R38021 last accessed: 2021-09-29

phytozome
metasource: bio.tools
version: extracted_at: 2021-09-29T12:14:50.614025

Other names: The JGI Comparative Plant Genomics Portal, phytozome

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. Search and visualization tools let users quickly find and analyze genes or genomic regions of interest.

Webpage:

https://phytozome.jgi.doe.gov/pz/portal.html

Licence:

Name: JGI disclaimer
URL: https://jgi.doe.gov/disclaimer/

Publications:

Publications
More detailed information about this field from each metasource.

Phytozome: a comparative platform for green plant genomics
PMID: 22110026
metasource: Fairsharing.org
version: None

metasource: bio.tools
version: extracted_at: 2021-09-29T12:14:50.614025

http://dx.doi.org/10.1093/nar/GKR944
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-09-29T11:57:30.286481

Phytozome: a comparative platform for green plant genomics PubMed citations: 1517.

1517 articles citing: Phytozome: a comparative platform for green plant genomics

Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships. PMID:34561450
Development of molecular markers based on LTR retrotransposon in the Cleistogenes songorica genome. PMID:34554437
Reference Genes and Expression Analysis of Seed Desaturases Genes in Soybean Mutant Accessions. PMID:34554351
Data Management and Modeling in Plant Biology. PMID:34539712
Genome-Wide Association Study of Seed Folate Content in Common Bean. PMID:34531882
Membrane anchoring facilitates colocalization of enzymes in plant cytochrome P450 redox systems. PMID:34504298
Genome-Wide Identification and Analysis of the Metallothionein Genes in Oryza Genus. PMID:34502554
Biochar-Enhanced Resistance to Botrytis cinerea in Strawberry Fruits (But Not Leaves) Is Associated With Changes in the Rhizosphere Microbiome. PMID:34497619
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Genome-wide identification, characterization and expression analysis of MATE family genes in apple (Malus × domestica Borkh). PMID:34461821
Genome-Wide Analysis of Glycoside Hydrolase Family 35 Genes and Their Potential Roles in Cell Wall Development in Medicago truncatula. PMID:34451684
Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.). PMID:34446782
Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions. PMID:34439430
Conserved oligomeric Golgi (COG) complex genes functioning in defense are expressed in root cells undergoing a defense response to a pathogenic infection and exhibit regulation my MAPKs. PMID:34437620
Molecular Mechanisms Underlying the Acclimation of Chlamydomonas reinhardtii Against Nitric Oxide Stress. PMID:34421944
GWAS provides biological insights into mechanisms of the parasitic plant (Striga) resistance in sorghum. PMID:34418971
Pathogen and drought stress affect cell wall and phytohormone signaling to shape host responses in a sorghum COMT bmr12 mutant. PMID:34418969
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. PMID:34417604
Whole-Genome Duplication and Purifying Selection Contributes to the Functional Redundancy of Auxin Response Factor (ARF) Genes in Foxtail Millet (Setaria italica L.). PMID:34414231
Genome Identification and Expression Profiles in Response to Nitrogen Treatment Analysis of the Class I CCoAOMT Gene Family in Populus. PMID:34410559
Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes. PMID:34400697
Genome-wide identification of serine acetyltransferase (SAT) gene family in rice (Oryza sativa) and their expressions under salt stress. PMID:34389920
Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max. PMID:34371668
Sorghum's Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review. PMID:34357076
The RGF/GLV/CLEL Family of Short Peptides Evolved Through Lineage-Specific Losses and Diversification and Yet Conserves Its Signaling Role Between Vascular Plants and Bryophytes. PMID:34354727
Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum. PMID:34354159
Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba. PMID:34344949
SorGSD: updating and expanding the sorghum genome science database with new contents and tools. PMID:34344425
An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis). PMID:34333548
An optimized protocol for stepwise optimization of real-time RT-PCR analysis. PMID:34333545
Genomic identification of nitrogen assimilation-related genes and transcriptional characterization of their responses to nitrogen in allotetraploid rapeseed. PMID:34327662
Localised expression of OsIAA29 suggests a key role for auxin in regulating development of the dorsal aleurone of early rice grains. PMID:34324072
Allele mining in diverse accessions of tropical grasses to improve forage quality and reduce environmental impact. PMID:34320174
Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination. PMID:34305984
The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. PMID:34305969
Bioinformatics analysis of PAE family in Populus trichocarpa and responsiveness to carbon and nitrogen treatment. PMID:34295610
Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes. PMID:34288936
Genome-wide association mapping reveals new loci associated with light-colored seed coat at harvest and slow darkening in carioca beans. PMID:34284717
Identification and Characterization of SRS Genes in Phaseolus vulgaris Genome and Their Responses Under Salt Stress. PMID:34282530
Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica. PMID:34281524
The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress. PMID:34275454
ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. PMID:34273949
Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L. PMID:34273948
A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes. PMID:34267227
Genome-Wide Analysis of MADS-Box Genes in Foxtail Millet (Setaria italica L.) and Functional Assessment of the Role of SiMADS51 in the Drought Stress Response. PMID:34262576
Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. PMID:34249082
Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity. PMID:34249030
The evolution of convex trade-offs enables the transition towards multicellularity. PMID:34244514
Plasticity in plastid redox networks: evolution of glutathione-dependent redox cascades and glutathionylation sites. PMID:34225654
Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum. PMID:34221730
Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis. PMID:34206279
In silico analysis of glycosyltransferase 2 family genes in duckweed (Spirodela polyrhiza) and its role in salt stress tolerance. PMID:34179502
Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis). PMID:34177145
Molecular Traits and Functional Analysis of the CLAVATA3/Endosperm Surrounding Region-Related Small Signaling Peptides in Three Species of Gossypium Genus. PMID:34149772
Phylogenetic and Structural Analysis of NIN-Like Proteins With a Type I/II PB1 Domain That Regulates Oligomerization for Nitrate Response. PMID:34135927
Flower Development in Cassava Is Feminized by Cytokinin, While Proliferation Is Stimulated by Anti-Ethylene and Pruning: Transcriptome Responses. PMID:34122486
PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses. PMID:34122478
Genome-wide characterization, evolution, and expression profiling of FBA gene family in response to light treatments and abiotic stress in Nicotiana tabacum. PMID:34120568
NF-YB-Mediated Active Responses of Plant Growth under Salt and Temperature Stress in Eucalyptus grandis. PMID:34072675
Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean. PMID:34069884
Sources of Resistance to Common Bacterial Blight and Charcoal Rot Disease for the Production of Mesoamerican Common Beans in the Southern United States. PMID:34067661
Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. PMID:34059650
New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis. PMID:34054921
Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. PMID:34050180
Lipid Pathway Databases with a Focus on Algae. PMID:34047993
Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana. PMID:34039279
Diversified amino acid-mediated allosteric regulation of phosphoglycerate dehydrogenase for serine biosynthesis in land plants. PMID:34032263
Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans. PMID:34010322
Super determinant1A, a RAWULdomain-containing protein, modulates axillary meristem formation and compound leaf development in tomato. PMID:34009392
Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean. PMID:34006214
Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types. PMID:33995436
Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. PMID:33980999
Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. PMID:33972666
The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation. PMID:33955484
De Novo Mutation Rate Variation and Its Determinants in Chlamydomonas. PMID:33950243
The pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content. PMID:33942475
Cell Wall Layer Induced in Xylem Fibers of Flax Upon Gravistimulation Is Similar to Constitutively Formed Cell Walls of Bast Fibers. PMID:33936149
Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum. PMID:33931706
Angular Leaf Spot Resistance Loci Associated With Different Plant Growth Stages in Common Bean. PMID:33927738
Genome-Wide Investigation of the NF-X1 Gene Family in Populus trichocarpa Expression Profiles during Development and Stress. PMID:33925110
Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly. PMID:33919286
CRISPR/Cas9-Mediated Knockout of GmFATB1 Significantly Reduced the Amount of Saturated Fatty Acids in Soybean Seeds. PMID:33918544
Transcriptional profile of AvrRpt2EA-mediated resistance and susceptibility response to Erwinia amylovora in apple. PMID:33888770
Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea. PMID:33883595
Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids. PMID:33874976
Predictive Models of Genetic Redundancy in Arabidopsis thaliana. PMID:33871641
An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals. PMID:33868343
Genome-wide identification of heat shock factors and heat shock proteins in response to UV and high intensity light stress in lettuce. PMID:33865315
The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. PMID:33863805
Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. PMID:33852055
Evolutionary diversification of cytokinin-specific glucosyltransferases in angiosperms and enigma of missing cis-zeatin O-glucosyltransferase gene in Brassicaceae. PMID:33846460
Topological clustering of regulatory genes confers pathogenic tolerance to cassava brown streak virus (CBSV) in cassava. PMID:33846415
The Phosphofructokinase Isoform AtPFK5 Is a Novel Target of Plastidic Thioredoxin-f-Dependent Redox Regulation. PMID:33800095
Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.). PMID:33781207
Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. PMID:33781078
Multimerization variants as potential drivers of neofunctionalization. PMID:33771868
Genomic-Wide Analysis of the PLC Family and Detection of GmPI-PLC7 Responses to Drought and Salt Stresses in Soybean. PMID:33763092
The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived F1 population. PMID:33753876
Identification of the PP2C gene family in paper mulberry (Broussonetia papyrifera) and its roles in the regulation mechanism of the response to cold stress. PMID:33751277
A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max). PMID:33742087
Genome-wide analysis of UGDH genes in Populus trichocarpa and responsiveness to nitrogen treatment. PMID:33732570
Genome-wide identification and expression profiling of chitinase genes in tea (Camellia sinensis (L.) O. Kuntze) under biotic stress conditions. PMID:33707875
Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest. PMID:33680580
Mapping Quantitative Trait Loci Associated With Graft (In)Compatibility in Apricot (Prunus armeniaca L.). PMID:33679836
Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species. PMID:33676571
Genome-Wide Identification and Characterization of Wheat 14-3-3 Genes Unravels the Role of TaGRF6-A in Salt Stress Tolerance by Binding MYB Transcription Factor. PMID:33673010
Plant HKT Channels: An Updated View on Structure, Function and Gene Regulation. PMID:33672907
Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat (Triticum aestivum L.). PMID:33671285
Posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression in Arabidopsis. PMID:33649234
Genome-wide analysis and expression profile of the bZIP gene family in poplar. PMID:33648455
Genome-wide analysis of fluoride exporter genes in plants. PMID:33643759
Lasting consequences of psyllid (Bactericera cockerelli L.) infestation on tomato defense, gene expression, and growth. PMID:33627099
Insights into the diversification of subclade IVa bHLH transcription factors in Fabaceae. PMID:33622255
Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes. PMID:33619356
Current status and impending progress for cassava structural genomics. PMID:33604743
Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). PMID:33588756
Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.]. PMID:33584812
ARF2 represses expression of plant GRF transcription factors in a complementary mechanism to microRNA miR396. PMID:33580700
Domain Unknown Function DUF1668-Containing Genes in Multiple Lineages Are Responsible for F1 Pollen Sterility in Rice. PMID:33574828
Orthology and synteny analysis of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. PMID:33568053
Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes. PMID:33568051
Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. PMID:33558550
Changes in the Plant β-Sitosterol/Stigmasterol Ratio Caused by the Plant Parasitic Nematode Meloidogyne incognita. PMID:33557005
Kleisin NSE4 of the SMC5/6 complex is necessary for DNA double strand break repair, but not for recovery from DNA damage in Physcomitrella (Physcomitrium patens). PMID:33550456
Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines. PMID:33546584
Regulation of Exocyst Function in Pollen Tube Growth by Phosphorylation of Exocyst Subunit EXO70C2. PMID:33519861
Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.). PMID:33519852
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. PMID:33505029
Bryo-Activities: A Review on How Bryophytes Are Contributing to the Arsenal of Natural Bioactive Compounds against Fungi. PMID:33494524
Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections. PMID:33492369
Identification and Downstream Analyses of Domains Amplified in Plant Genomes: The Case of StAR-Related Lipid Transfer (START) Domains in Rice. PMID:33471342
Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum. PMID:33452894
Involvement of SUT1 and SUT2 Sugar Transporters in the Impairment of Sugar Transport and Changes in Phloem Exudate Contents in Phytoplasma-Infected Plants. PMID:33451049
Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm. PMID:33424928
Sucrose-phosphate phosphatase from sugarcane reveals an ancestral tandem duplication. PMID:33413115
Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening. PMID:33413072
Genome-wide characterization and analysis of the CCT motif family genes in soybean (Glycine max). PMID:33392793
PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. PMID:33392435
Stable Protein Sialylation in Physcomitrella. PMID:33391325
Refinement of Draft Genome Assemblies of Pigeonpea (Cajanus cajan). PMID:33384719
Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C4 rhizomatous grasses Miscanthus and switchgrass. PMID:33381230
Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum Lycopersicum L.). PMID:33375673
Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. PMID:33361111
An unbiased method for evaluating the genome-wide specificity of base editors in rice. PMID:33349703
Genome-wide identification and evolution of HECT genes in wheat. PMID:33344088
The Peptide PbrPSK2 From Phytosulfokine Family Induces Reactive Oxygen Species (ROS) Production to Regulate Pear Pollen Tube Growth. PMID:33329671
Sugar and Hormone Dynamics and the Expression Profiles of SUT/SUC and SWEET Sweet Sugar Transporters during Flower Development in Petunia axillaris. PMID:33327497
Helixer: Cross-species gene annotation of large eukaryotic genomes using deep learning. PMID:33325516
Genome-Wide Analysis of the Cyclin Gene Family and Their Expression Profile in Medicago truncatula. PMID:33322339
Systematic Analysis and Functional Validation of Citrus Pectin Acetylesterases (CsPAEs) Reveals that CsPAE2 Negatively Regulates Citrus Bacterial Canker Development. PMID:33322321
Genome-Wide Survey and Expression Analysis of the KT/HAK/KUP Family in Brassica napus and Its Potential Roles in the Response to K+ Deficiency. PMID:33322211
Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function. PMID:33320854
Unequal contribution of two paralogous CENH3 variants in cowpea centromere function. PMID:33319863
TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site. PMID:33304661
The vascular targeted citrus FLOWERING LOCUS T3 gene promotes non-inductive early flowering in transgenic Carrizo rootstocks and grafted juvenile scions. PMID:33293614
In silico prediction and segregation analysis of putative virus defense genes based on SSR markers in sweet potato F1 progenies of cultivars 'New Kawogo' and 'Resisto'. PMID:33281890
Genome-Wide Association Study for Biomass Related Traits in a Panel of Sorghum bicolor and S. bicolor × S. halepense Populations. PMID:33281836
The Glycine max Conserved Oligomeric Golgi (COG) Complex Functions During a Defense Response to Heterodera glycines. PMID:33262774
Genome-Wide Identification of the Vacuolar H+-ATPase Gene Family in Five Rosaceae Species and Expression Analysis in Pear (Pyrus bretschneideri). PMID:33261053
MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. PMID:33240618
Systems identification and characterization of β-glucuronosyltransferase genes involved in arabinogalactan-protein biosynthesis in plant genomes. PMID:33239665
GreenPhylDB v5: a comparative pangenomic database for plant genomes. PMID:33237299
The Arabidopsis V-ATPase is localized to the TGN/EE via a seed plant-specific motif. PMID:33236982
In-silico Exploration of Channel Type and Efflux Silicon Transporters and Silicification Proteins in 80 Sequenced Viridiplantae Genomes. PMID:33233677
SiMADS34, an E-class MADS-box transcription factor, regulates inflorescence architecture and grain yield in Setaria italica. PMID:33231834
Knowing When to Self-Eat - Fine-Tuning Autophagy Through ATG8 Iso-forms in Plants. PMID:33224169
The emergence and evolution of intron-poor and intronless genes in intron-rich plant gene families. PMID:33217085
Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance. PMID:33208862
A cellulose synthase-derived enzyme catalyses 3-O-glucuronosylation in saponin biosynthesis. PMID:33199711
Transcriptome-wide identification of MAPKKK genes in bermudagrass (Cynodon dactylon L.) and their potential roles in low temperature stress responses. PMID:33194398
Recurrent Drought Conditions Enhance the Induction of Drought Stress Memory Genes in Glycine max L. PMID:33193691
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
Endophyte-Promoted Phosphorus Solubilization in Populus. PMID:33193494
European landrace diversity for common bean biofortification: a genome-wide association study. PMID:33188249
CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages. PMID:33181825
Characterization of the Poplar R2R3-MYB Gene Family and Over-Expression of PsnMYB108 Confers Salt Tolerance in Transgenic Tobacco. PMID:33178243
Transcription Terminator-Mediated Enhancement in Transgene Expression in Maize: Preponderance of the AUGAAU Motif Overlapping With Poly(A) Signals. PMID:33178242
Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses. PMID:33178241
Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species. PMID:33171085
A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae. PMID:33163293
Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum. PMID:33143636
Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding. PMID:33143347
Genome-Wide Identification, Expression Profiling, and Evolution of Phosphate Transporter Gene Family in Green Algae. PMID:33133172
Toward the introgression of PvPdh1 for increased resistance to pod shattering in common bean. PMID:33130953
Evolution of the Brassicaceae-specific MS5-Like family and neofunctionalization of the novel MALE STERILITY 5 gene essential for male fertility in Brassica napus. PMID:33128826
Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum. PMID:33120967
Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest. PMID:33120946
Rapid metabolite response in leaf blade and petiole as a marker for shade avoidance syndrome. PMID:33117429
Prometheus, an omics portal for interkingdom comparative genomic analyses. PMID:33112870
Heat Stress Triggers Differential Protein Accumulation in the Extracellular Matrix of Sorghum Cell Suspension Cultures. PMID:33105781
PhycoCosm, a comparative algal genomics resource. PMID:33104790
Functional Analysis of the teosinte branched 1 Gene in the Tetraploid Switchgrass (Panicum virgatum L.) by CRISPR/Cas9-Directed Mutagenesis. PMID:33101338
In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues. PMID:33092180
Prediction of Dhurrin Metabolism by Transcriptome and Metabolome Analyses in Sorghum. PMID:33086681
Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica. PMID:33080620
NAMS webserver: coding potential assessment and functional annotation of plant transcripts. PMID:33080021
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs. PMID:33079992
Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.). PMID:33076828
Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin. PMID:33075080
Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (Glycine max) Tissues during Early Seed Development. PMID:33066688
Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean. PMID:33066482
EXO70A2 Is Critical for Exocyst Complex Function in Pollen Development. PMID:33051268
Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences. PMID:33045986
Genome-wide identification and analysis of high-affinity nitrate transporter 2 (NRT2) family genes in rapeseed (Brassica napus L.) and their responses to various stresses. PMID:33036562
Comprehensive transcriptome profiling of Caragana microphylla in response to salt condition using de novo assembly. PMID:33026585
Evolutionary aspects of the Viridiplantae nitroreductases. PMID:33025290
Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.). PMID:33024641
Structural Aspects of DNA Repair and Recombination in Crop Improvement. PMID:33024442
ARMADILLO REPEAT ONLY proteins confine Rho GTPase signalling to polar growth sites. PMID:33020609
Installation of C4 photosynthetic pathway enzymes in rice using a single construct. PMID:33016576
Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa. PMID:33013968
Biased Gene Retention in the Face of Introgression Obscures Species Relationships. PMID:33011798
Genome-wide characterization and expression profiling of Eucalyptus grandis HD-Zip gene family in response to salt and temperature stress. PMID:33004006
Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae. PMID:32988994
Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L. PMID:32961651
Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton. PMID:32948145
Ancestral function of the phytochelatin synthase C-terminal domain in inhibition of heavy metal-mediated enzyme overactivation. PMID:32936292
A Genomic Perspective on the Evolutionary Diversity of the Plant Cell Wall. PMID:32932717
Exocyst components promote an incompatible interaction between Glycine max (soybean) and Heterodera glycines (the soybean cyst nematode). PMID:32929168
The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection. PMID:32928117
Towards an understanding of the role of intrinsic protein disorder on plant adaptation to environmental challenges. PMID:32902806
Genome-Wide Characterization, Evolution, and Expression Analysis of the Leucine-Rich Repeat Receptor-Like Protein Kinase (LRR-RLK) Gene Family in Medicago truncatula. PMID:32899802
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce. PMID:32894759
Citrus Vascular Proteomics Highlights the Role of Peroxidases and Serine Proteases during Huanglongbing Disease Progression. PMID:32883801
Wheat Disease Resistance Genes and Their Diversification Through Integrated Domain Fusions. PMID:32849852
Aphid-Responsive Defense Networks in Hybrid Switchgrass. PMID:32849703
Elevated Temperatures Impose Transcriptional Constraints and Elicit Intraspecific Differences Between Coffee Genotypes. PMID:32849685
Two splice variants of the DsMEK1 mitogen-activated protein kinase kinase (MAPKK) are involved in salt stress regulation in Dunaliella salina in different ways. PMID:32843896
910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens. PMID:32843634
Isolation of novel citrus and plum fruit promoters and their functional characterization for fruit biotechnology. PMID:32819338
Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses. PMID:32811430
Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics. PMID:32794321
Genome-Wide Identification of Apple Ubiquitin SINA E3 Ligase and Functional Characterization of MdSINA2. PMID:32793265
Evolution and Expression of the Membrane Attack Complex and Perforin Gene Family in the Poaceae. PMID:32785137
Conserved sequence motifs in the abiotic stress response protein late embryogenesis abundant 3. PMID:32760115
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. PMID:32728126
The alcohol dehydrogenase gene family in sugarcane and its involvement in cold stress regulation. PMID:32727370
Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa. PMID:32722098
Network Modeling of Complex Data Sets. PMID:32720156
Molecular evolution and diversification of the GRF transcription factor family. PMID:32706846
Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum). PMID:32702710
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. PMID:32699173
DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems. PMID:32689934
Targeted suppression of soybean BAG6-induced cell death in yeast by soybean cyst nematode effectors. PMID:32686295
Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis. PMID:32674446
Genome-Wide Identification, Evolution, and Expression of GDSL-Type Esterase/Lipase Gene Family in Soybean. PMID:32670311
TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. PMID:32663247
Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence. PMID:32658273
Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome. PMID:32655308
Sympatric speciation in mountain roses (Metrosideros) on an oceanic island. PMID:32654651
Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids. PMID:32642754
Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality. PMID:32641089
Discovery and modification of cytochrome P450 for plant natural products biosynthesis. PMID:32637672
The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity. PMID:32636339
Volvox and volvocine green algae. PMID:32626570
Elongating maize root: zone-specific combinations of polysaccharides from type I and type II primary cell walls. PMID:32616810
Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. PMID:32605573
Evolutionary Understanding of Aquaporin Transport System in the Basal Eudicot Model Species Aquilegia coerulea. PMID:32604788
Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica. PMID:32587596
Photosynthetic Metabolism and Nitrogen Reshuffling Are Regulated by Reversible Cysteine Thiol Oxidation Following Nitrogen Deprivation in Chlamydomonas. PMID:32585825
Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.). PMID:32581321
Isolation, characterization and expression analysis of stress responsive plant nuclear transcriptional factor subunit (NF-YB2) from commercial Saccharum hybrid and wild relative Erianthus arundinaceus. PMID:32566442
Host plant genetic control of associated fungal and insect species in a Populus hybrid cross. PMID:32551087
Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens. PMID:32547597
Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato. PMID:32533036
MYB Superfamily in Brassica napus: Evidence for Hormone-Mediated Expression Profiles, Large Expansion, and Functions in Root Hair Development. PMID:32517318
Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress. PMID:32513102
OsCpn60β1 is Essential for Chloroplast Development in Rice (Oryza sativa L.). PMID:32512821
What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination? PMID:32508870
Evolution and Functional Divergence of the Fructokinase Gene Family in Populus. PMID:32499793
A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. PMID:32497070
Functional Divergence of the Arabidopsis Florigen-Interacting bZIP Transcription Factors FD and FDP. PMID:32492426
NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs. PMID:32463462
Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis. PMID:32457808
Convergent molecular evolution among ash species resistant to the emerald ash borer. PMID:32451426
Structural and functional similarities and differences in nucleolar Pumilio RNA-binding proteins between Arabidopsis and the charophyte Chara corallina. PMID:32448230
Molecular diversity and genetic structure of Saccharum complex accessions. PMID:32442233
Global Landscapes of the Na+/H+ Antiporter (NHX) Family Members Uncover their Potential Roles in Regulating the Rapeseed Resistance to Salt Stress. PMID:32408717
Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate. PMID:32398676
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
An Acyl-CoA N-Acyltransferase Regulates Meristem Phase Change and Plant Architecture in Barley. PMID:32376761
Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins. PMID:32371491
The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. PMID:32355217
Genetic Architecture of Early Vigor Traits in Wild Soybean. PMID:32354037
Proteomic analysis and interactions network in leaves of mycorrhizal and nonmycorrhizal sorghum plants under water deficit. PMID:32351787
Structure-Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes. PMID:32350121
Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed Down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.). PMID:32340299
Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.). PMID:32331491
Dataset for the combined transcriptome assembly of M. oleifera and functional annotation. PMID:32309524
Exploring dynamic protein-protein interactions in cassava through the integrative interactome network. PMID:32300157
Identification and validation of mutation points associated with waxy phenotype in cassava. PMID:32293293
An RNA thermoswitch regulates daytime growth in Arabidopsis. PMID:32284544
Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus. PMID:32280432
A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.). PMID:32276381
Genomics, molecular and evolutionary perspective of NAC transcription factors. PMID:32275733
Evolutionary and biochemical analyses reveal conservation of the Brassicaceae telomerase ribonucleoprotein complex. PMID:32271752
Genome-wide identification of the amino acid permease genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed. PMID:32268885
Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. PMID:32267233
IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix. PMID:32265990
Genome-wide identification and expression analysis of the NAC transcription factor family in tomato (Solanum lycopersicum) during aluminum stress. PMID:32264854
The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage. PMID:32260156
The Mitochondrial Iron-Regulated (MIR) gene is Oryza genus specific and evolved before speciation within the Oryza sativa complex. PMID:32253515
Genome-wide analysis of Myo-inositol oxygenase gene family in tomato reveals their involvement in ascorbic acid accumulation. PMID:32252624
NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification. PMID:32245073
Water lily (Nymphaea thermarum) genome reveals variable genomic signatures of ancient vascular cambium losses. PMID:32234787
Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA. PMID:32228449
Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum. PMID:32217633
Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms. PMID:32206771
Genome-wide characterization and expression analysis of soybean trihelix gene family. PMID:32206450
Biological and Cellular Functions of the Microdomain-Associated FWL/CNR Protein Family in Plants. PMID:32204387
A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. PMID:32191846
Evolutionary History and Activity of RNase H1-Like Proteins in Arabidopsis thaliana. PMID:32191307
PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants. PMID:32185394
Actin Depolymerizing Factor Modulates Rhizobial Infection and Nodule Organogenesis in Common Bean. PMID:32183068
Reconstruction of the Evolutionary Histories of UGT Gene Superfamily in Legumes Clarifies the Functional Divergence of Duplicates in Specialized Metabolism. PMID:32182686
Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach. PMID:32180783
Genome-wide identification and expression analysis of WRKY transcription factors in pearl millet (Pennisetum glaucum) under dehydration and salinity stress. PMID:32171257
Rapid identification of an Arabidopsis NLR gene as a candidate conferring susceptibility to Sclerotinia sclerotiorum using time-resolved automated phenotyping. PMID:32170798
Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. PMID:32170292
The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae. PMID:32164546
Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes. PMID:32161609
High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Megathyrsus maximus). PMID:32161603
Global Survey and Expressions of the Phosphate Transporter Gene Families in Brassica napus and Their Roles in Phosphorus Response. PMID:32143436
Successful field performance in warm and dry environments of soybean expressing the sunflower transcription factor HB4. PMID:32140724
Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor. PMID:32132167
In the presence of population structure: From genomics to candidate genes underlying local adaptation. PMID:32128123
Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway. PMID:32121542
Genome-wide identification and expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula. PMID:32117614
A xylan glucuronosyltransferase gene exhibits pleiotropic effects on cellular composition and leaf development in rice. PMID:32111928
Genomewide analysis of the CIII peroxidase family in sweet orange (Citrus sinensis) and expression profiles induced by Xanthomonas citri subsp. citri and hormones. PMID:32089529
Evolution of the Small Family of Alternative Splicing Modulators Nuclear Speckle RNA-binding Proteins in Plants. PMID:32085457
Hydrogen peroxide sensor HPCA1 is an LRR receptor kinase in Arabidopsis. PMID:32076270
The Floral Repressor GmFLC-like Is Involved in Regulating Flowering Time Mediated by Low Temperature in Soybean. PMID:32075331
Genetic analysis of the Arabidopsis TIR1/AFB auxin receptors reveals both overlapping and specialized functions. PMID:32067636
Molecular characterization of teosinte branched1 gene governing branching architecture in cultivated maize and wild relatives. PMID:32058540
Identification of eukaryotic translation initiation factors and the temperature-dependent nature of Turnip mosaic virus epidemics in allopolyploid Brassica juncea. PMID:32051808
Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions. PMID:32043527
The Genome-Wide Analysis of RALF-Like Genes in Strawberry (Wild and Cultivated) and Five Other Plant Species (Rosaceae). PMID:32041308
Systematic Analysis of the DNA Methylase and Demethylase Gene Families in Rapeseed (Brassica napus L.) and Their Expression Variations After Salt and Heat stresses. PMID:32023925
Genome-wide identification of BXL genes in Populus trichocarpa and their expression under different nitrogen treatments. PMID:32015953
Insights obtained using different modules of the cotton uceA1.7 promoter. PMID:32006110
Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor). PMID:32005168
Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid. PMID:31996126
Structural evolution drives diversification of the large LRR-RLK gene family. PMID:31990988
Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. PMID:31988262
Heating quinoa shoots results in yield loss by inhibiting fruit production and delaying maturity. PMID:31971639
Generation of fruit postharvest gene datasets and a novel motif analysis tool for functional studies: uncovering links between peach fruit heat treatment and cold storage responses. PMID:31950388
Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon. PMID:31948407
The genome sequence of celery (Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae family. PMID:31934340
A Snapshot of the Trehalose Pathway During Seed Imbibition in Medicago truncatula Reveals Temporal- and Stress-Dependent Shifts in Gene Expression Patterns Associated With Metabolite Changes. PMID:31921241
Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses. PMID:31900112
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana. PMID:31887137
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. PMID:31885040
Analysis of Soybean Long Non-Coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts. PMID:31882456
Direct visualization of degradation microcompartments at the ER membrane. PMID:31882451
Genomic resources for energy cane breeding in the post genomics era. PMID:31871586
Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. PMID:31871489
Domesticating Vigna Stipulacea: A Potential Legume Crop With Broad Resistance to Biotic Stresses. PMID:31867036
Genetic Correlation, Genome-Wide Association and Genomic Prediction of Portable NIRS Predicted Carotenoids in Cassava Roots. PMID:31867030
The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. PMID:31861318
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries. PMID:31856718
A Bioinformatics Approach to Explore MicroRNAs as Tools to Bridge Pathways Between Plants and Animals. Is DNA Damage Response (DDR) a Potential Target Process? PMID:31850028
Transcriptional, metabolic and DNA methylation changes underpinning the response of Arundo donax ecotypes to NaCl excess. PMID:31848729
Compensatory sequence variation between trans-species small RNAs and their target sites. PMID:31845648
Investigations into a putative role for the novel BRASSIKIN pseudokinases in compatible pollen-stigma interactions in Arabidopsis thaliana. PMID:31829135
Phylogenetic analysis of ABCG subfamily proteins in plants: functional clustering and coevolution with ABCGs of pathogens. PMID:31828796
Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max). PMID:31824753
Genome-wide association analyses reveal the genetic basis of biomass accumulation under symbiotic nitrogen fixation in African soybean. PMID:31822937
Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). PMID:31822760
Unraveling candidate genes underlying biomass digestibility in elephant grass (Cenchrus purpureus). PMID:31822283
The Chalcone Isomerase Family in Cotton: Whole-Genome Bioinformatic and Expression Analyses of the Gossypium barbadense L. Response to Fusarium Wilt Infection. PMID:31817162
TILLING by Sequencing: A Successful Approach to Identify Rare Alleles in Soybean Populations. PMID:31817015
Genome-wide association mapping of total antioxidant capacity, phenols, tannins, and flavonoids in a panel of Sorghum bicolor and S. bicolor × S. halepense populations using multi-locus models. PMID:31805171
The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons. PMID:31789592
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. PMID:31782791
Glycerol-3-phosphate mediates rhizobia-induced systemic signaling in soybean. PMID:31757957
Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles. PMID:31750917
Identification and characterization of the GmRD26 soybean promoter in response to abiotic stresses: potential tool for biotechnological application. PMID:31747926
The ABA-induced soybean ERF transcription factor gene GmERF75 plays a role in enhancing osmotic stress tolerance in Arabidopsis and soybean. PMID:31747904
Sequence characteristics of Medicago truncatula cyclophilin family members and function analysis of MsCYP20-3B involved in axillary shoot development. PMID:31741262
Identifying Temporally Regulated Root Nodulation Biomarkers Using Time Series Gene Co-Expression Network Analysis. PMID:31737022
PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis. PMID:31732705
Genome-Wide Analysis of the DYW Subgroup PPR Gene Family and Identification of GmPPR4 Responses to Drought Stress. PMID:31726763
Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand's high ultraviolet B radiation environment. PMID:31718535
SH3Ps-Evolution and Diversity of a Family of Proteins Engaged in Plant Cytokinesis. PMID:31717902
Genome-Wide Analysis of Basic Helix-Loop-Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.). PMID:31717469
PdWND3A, a wood-associated NAC domain-containing protein, affects lignin biosynthesis and composition in Populus. PMID:31711424
Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations. PMID:31711416
Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon. PMID:31708948
PlantRegMap: charting functional regulatory maps in plants. PMID:31701126
Isocitrate lyase plays important roles in plant salt tolerance. PMID:31694539
Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum. PMID:31681373
Evolution of the Cell Wall Gene Families of Grasses. PMID:31681352
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
Differential gene expression in non-transgenic and transgenic "M.26" apple overexpressing a peach CBF gene during the transition from eco-dormancy to bud break. PMID:31666956
Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.). PMID:31651257
Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence. PMID:31649710
One thousand plant transcriptomes and the phylogenomics of green plants. PMID:31645766
Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). PMID:31644802
A Sequence-Indexed Mutator Insertional Library for Maize Functional Genomics Study. PMID:31636104
An Optimized Screen Reduces the Number of GA Transporters and Provides Insights Into Nitrate Transporter 1/Peptide Transporter Family Substrate Determinants. PMID:31632416
Mutations in sorghum SBEIIb and SSIIa affect alkali spreading value, starch composition, thermal properties and flour viscosity. PMID:31624872
De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway. PMID:31619732
Changes in gene expression and metabolic profile of drupes of Olea europaea L. cv Carolea in relation to maturation stage and cultivation area. PMID:31619170
A modular steroid-inducible gene expression system for use in rice. PMID:31615413
Systematic Analysis and Functional Validation of Citrus XTH Genes Reveal the Role of Csxth04 in Citrus Bacterial Canker Resistance and Tolerance. PMID:31611887
Data Integration in Poplar: 'Omics Layers and Integration Strategies. PMID:31608114
Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots. PMID:31606033
Evolutionary flexibility in flooding response circuitry in angiosperms. PMID:31604238
PmiREN: a comprehensive encyclopedia of plant miRNAs. PMID:31602478
A Mitochondrial LYR Protein Is Required for Complex I Assembly. PMID:31601645
Natural variation and selection in GmSWEET39 affect soybean seed oil content. PMID:31596499
Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses. PMID:31589325
CsBZIP40, a BZIP transcription factor in sweet orange, plays a positive regulatory role in citrus bacterial canker response and tolerance. PMID:31584990
The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PMID:31579570
Sugar transporters in Fabaceae, featuring SUT MST and SWEET families of the model plant Medicago truncatula and the agricultural crop Pisum sativum. PMID:31568488
NODULE INCEPTION Recruits the Lateral Root Developmental Program for Symbiotic Nodule Organogenesis in Medicago truncatula. PMID:31543454
Analysis of Orthologous SECONDARY WALL-ASSOCIATED NAC DOMAIN1 (SND1) Promotor Activity in Herbaceous and Woody Angiosperms. PMID:31540430
Genome-Wide Analysis Reveals the Role of Mediator Complex in the Soybean-Phytophthora sojae Interaction. PMID:31540158
Molecular Evolution in Small Steps under Prevailing Negative Selection: A Nearly Universal Rule of Codon Substitution. PMID:31504473
Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max). PMID:31497394
Identification and characterization of the MADS-box genes highly expressed in the laticifer cells of Hevea brasiliensis. PMID:31481699
The Evolution of the KANADI Gene Family and Leaf Development in Lycophytes and Ferns. PMID:31480252
Prospects of genomic resources available at the global databases for the flora of United Arab Emirates. PMID:31475085
The rhg1-a (Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene. PMID:31468029
Identification and in Silico Characterization of GT Factors Involved in Phytohormone and Abiotic Stresses Responses in Brachypodium distachyon. PMID:31450734
Different regulations of cell-type transcription by UV-B in multicellular green alga Volvox carteri. PMID:31446835
Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). PMID:31438854
Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae. PMID:31431676
TDNAscan: A Software to Identify Complete and Truncated T-DNA Insertions. PMID:31428129
Genome-Wide Association Study Reveals Candidate Genes for Flowering Time Variation in Common Bean (Phaseolus vulgaris L.). PMID:31428109
Genome-Wide Transcription Factor Binding in Leaves from C3 and C4 Grasses. PMID:31427470
New perspectives on the plant PARP family: Arabidopsis PARP3 is inactive, and PARP1 exhibits predominant poly (ADP-ribose) polymerase activity in response to DNA damage. PMID:31426748
Compartmentalized Synthesis of Triacylglycerol at the Inner Nuclear Membrane Regulates Nuclear Organization. PMID:31422915
Epistasis Detection and Modeling for Genomic Selection in Cowpea (Vigna unguiculata L. Walp.). PMID:31417604
The Roles of GmERF135 in Improving Salt Tolerance and Decreasing ABA Sensitivity in Soybean. PMID:31396249
Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology. PMID:31390788
Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean. PMID:31373320
Identifying genetic markers for a range of phylogenetic utility-From species to family level. PMID:31369563
Molecular Characterization of ZosmaNRT2, the Putative Sodium Dependent High-Affinity Nitrate Transporter of Zostera marina L. PMID:31357380
The Conservation of VIT1-Dependent Iron Distribution in Seeds. PMID:31354774
Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. PMID:31340456
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers. PMID:31339877
Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean. PMID:31338257
Flower bud proteome reveals modulation of sex-biased proteins potentially associated with sex expression and modification in dioecious Coccinia grandis. PMID:31337343
Gene Expression Profiling and Fine Mapping Identifies a Gibberellin 2-Oxidase Gene Co-segregating With the Dominant Dwarfing Gene Ddw1 in Rye (Secale cereale L.). PMID:31333700
Identification and characterization of a fast-neutron-induced mutant with elevated seed protein content in soybean. PMID:31324928
Characterization and Expression Analysis of Heme Oxygenase Genes from Sorghum bicolor. PMID:31320797
A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.). PMID:31318931
Genome-wide in silico identification of LysM-RLK genes in potato (Solanum tuberosum L.). PMID:31317454
Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid. PMID:31311507
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. PMID:31293610
Overexpression of Acyl-ACP Thioesterases, CpFatB4 and CpFatB5, Induce Distinct Gene Expression Reprogramming in Developing Seeds of Brassica napus. PMID:31284614
Genome-wide identification and functional analysis of oleosin genes in Brassica napus L. PMID:31272381
Genome-Wide Identification and Expression Profiling of the Polygalacturonase (PG) and Pectin Methylesterase (PME) Genes in Grapevine (Vitis vinifera L.). PMID:31261768
Site-specific cleavage of bacterial MucD by secreted proteases mediates antibacterial resistance in Arabidopsis. PMID:31253808
DREB Genes from Common Bean (Phaseolus vulgaris L.) Show Broad to Specific Abiotic Stress Responses and Distinct Levels of Nucleotide Diversity. PMID:31249842
The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling. PMID:31248964
The Elongation Factor GmEF4 Is Involved in the Response to Drought and Salt Tolerance in Soybean. PMID:31248195
Genome-Wide Analysis of Serine/Arginine-Rich Protein Family in Wheat and Brachypodium distachyon. PMID:31247888
Flowering plant immune repertoires expand under mycorrhizal symbiosis. PMID:31245768
Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). PMID:31245718
Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated PHAS loci. PMID:31245701
Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance. PMID:31245692
Conserved redox-dependent DNA binding of ROXY glutaredoxins with TGA transcription factors. PMID:31245678
Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. PMID:31245666
Downregulation of Orco and 5-HTT Alters Nestmate Discrimination in the Subterranean Termite Odontotermes formosanus (Shiraki). PMID:31244679
Redundant SCARECROW genes pattern distinct cell layers in roots and leaves of maize. PMID:31235633
Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation. PMID:31234799
Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion. PMID:31231410
Soybean (Glycine max L.) triacylglycerol lipase GmSDP1 regulates the quality and quantity of seed oil. PMID:31222045
Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen. PMID:31222001
Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation. PMID:31214244
NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches. PMID:31201314
A Large-Scale Genome-Wide Association Analyses of Ethiopian Sorghum Landrace Collection Reveal Loci Associated With Important Traits. PMID:31191590
Butterfly Pea (Clitoria ternatea), a Cyclotide-Bearing Plant With Applications in Agriculture and Medicine. PMID:31191573
Functional Analysis of the PgCesA3 White Spruce Cellulose Synthase Gene Promoter in Secondary Xylem. PMID:31191566
Functional, Structural and Biochemical Features of Plant Serinyl-Glutathione Transferases. PMID:31191562
Genomic Selection with Allele Dosage in Panicum maximum Jacq. PMID:31171567
Comparing time series transcriptome data between plants using a network module finding algorithm. PMID:31164912
Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal. PMID:31161017
Gene Expression analysis associated with salt stress in a reciprocally crossed rice population. PMID:31160691
CRISPR-Based Assessment of Gene Specialization in the Gibberellin Metabolic Pathway in Rice. PMID:31160507
Evolution and functional differentiation of recently diverged phytochelatin synthase genes from Arundo donax L. PMID:31145784
PEST sequences from a cactus dehydrin regulate its proteolytic degradation. PMID:31143531
Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family in Oryza Genus. PMID:31139200
Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships. PMID:31134130
Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions. PMID:31134109
A genome-wide approach to the comprehensive analysis of GASA gene family in Glycine max. PMID:31123969
Production of the cyanogenic glycoside dhurrin in yeast. PMID:31110942
Lateral Root Initiation in the Parental Root Meristem of Cucurbits: Old Players in a New Position. PMID:31110507
Whirly (Why) transcription factors in tomato (Solanum lycopersicum L.): genome-wide identification and transcriptional profiling under drought and salt stresses. PMID:31089915
Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism. PMID:31088371
Genome-Wide Identification, Evolution, and Transcriptional Profiling of PP2C Gene Family in Brassica rapa. PMID:31073524
Identification of a role for an E6-like 1 gene in early pollen-stigma interactions in Arabidopsis thaliana. PMID:31069543
Genome-wide identification and characterization of the metal tolerance protein (MTP) family in grape (Vitis vinifera L.). PMID:31065499
Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus). PMID:31060501
Dynamic Transcriptome Changes Related to Oil Accumulation in Developing Soybean Seeds. PMID:31060266
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. PMID:31049561
Genome-wide identification and gene expression pattern of ABC transporter gene family in Capsicum spp. PMID:31039176
Genome-wide analysis of maize GPAT gene family and cytological characterization and breeding application of ZmMs33/ZmGPAT6 gene. PMID:31016347
Quantitative Trait Loci for Freezing Tolerance in a Lowland x Upland Switchgrass Population. PMID:30984223
Functional conservation of EXA1 among diverse plant species for the infection by a family of plant viruses. PMID:30976020
Prunus genetics and applications after de novo genome sequencing: achievements and prospects. PMID:30962943
The auxin response factor gene family in allopolyploid Brassica napus. PMID:30958842
Populus trichocarpa clade A PP2C protein phosphatases: their stress-induced expression patterns, interactions in core abscisic acid signaling, and potential for regulation of growth and development. PMID:30945147
Genome-wide association study for kernel composition and flour pasting behavior in wholemeal maize flour. PMID:30940081
The Molecular and Structural Basis of O-methylation Reaction in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn. PMID:30934718
Comparative Genomics Analysis Provides New Insight Into Molecular Basis of Stomatal Movement in Kalanchoë fedtschenkoi. PMID:30930922
Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana. PMID:30913563
Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress. PMID:30901839
Impact of Stomatal Density and Morphology on Water-Use Efficiency in a Changing World. PMID:30894867
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. PMID:30886425
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug (Notozulia entreriana Berg) Resistance. PMID:30873183
Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions. PMID:30871456
Angiosperm-Wide and Family-Level Analyses of AP2/ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication. PMID:30863419
Unbiased subgenome evolution following a recent whole-genome duplication in pear (Pyrus bretschneideri Rehd.). PMID:30854211
Genome-wide identification of CAMTA gene family members in Phaseolus vulgaris L. and their expression profiling during salt stress. PMID:30843175
Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae. PMID:30842619
Comparative genomics reveals origin of MIR159A-MIR159B paralogy, and complexities of PTGS interaction between miR159 and target GA-MYBs in Brassicaceae. PMID:30840147
Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins. PMID:30828723
Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum). PMID:30823433
Evolutionary Insight into the Clock-Associated PRR5 Transcriptional Network of Flowering Plants. PMID:30814643
Analysis of wheat gene expression related to the oxidative stress response and signal transduction under short-term osmotic stress. PMID:30808876
Origin and evolution of the octoploid strawberry genome. PMID:30804557
Technological advances in maize breeding: past, present and future. PMID:30798332
SuCComBase: a manually curated repository of plant sulfur-containing compounds. PMID:30793170
Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles. PMID:30791461
Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway. PMID:30789903
RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines. PMID:30777012
Mechanistic insights into the evolution of DUF26-containing proteins in land plants. PMID:30775457
Cold Induced Antisense Transcription of FLOWERING LOCUS C in Distant Grasses. PMID:30774642
Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species. PMID:30769903
Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler. PMID:30768175
In Silico Genome-Wide Analysis of the ATP-Binding Cassette Transporter Gene Family in Soybean (Glycine max L.) and Their Expression Profiling. PMID:30766888
Messages From the Past: New Insights in Plant Lectin Evolution. PMID:30761173
A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants. PMID:30761165
Deletion of BSG1 in Chlamydomonas reinhardtii leads to abnormal starch granule size and morphology. PMID:30760823
Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Black Cottonwood (Populus trichocarpa). PMID:30755461
Genome reorganization of the GmSHMT gene family in soybean showed a lack of functional redundancy in resistance to soybean cyst nematode. PMID:30728404
Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L. PMID:30723620
Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants. PMID:30723486
Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants. PMID:30723229
Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination. PMID:30719568
The Systems Architecture of Molecular Memory in Poplar after Abiotic Stress. PMID:30705134
SNARE Proteins LjVAMP72a and LjVAMP72b Are Required for Root Symbiosis and Root Hair Formation in Lotus japonicus. PMID:30700990
Agrobacterium-mediated Tnt1 mutagenesis of moss protonemal filaments and generation of stable mutants with impaired gametophyte. PMID:30689096
Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). PMID:30678298
Genome-wide identification and characterization of CKIN/SnRK gene family in Chlamydomonas reinhardtii. PMID:30674892
Involving community in genes and pathway curation. PMID:30649295
Genome-Wide Characterization and Identification of Trihelix Transcription Factor and Expression Profiling in Response to Abiotic Stresses in Rice (Oryza sativa L.). PMID:30634597
Systematic analysis of NAC transcription factors' gene family and identification of post-flowering drought stress responsive members in sorghum. PMID:30627770
Analysis of the distribution of assimilation products and the characteristics of transcriptomes in rice by submergence during the ripening stage. PMID:30621581
Integrated Transcriptome Analysis Reveals Plant Hormones Jasmonic Acid and Salicylic Acid Coordinate Growth and Defense Responses upon Fungal Infection in Poplar. PMID:30609760
The control of endopolygalacturonase expression by the sugarcane RAV transcription factor during aerenchyma formation. PMID:30605523
Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events. PMID:30590727
Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells. PMID:30587128
Genome-Wide Identification and Comparative Analysis for OPT Family Genes in Panax ginseng and Eleven Flowering Plants. PMID:30577553
Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. PMID:30576513
PhytoTypeDB: a database of plant protein inter-cultivar variability and function. PMID:30576486
Genome-scale characterization of the vacuole nitrate transporter Chloride Channel (CLC) genes and their transcriptional responses to diverse nutrient stresses in allotetraploid rapeseed. PMID:30571734
Genome-wide analysis of the pentatricopeptide repeat gene family in different maize genomes and its important role in kernel development. PMID:30567489
The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA Methylation Changes at a Linked Transposon. PMID:30563848
DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data. PMID:30559761
PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. PMID:30555515
Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant Kalanchoë fedtschenkoi and a Model C3 Photosynthesis Plant Arabidopsis thaliana. PMID:30546378
Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra. PMID:30541448
Fluctuating selection on migrant adaptive sodium transporter alleles in coastal Arabidopsis thaliana. PMID:30530653
Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. PMID:30520727
Downregulation of RdDM during strawberry fruit ripening. PMID:30514401
Genome-wide identification and localization of chalcone synthase family in soybean (Glycine max [L]Merr). PMID:30509179
Integrated physiologic, genomic and transcriptomic strategies involving the adaptation of allotetraploid rapeseed to nitrogen limitation. PMID:30509163
RAD-seq reveals genetic structure of the F2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression. PMID:30509159
Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses. PMID:30501109
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. PMID:30497367
OXA2b is Crucial for Proper Membrane Insertion of COX2 during Biogenesis of Complex IV in Plant Mitochondria. PMID:30487140
Engineering modular diterpene biosynthetic pathways in Physcomitrella patens. PMID:30470899
Uncovering Bax inhibitor-1 dual role in the legume-rhizobia symbiosis in common bean roots. PMID:30462254
Genome-wide identification and analysis of non-specific Lipid Transfer Proteins in hexaploid wheat. PMID:30459322
Genome-wide analysis reveals the evolution and structural features of WRINKLED1 in plants. PMID:30446819
Identification of O-acetylserine(thiol)lyase (OASTL) genes in sorghum (Sorghum bicolor) and gene expression analysis under cadmium stress. PMID:30443823
Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach. PMID:30413726
Dissecting the Genomic Diversification of Late Embryogenesis Abundant (LEA) Protein Gene Families in Plants. PMID:30407531
Proteome evolution under non-substitutable resource limitation. PMID:30405128
Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing. PMID:30397543
RNA uridylation and decay in plants. PMID:30397100
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
New insights into tomato microRNAs. PMID:30375421
Gene-guided discovery and engineering of branched cyclic peptides in plants. PMID:30373830
Bottlenecks for genome-edited crops on the road from lab to farm. PMID:30367679
Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots. PMID:30364940
Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. PMID:30353370
Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicago truncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms. PMID:30349546
RAMOSA1 ENHANCER LOCUS2-Mediated Transcriptional Repression Regulates Vegetative and Reproductive Architecture. PMID:30348817
The nitrilase PtNIT1 catabolizes herbivore-induced nitriles in Populus trichocarpa. PMID:30348089
GFDP: the gene family database in poplar. PMID:30339216
Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole-Genome Duplication. PMID:30333148
Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events. PMID:30319674
DREB2 (dehydration-responsive element-binding protein 2) type transcription factor in sorghum (Sorghum bicolor): genome-wide identification, characterization and expression profiles under cadmium and salt stresses. PMID:30305995
A Musashi Splice Variant and Its Interaction Partners Influence Temperature Acclimation in Chlamydomonas. PMID:30301774
Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes. PMID:30297664
Reconfigured Cyanogenic Glucoside Biosynthesis in Eucalyptus cladocalyx Involves a Cytochrome P450 CYP706C55. PMID:30297456
A SOC1-like gene MtSOC1a promotes flowering and primary stem elongation in Medicago. PMID:30295903
Genome-Wide Association Study in Pseudo-F2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates. PMID:30271414
Transcriptomics and co-expression networks reveal tissue-specific responses and regulatory hubs under mild and severe drought in papaya (Carica papaya L.). PMID:30267030
Bona fide choline monoxygenases evolved in Amaranthaceae plants from oxygenases of unknown function: Evidence from phylogenetics, homology modeling and docking studies. PMID:30256846
Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus). PMID:30248137
Maintaining Genome Integrity during Seed Development in Phaseolus vulgaris L.: Evidence from a Transcriptomic Profiling Study. PMID:30241355
Growing and cultivating the forest genomics database, TreeGenes. PMID:30239664
Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress. PMID:30238225
Molecular Evolution of GDP-D-Mannose Epimerase (GME), a Key Gene in Plant Ascorbic Acid Biosynthesis. PMID:30233629
Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage. PMID:30228108
A Trihelix Family Transcription Factor Is Associated with Key Genes in Mixed-Linkage Glucan Accumulation. PMID:30224432
Discovery and characterization of conserved binding of eIF4E 1 (CBE1), a eukaryotic translation initiation factor 4E-binding plant protein. PMID:30213859
Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production. PMID:30206304
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome. PMID:30184069
Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification. PMID:30180895
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species. PMID:30158558
Genome-wide Identification of PP2C Genes and Their Expression Profiling in Response to Drought and Cold Stresses in Medicago truncatula. PMID:30150630
Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants. PMID:30139765
---A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants. PMID:30135718
QTL mapping and validation of fertility restoration in West African sorghum A1 cytoplasm and identification of a potential causative mutation for Rf2. PMID:30132022
Defining the genetic components of callus formation: A GWAS approach. PMID:30118526
Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans. PMID:30113693
Assessing genome assembly quality using the LTR Assembly Index (LAI). PMID:30107434
Genomic Signatures of Adaptation to a Precipitation Gradient in Nigerian Sorghum. PMID:30097471
Response of cell-wall composition and RNA-seq transcriptome to methyl-jasmonate in Brachypodium distachyon callus. PMID:30094490
Genome wide association mapping of agro-morphological traits among a diverse collection of finger millet (Eleusine coracana L.) genotypes using SNP markers. PMID:30092057
Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes. PMID:30078073
Genome-wide identification and analysis of the ALTERNATIVE OXIDASE gene family in diploid and hexaploid wheat. PMID:30074999
Molecular characterization, modeling, and docking analysis of late phytic acid biosynthesis pathway gene, inositol polyphosphate 6-/3-/5-kinase, a potential candidate for developing low phytate crops. PMID:30073129
Evolution and diversification of the plant gibberellin receptor GID1. PMID:30068603
A Rice B-Box Protein, OsBBX14, Finely Regulates Anthocyanin Biosynthesis in Rice. PMID:30060460
Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops. PMID:30053133
Genome sequence and genetic transformation of a widely distributed and cultivated poplar. PMID:30044051
Rice with reduced stomatal density conserves water and has improved drought tolerance under future climate conditions. PMID:30043395
Identification and expression of genes in response to cassava bacterial blight infection. PMID:30039242
Effect of 1-aminocyclopropane-1-carboxylic acid (ACC)-induced ethylene on cellulose synthase A (CesA) genes in flax (Linum usitatissimum L. 'Nike') seedlings. PMID:30032481
Transcriptome Profiles of Nod Factor-independent Symbiosis in the Tropical Legume Aeschynomene evenia. PMID:30026595
MtNODULE ROOT1 and MtNODULE ROOT2 Are Essential for Indeterminate Nodule Identity. PMID:30026291
Characterization of a large sex determination region in Salix purpurea L. (Salicaceae). PMID:30022352
Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 reduces cassava brown streak disease symptom severity and incidence. PMID:30019807
MORC Domain Definition and Evolutionary Analysis of the MORC Gene Family in Green Plants. PMID:29982569
KBase: The United States Department of Energy Systems Biology Knowledgebase. PMID:29979655
Fern genomes elucidate land plant evolution and cyanobacterial symbioses. PMID:29967517
Genome-wide analysis of the invertase gene family from maize. PMID:29948658
RNA-Seq in the discovery of a sparsely expressed scent-determining monoterpene synthase in lavender (Lavandula). PMID:29948128
Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii. PMID:29931069
TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms. PMID:29929474
Comparative transcriptome analysis of Haematococcus pluvialis on astaxanthin biosynthesis in response to irradiation with red or blue LED wavelength. PMID:29916185
Oak genome reveals facets of long lifespan. PMID:29915331
In situ architecture of the algal nuclear pore complex. PMID:29915221
Genome-wide identification and characterization of the RIO atypical kinase family in plants. PMID:29892951
A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein. PMID:29884614
Comparative transcriptomics reveals shared gene expression changes during independent evolutionary origins of stem and hypocotyl/root tubers in Brassica (Brassicaceae). PMID:29856865
Comparative analysis of plant MKK gene family reveals novel expansion mechanism of the members and sheds new light on functional conservation. PMID:29843611
The effects of repeated whole genome duplication events on the evolution of cytokinin signaling pathway. PMID:29843594
Function of the evolutionarily conserved plant methionine-S-sulfoxide reductase without the catalytic residue. PMID:29808313
Characterization of gossypol biosynthetic pathway. PMID:29784821
Revised Phylogeny of the Cellulose Synthase Gene Superfamily: Insights into Cell Wall Evolution. PMID:29780036
Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch). PMID:29776387
De novo genome assembly of the red silk cotton tree (Bombax ceiba). PMID:29757382
Comparative in Silico Analysis of Ferric Reduction Oxidase (FRO) Genes Expression Patterns in Response to Abiotic Stresses, Metal and Hormone Applications. PMID:29757203
Meta-QTL analysis of seed iron and zinc concentration and content in common bean (Phaseolus vulgaris L.). PMID:29752522
Transport and Use of Bicarbonate in Plants: Current Knowledge and Challenges Ahead. PMID:29751549
Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species. PMID:29743014
Prediction of plant lncRNA by ensemble machine learning classifiers. PMID:29720103
psRNATarget: a plant small RNA target analysis server (2017 release). PMID:29718424
A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation. PMID:29713868
The Sequenced Angiosperm Genomes and Genome Databases. PMID:29706973
OMGene: mutual improvement of gene models through optimisation of evolutionary conservation. PMID:29703150
Enhanced JBrowse plugins for epigenomics data visualization. PMID:29699480
An atypical N-ethylmaleimide sensitive factor enables the viability of nematode-resistant Rhg1 soybeans. PMID:29695628
Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes. PMID:29692796
Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery. PMID:29686853
The Amount of Nitrogen Used for Photosynthesis Modulates Molecular Evolution in Plants. PMID:29684170
The nonstop decay and the RNA silencing systems operate cooperatively in plants. PMID:29672715
Genomic prediction applied to high-biomass sorghum for bioenergy production. PMID:29670457
Synergistic Binding of bHLH Transcription Factors to the Promoter of the Maize NADP-ME Gene Used in C4 Photosynthesis Is Based on an Ancient Code Found in the Ancestral C3 State. PMID:29659975
Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs). PMID:29659815
Present Scenario of Long Non-Coding RNAs in Plants. PMID:29657289
Duplication and diversification of lectin receptor-like kinases (LecRLK) genes in soybean. PMID:29651041
Genome-wide (ChIP-seq) identification of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress. PMID:29636001
Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.). PMID:29626084
Global gene regulation in tomato plant (Solanum lycopersicum) responding to vector (Bactericera cockerelli) feeding and pathogen ('Candidatus Liberibacter solanacearum') infection. PMID:29619663
IPD3 and IPD3L Function Redundantly in Rhizobial and Mycorrhizal Symbioses. PMID:29616050
Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes. PMID:29597290
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
Characterization of the basic helix-loop-helix gene family and its tissue-differential expression in response to salt stress in poplar. PMID:29576971
Ribosome profiling reveals changes in translational status of soybean transcripts during immature cotyledon development. PMID:29570733
Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story. PMID:29568308
Biochemical and genetic analyses of N metabolism in maize testcross seedlings: 2. Roots. PMID:29541827
A microtubule-dynein tethering complex regulates the axonemal inner dynein f (I1). PMID:29540525
Genome-Wide Transcriptome Analysis Reveals the Comprehensive Response of Two Susceptible Poplar Sections to Marssonina brunnea Infection. PMID:29534547
Genome-wide identification and characterization of Dof transcription factors in eggplant (Solanum melongena L.). PMID:29527420
RecQ Helicases Function in Development, DNA Repair, and Gene Targeting in Physcomitrella patens. PMID:29514942
Phytochrome B regulates resource allocation in Brassica rapa. PMID:29514292
Comparative transcriptome analysis provides key insights into gene expression pattern during the formation of nodule-like structures in Brachypodium. PMID:29511998
Up-regulation of GhTT2-3A in cotton fibres during secondary wall thickening results in brown fibres with improved quality. PMID:29509985
Simultaneous imaging and functional studies reveal a tight correlation between calcium and actin networks. PMID:29507239
Regional Heritability Mapping Provides Insights into Dry Matter Content in African White and Yellow Cassava Populations. PMID:29505634
Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement. PMID:29503654
The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants. PMID:29495437
Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri). PMID:29487610
Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching. PMID:29483921
Synopsis of the SOFL Plant-Specific Gene Family. PMID:29467189
Diel pattern of circadian clock and storage protein gene expression in leaves and during seed filling in cowpea (Vigna unguiculata). PMID:29444635
Ancient duons may underpin spatial patterning of gene expression in C4 leaves. PMID:29432183
Characterization of a new GmFAD3A allele in Brazilian CS303TNKCA soybean cultivar. PMID:29397403
Survey of Candidate Genes for Maize Resistance to Infection by Aspergillus flavus and/or Aflatoxin Contamination. PMID:29385107
Genome-wide identification, classification, and expression of phytocyanins in Populus trichocarpa. PMID:29383450
Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function. PMID:29382771
Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized Sorghum. PMID:29378822
Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta. PMID:29367617
Specific Upregulation of a Cotton Phytoene Synthase Gene Produces Golden Cottonseeds with Enhanced Provitamin A. PMID:29358599
Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut. PMID:29321580
Suppression of a single BAHD gene in Setaria viridis causes large, stable decreases in cell wall feruloylation and increases biomass digestibility. PMID:29315591
Quantile regression for genome-wide association study of flowering time-related traits in common bean. PMID:29300788
Correction: Wentao Wu, et al. Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals. Int. J. Mol. Sci. 2017, 18, 2107. PMID:29300308
A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees. PMID:29298676
Root lodging is a physical stress that changes gene expression from sucrose accumulation to degradation in sorghum. PMID:29298675
Divergent evolutionary patterns of the MAPK cascade genes in Brassica rapa and plant phylogenetics. PMID:29285397
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench). PMID:29273003
Parallel evolution of the POQR prolyl oligo peptidase gene conferring plant quantitative disease resistance. PMID:29272270
Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. PMID:29259172
Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree. PMID:29253216
Molecular Characterization and Co-expression Analysis of the SnRK2 Gene Family in Sugarcane (Saccharum officinarum L.). PMID:29247208
Mutations in the Arabidopsis AtMRS2-11/AtMGT10/VAR5 Gene Cause Leaf Reticulation. PMID:29234332
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. PMID:29233850
Prediction of cassava protein interactome based on interolog method. PMID:29222529
EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species. PMID:29220468
MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. PMID:29220435
Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population. PMID:29217731
Agronomic performance of Populus deltoides trees engineered for biofuel production. PMID:29213313
Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs. PMID:29208647
Accuracies of univariate and multivariate genomic prediction models in African cassava. PMID:29202685
Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47. PMID:29196940
Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri. PMID:29179763
Rama: a machine learning approach for ribosomal protein prediction in plants. PMID:29176736
The Terpene Synthase Gene Family of Carrot (Daucus carota L.): Identification of QTLs and Candidate Genes Associated with Terpenoid Volatile Compounds. PMID:29170675
A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.). PMID:29166879
Mannans and endo-β-mannanase transcripts are located in different seed compartments during Brassicaceae germination. PMID:29164367
PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes. PMID:29156057
Genetic dissection of early-season cold tolerance in sorghum: genome-wide association studies for seedling emergence and survival under field and controlled environment conditions. PMID:29147737
SHORTROOT-Mediated Increase in Stomatal Density Has No Impact on Photosynthetic Efficiency. PMID:29127261
Genome-Wide Identification and Expression, Protein-Protein Interaction and Evolutionary Analysis of the Seed Plant-Specific BIG GRAIN and BIG GRAIN LIKE Gene Family. PMID:29118774
Surviving a Dry Future: Abscisic Acid (ABA)-Mediated Plant Mechanisms for Conserving Water under Low Humidity. PMID:29113039
Genome-wide analysis of MATE transporters and molecular characterization of aluminum resistance in Populus. PMID:29099944
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains. PMID:29097748
Genome-wide identification and expression profile analysis of CCH gene family in Populus. PMID:29085758
Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development. PMID:29085379
Shaping the evolutionary tree of green plants: evidence from the GST family. PMID:29084977
Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation. PMID:29084582
Characterization of the lamin analogue NMCP2 in the monocot Allium cepa. PMID:29079971
A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes. PMID:29071392
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. PMID:29069403
The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire. PMID:29055088
PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. PMID:29036354
STRIDE: Species Tree Root Inference from Gene Duplication Events. PMID:29029342
Targeted Next-Generation Sequencing Identification of Mutations in Disease Resistance Gene Analogs (RGAs) in Wild and Cultivated Beets. PMID:29019931
Dissecting the 'bacon and eggs' phenotype: transcriptomics of post-anthesis colour change in Lotus. PMID:28981620
Origin of TAA Genes in Charophytes: New Insights into the Controversy over the Origin of Auxin Biosynthesis. PMID:28979280
qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms. PMID:28977518
Rootstock influence on iron uptake responses in Citrus leaves and their regulation under the Fe paradox effect. PMID:28966887
A database for orphan genes in Poaceae. PMID:28966675
The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves. PMID:28957460
Genome-wide analysis of Phaseolus vulgaris C2C2-YABBY transcription factors under salt stress conditions. PMID:28955602
A Transcriptome Approach Toward Understanding Fruit Softening in Persimmon. PMID:28955353
PEG Induces High Expression of the Cell Cycle Checkpoint Gene WEE1 in Embryogenic Callus of Medicago truncatula: Potential Link between Cell Cycle Checkpoint Regulation and Osmotic Stress. PMID:28928753
The meiotic regulator JASON utilizes alternative translation initiation sites to produce differentially localized forms. PMID:28922756
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico. PMID:28886704
Systems Identification and Characterization of Cell Wall Reassembly and Degradation Related Genes in Glycine max (L.) Merill, a Bioenergy Legume. PMID:28883533
Comprehensive description of genomewide nucleotide and structural variation in short-season soya bean. PMID:28869792
Protoplast Swelling and Hypocotyl Growth Depend on Different Auxin Signaling Pathways. PMID:28860155
Vitamin B1 diversity and characterization of biosynthesis genes in cassava. PMID:28859374
Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution. PMID:28854926
Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice. PMID:28846681
CLE peptide-encoding gene families in Medicago truncatula and Lotus japonicus, compared with those of soybean, common bean and Arabidopsis. PMID:28839170
Ancestor of land plants acquired the DNA-3-methyladenine glycosylase (MAG) gene from bacteria through horizontal gene transfer. PMID:28839126
Evolutionarily Conserved Alternative Splicing Across Monocots. PMID:28839042
Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis. PMID:28820887
Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato. PMID:28819320
Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production. PMID:28817696
Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. PMID:28814974
Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of A. hypochondriacus. PMID:28786999
Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs. PMID:28786034
QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii. PMID:28785268
OsbZIP48, a HY5 Transcription Factor Ortholog, Exerts Pleiotropic Effects in Light-Regulated Development. PMID:28775143
Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. PMID:28768484
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. PMID:28756775
Evolution of Daily Gene Co-expression Patterns from Algae to Plants. PMID:28751903
Antarctic Moss Multiprotein Bridging Factor 1c Overexpression in Arabidopsis Resulted in Enhanced Tolerance to Salt Stress. PMID:28744295
Genome-wide Analysis and Expression Divergence of the Trihelix family in Brassica Rapa: Insight into the Evolutionary Patterns in Plants. PMID:28743951
Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen. PMID:28736566
Systematic Analysis of Hsf Family Genes in the Brassica napus Genome Reveals Novel Responses to Heat, Drought and High CO2 Stresses. PMID:28729874
Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production. PMID:28724386
Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls. PMID:28720072
miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation. PMID:28710366
Spatial regulation of monolignol biosynthesis and laccase genes control developmental and stress-related lignin in flax. PMID:28705193
Characterization and Functional Analysis of the Poplar Pectate Lyase-Like Gene PtPL1-18 Reveal Its Role in the Development of Vascular Tissues. PMID:28702042
Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton. PMID:28693426
Genome-wide characterization of the aldehyde dehydrogenase gene superfamily in soybean and its potential role in drought stress response. PMID:28687067
Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants. PMID:28671678
Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences. PMID:28662199
AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula. PMID:28655750
Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. PMID:28651538
Data on the genome-wide identification of CNL R-genes in Setaria italica (L.) P. Beauv. PMID:28649585
Genome-wide analysis of UDP-glycosyltransferase super family in Brassica rapa and Brassica oleracea reveals its evolutionary history and functional characterization. PMID:28645261
Analysis of MAP kinase MPK4/MEKK1/MKK genes of Carica papaya L. comparative to other plant homologues. PMID:28642634
A sorghum (Sorghum bicolor) mutant with altered carbon isotope ratio. PMID:28640841
Genome-Wide Analysis of the RAV Family in Soybean and Functional Identification of GmRAV-03 Involvement in Salt and Drought Stresses and Exogenous ABA Treatment. PMID:28634481
OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement. PMID:28633662
Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants. PMID:28630437
A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. PMID:28625162
A Transcriptomics and Comparative Genomics Analysis Reveals Gene Families with a Role in Body Plan Complexity. PMID:28611798
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
Genome-wide survey of switchgrass NACs family provides new insights into motif and structure arrangements and reveals stress-related and tissue-specific NACs. PMID:28596552
CottonFGD: an integrated functional genomics database for cotton. PMID:28595571
Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis. PMID:28595570
Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population. PMID:28592497
Detecting early signs of heat and drought stress in Phoenix dactylifera (date palm). PMID:28570677
In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. PMID:28558696
A parts list for fungal cellulosomes revealed by comparative genomics. PMID:28555641
Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens. PMID:28549175
Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants. PMID:28523013
PSA3, a Protein on the Stromal Face of the Thylakoid Membrane, Promotes Photosystem I Accumulation in Cooperation with the Assembly Factor PYG7. PMID:28522455
OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations. PMID:28521726
Pyrenoid loss impairs carbon-concentrating mechanism induction and alters primary metabolism in Chlamydomonas reinhardtii. PMID:28520898
Genetic analysis of the Lf1 gene that controls leaflet number in soybean. PMID:28516383
Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth. PMID:28499078
Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. PMID:28498906
Evolutionary Analysis of DELLA-Associated Transcriptional Networks. PMID:28487716
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. PMID:28472432
Genome-wide analysis and expression patterns of the NAC transcription factor family in Medicago truncatula. PMID:28461723
Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis. PMID:28461722
Concerted Divergence after Gene Duplication in Polycomb Repressive Complexes. PMID:28455403
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. PMID:28453650
Functional characterization of the pinoresinol-lariciresinol reductase-2 gene reveals its roles in yatein biosynthesis and flax defense response. PMID:28451749
Pipeline to Identify Hydroxyproline-Rich Glycoproteins. PMID:28446635
The plant cell-wall enzyme AtXTH3 catalyses covalent cross-linking between cellulose and cello-oligosaccharide. PMID:28443615
Evolutionary Analysis of Snf1-Related Protein Kinase2 (SnRK2) and Calcium Sensor (SCS) Gene Lineages, and Dimerization of Rice Homologs, Suggest Deep Biochemical Conservation across Angiosperms. PMID:28424709
New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms. PMID:28424707
Regulation of CONIFERALDEHYDE 5-HYDROXYLASE expression to modulate cell wall lignin structure in rice. PMID:28421330
Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress. PMID:28417911
HopBase: a unified resource for Humulus genomics. PMID:28415075
Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli. PMID:28412928
Reproductive stage physiological and transcriptional responses to salinity stress in reciprocal populations derived from tolerant (Horkuch) and susceptible (IR29) rice. PMID:28397857
Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon. PMID:28391293
Origins and Evolution of Stomatal Development. PMID:28356502
Isolation and characterization of a promoter responsive to salt, osmotic and dehydration stresses in soybean. PMID:28350037
Virus-induced gene silencing of the two squalene synthase isoforms of apple tree (Malus × domestica L.) negatively impacts phytosterol biosynthesis, plastid pigmentation and leaf growth. PMID:28349256
Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus. PMID:28344649
Cross-Species Genome-Wide Identification of Evolutionary Conserved MicroProteins. PMID:28338802
The legume miR1514a modulates a NAC transcription factor transcript to trigger phasiRNA formation in response to drought. PMID:28338719
An efficient field and laboratory workflow for plant phylotranscriptomic projects. PMID:28337391
Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. PMID:28334050
Electromagnetic Field Seems to Not Influence Transcription via CTCT Motif in Three Plant Promoters. PMID:28326086
RNAi inhibition of feruloyl CoA 6'-hydroxylase reduces scopoletin biosynthesis and post-harvest physiological deterioration in cassava (Manihot esculenta Crantz) storage roots. PMID:28315989
Natural haplotypes of FLM non-coding sequences fine-tune flowering time in ambient spring temperatures in Arabidopsis. PMID:28294941
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. PMID:28284188
De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome. PMID:28276452
Origin and evolution of transporter substrate specificity within the NPF family. PMID:28257001
Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes. PMID:28250580
Proteome Characterization of Leaves in Common Bean. PMID:28248269
Arabidopsis Regenerating Protoplast: A Powerful Model System for Combining the Proteomics of Cell Wall Proteins and the Visualization of Cell Wall Dynamics. PMID:28248244
Comprehensive Analysis of the CDPK-SnRK Superfamily Genes in Chinese Cabbage and Its Evolutionary Implications in Plants. PMID:28239387
Gene coding for an elongation factor is involved in resistance against powdery mildew in common bean. PMID:28233030
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. PMID:28228535
Computational Tools for Genomic Studies in Plants. PMID:28217007
Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs. PMID:28209137
Experimental Evidence and In Silico Identification of Tryptophan Decarboxylase in Citrus Genus. PMID:28208655
A sweet story: Bean pod mottle virus transmission dynamics by Mexican bean beetles (Epilachna varivestis). PMID:28204501
Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.). PMID:28193168
NorWood: a gene expression resource for evo-devo studies of conifer wood development. PMID:28186632
Mitochondrial AtTrxo1 is transcriptionally regulated by AtbZIP9 and AtAZF2 and affects seed germination under saline conditions. PMID:28184497
A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups. PMID:28174582
Survey of the rubber tree genome reveals a high number of cysteine protease-encoding genes homologous to Arabidopsis SAG12. PMID:28166280
Loss of the Chloroplast Transit Peptide from an Ancestral C3 Carbonic Anhydrase Is Associated with C4 Evolution in the Grass Genus Neurachne. PMID:28153918
De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens. PMID:28140388
Characterization and Expression Analysis of Common Bean Histone Deacetylase 6 during Development and Cold Stress Response. PMID:28127547
An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance. PMID:28111887
MarpoDB: An Open Registry for Marchantia Polymorpha Genetic Parts. PMID:28100647
Evolution and structural diversification of Nictaba-like lectin genes in food crops with a focus on soybean (Glycine max). PMID:28087663
Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum. PMID:28082603
GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. PMID:28077090
Transcriptomic evidence for the control of soybean root isoflavonoid content by regulation of overlapping phenylpropanoid pathways. PMID:28077078
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
An incoherent feed-forward loop mediates robustness and tunability in a plant immune network. PMID:28069610
Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits. PMID:28068350
Duplication and Divergence of Leucine-Rich Repeat Receptor-Like Protein Kinase (LRR-RLK) Genes in Basal Angiosperm Amborella trichopoda. PMID:28066499
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
Genetic architecture of kernel composition in global sorghum germplasm. PMID:28056770
PceRBase: a database of plant competing endogenous RNA. PMID:28053167
Cytokinin Response Factor 5 has transcriptional activity governed by its C-terminal domain. PMID:28045578
Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. PMID:28043950
Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines. PMID:28040779
SDH6 and SDH7 Contribute to Anchoring Succinate Dehydrogenase to the Inner Mitochondrial Membrane in Arabidopsis thaliana. PMID:28039307
Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max. PMID:28025595
Reefgenomics.Org - a repository for marine genomics data. PMID:28025343
Developing integrated crop knowledge networks to advance candidate gene discovery. PMID:28018846
Molecular Evolution and Expression Divergence of the Aconitase (ACO) Gene Family in Land Plants. PMID:28018410
Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula. PMID:28018393
Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq. PMID:28018382
Lotus Base: An integrated information portal for the model legume Lotus japonicus. PMID:28008948
Structure and Function of the TIR Domain from the Grape NLR Protein RPV1. PMID:28008335
Concerted Up-regulation of Aldehyde/Alcohol Dehydrogenase (ADHE) and Starch in Chlamydomonas reinhardtii Increases Survival under Dark Anoxia. PMID:28007962
Genome-Wide Survey of Flavonoid Biosynthesis Genes and Gene Expression Analysis between Black- and Yellow-Seeded Brassica napus. PMID:27999578
Evolution of floral diversity: genomics, genes and gamma. PMID:27994132
RNAseq Analysis of Endornavirus-Infected vs. Endornavirus-Free Common Bean (Phaseolus vulgaris) Cultivar Black Turtle Soup. PMID:27965640
Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions. PMID:27927184
Genome-wide Analysis of Phosphoenolpyruvate Carboxylase Gene Family and Their Response to Abiotic Stresses in Soybean. PMID:27924923
Functional Analysis of Cellulose Synthase (CESA) Protein Class Specificity. PMID:27923988
Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum. PMID:27917941
Expression of Flavone Synthase II and Flavonoid 3'-Hydroxylase Is Associated with Color Variation in Tan-Colored Injured Leaves of Sorghum. PMID:27917182
Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases. PMID:27859885
Differences in glycosyltransferase family 61 accompany variation in seed coat mucilage composition in Plantago spp. PMID:27856710
Novel Genomic and Evolutionary Insight of WRKY Transcription Factors in Plant Lineage. PMID:27853303
The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development. PMID:27837089
Membrane Proteomic Insights into the Physiology and Taxonomy of an Oleaginous Green Microalga. PMID:27837088
Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas. PMID:27835957
Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination. PMID:27824062
Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. PMID:27821048
Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass. PMID:27812750
RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants. PMID:27806688
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. PMID:27803309
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
Integration of omics approaches to understand oil/protein content during seed development in oilseed crops. PMID:27796489
Eleven years of breeding efforts to combat cassava brown streak disease. PMID:27795681
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. PMID:27791167
Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation. PMID:27791104
Plant-Specific Preprotein and Amino Acid Transporter Proteins Are Required for tRNA Import into Mitochondria. PMID:27789739
Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum. PMID:27782130
PGen: large-scale genomic variations analysis workflow and browser in SoyKB. PMID:27766951
RAP2.4a Is Transported through the Phloem to Regulate Cold and Heat Tolerance in Papaya Tree (Carica papaya cv. Maradol): Implications for Protection Against Abiotic Stress. PMID:27764197
Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants. PMID:27760179
Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants. PMID:27760122
PIECE 2.0: an update for the plant gene structure comparison and evolution database. PMID:27742820
Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon. PMID:27742753
PMDBase: a database for studying microsatellite DNA and marker development in plants. PMID:27733507
Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. PMID:27729060
A transcriptomic resource for Douglas-fir seed development and analysis of transcription during late megagametophyte development. PMID:27699505
Tomato phyE Is Required for Shade Avoidance in the Absence of phyB1 and phyB2. PMID:27695458
Genome-wide identification of multifunctional laccase gene family in cotton (Gossypium spp.); expression and biochemical analysis during fiber development. PMID:27679939
Widespread natural variation of DNA methylation within angiosperms. PMID:27671052
Phosphate uptake kinetics and tissue-specific transporter expression profiles in poplar (Populus × canescens) at different phosphorus availabilities. PMID:27663513
Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera. PMID:27659322
Origin of the plant Tm-1-like gene via two independent horizontal transfer events and one gene fusion event. PMID:27647002
Genome-wide identification and characterization of GRAS transcription factors in sacred lotus (Nelumbo nucifera). PMID:27635351
Identification, Characterization, and Expression Analysis of Cell Wall Related Genes in Sorghum bicolor (L.) Moench, a Food, Fodder, and Biofuel Crop. PMID:27630645
Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification. PMID:27625671
A Conserved cis-Regulatory Module Determines Germline Fate through Activation of the Transcription Factor DUO1 Promoter. PMID:27624837
The Arabidopsis sickle Mutant Exhibits Altered Circadian Clock Responses to Cool Temperatures and Temperature-Dependent Alternative Splicing. PMID:27624757
De novo Transcriptome Analysis Reveals Distinct Defense Mechanisms by Young and Mature Leaves of Hevea brasiliensis (Para Rubber Tree). PMID:27619402
Genome-wide Identification of TCP Family Transcription Factors from Populus euphratica and Their Involvement in Leaf Shape Regulation. PMID:27605130
Genome-wide analysis of lectin receptor-like kinases in Populus. PMID:27580945
Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus. PMID:27570529
Metabolic Reconstruction of Setaria italica: A Systems Biology Approach for Integrating Tissue-Specific Omics and Pathway Analysis of Bioenergy Grasses. PMID:27559337
Genome-wide identification of salinity responsive HSP70s in common bean. PMID:27558093
The Gene Encoding Dihydroflavonol 4-Reductase Is a Candidate for the anthocyaninless Locus of Rapid Cycling Brassica rapa (Fast Plants Type). PMID:27548675
Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools. PMID:27542599
Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4. PMID:27540766
3D Sorghum Reconstructions from Depth Images Identify QTL Regulating Shoot Architecture. PMID:27528244
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure. PMID:27527578
PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants. PMID:27515999
Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica). PMID:27503335
Bioinformatics Approach in Plant Genomic Research. PMID:27499685
SoyNet: a database of co-functional networks for soybean Glycine max. PMID:27492285
Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii. PMID:27487948
Global identification and expression analysis of stress-responsive genes of the Argonaute family in apple. PMID:27475441
Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.). PMID:27473680
The Evolution of the FT/TFL1 Genes in Amaranthaceae and Their Expression Patterns in the Course of Vegetative Growth and Flowering in Chenopodium rubrum. PMID:27473314
Re-Evaluation of Reportedly Metal Tolerant Arabidopsis thaliana Accessions. PMID:27467746
IGDD: a database of intronless genes in dicots. PMID:27465544
On the origin and evolutionary consequences of gene body DNA methylation. PMID:27457936
The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. PMID:27457880
Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients. PMID:27452947
Analyses of Physcomitrella patens Ankyrin Repeat Proteins by Computational Approach. PMID:27429806
Grasses suppress shoot-borne roots to conserve water during drought. PMID:27422554
Genome-wide identification and characterization of R2R3MYB family in Rosaceae. PMID:27408811
An ancestral stomatal patterning module revealed in the non-vascular land plant Physcomitrella patens. PMID:27407102
Long-Term Growth of Moss in Microfluidic Devices Enables Subcellular Studies in Development. PMID:27406170
Genome-scale DNA variant analysis and functional validation of a SNP underlying yellow fruit color in wild strawberry. PMID:27377763
Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae. PMID:27364496
A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy. PMID:27356613
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors. PMID:27338344
The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling. PMID:27330561
Rice bifunctional phytocystatin is a dual modulator of legumain and papain-like proteases. PMID:27325119
Conservation and Expression Patterns Divergence of Ascorbic Acid d-mannose/l-galactose Pathway Genes in Brassica rapa. PMID:27313597
A comprehensive view of the web-resources related to sericulture. PMID:27307138
Systematic Identification, Evolution and Expression Analysis of the Zea mays PHT1 Gene Family Reveals Several New Members Involved in Root Colonization by Arbuscular Mycorrhizal Fungi. PMID:27304955
Evolution of Gene Duplication in Plants. PMID:27288366
nana plant2 Encodes a Maize Ortholog of the Arabidopsis Brassinosteroid Biosynthesis Gene DWARF1, Identifying Developmental Interactions between Brassinosteroids and Gibberellins. PMID:27288361
Structure of a Berberine Bridge Enzyme-Like Enzyme with an Active Site Specific to the Plant Family Brassicaceae. PMID:27276217
Bioinformatics resources for pollen. PMID:27271281
Genome-Wide Association Study of Anthracnose Resistance in Andean Beans (Phaseolus vulgaris). PMID:27270627
Promises and Challenges of Eco-Physiological Genomics in the Field: Tests of Drought Responses in Switchgrass. PMID:27246097
Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. PMID:27245738
Tissue- and Cell-Specific Cytokinin Activity in Populus × canescens Monitored by ARR5::GUS Reporter Lines in Summer and Winter. PMID:27242853
Orthology Analysis and In Vivo Complementation Studies to Elucidate the Role of DIR1 during Systemic Acquired Resistance in Arabidopsis thaliana and Cucumis sativus. PMID:27200039
Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor. PMID:27194807
Heat shock factors in tomatoes: genome-wide identification, phylogenetic analysis and expression profiling under development and heat stress. PMID:27190703
Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae. PMID:27190001
Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization. PMID:27189060
Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses. PMID:27176476
Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.). PMID:27168720
Analysis of gene expression and histone modification between C4 and non-C4 homologous genes of PPDK and PCK in maize. PMID:27161567
An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants. PMID:27159078
In situ embryo rescue for generation of wide intra- and interspecific hybrids of Panicum virgatum L. PMID:27154282
Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean. PMID:27152109
Molecular evolution analysis of WUSCHEL-related homeobox transcription factor family reveals functional divergence among clades in the homeobox region. PMID:27150824
SpinachDB: A Well-Characterized Genomic Database for Gene Family Classification and SNP Information of Spinach. PMID:27148975
Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. PMID:27138000
Abaxial Greening Phenotype in Hybrid Aspen. PMID:27137376
Auxin and Cell Wall Invertase Related Signaling during Rice Grain Development. PMID:27135493
ExactSearch: a web-based plant motif search tool. PMID:27134638
The N-Terminus of the Floral Arabidopsis TGA Transcription Factor PERIANTHIA Mediates Redox-Sensitive DNA-Binding. PMID:27128442
Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns. PMID:27112365
Learning from Co-expression Networks: Possibilities and Challenges. PMID:27092161
JBrowse: a dynamic web platform for genome visualization and analysis. PMID:27072794
Microsomal Omega-3 Fatty Acid Desaturase Genes in Low Linolenic Acid Soybean Line RG10 and Validation of Major Linolenic Acid QTL. PMID:27066063
Identification and Comparative Analysis of H2O2-Scavenging Enzymes (Ascorbate Peroxidase and Glutathione Peroxidase) in Selected Plants Employing Bioinformatics Approaches. PMID:27047498
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. PMID:27029936
Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species. PMID:27016024
MicroProtein-Mediated Recruitment of CONSTANS into a TOPLESS Trimeric Complex Represses Flowering in Arabidopsis. PMID:27015278
Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence. PMID:27014316
Knockdown of a laccase in Populus deltoides confers altered cell wall chemistry and increased sugar release. PMID:26997157
Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria. PMID:26985990
RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases. PMID:26979928
Structural modelling and transcriptional responses highlight a clade of PpKAI2-LIKE genes as candidate receptors for strigolactones in Physcomitrella patens. PMID:26979323
Functionally Similar WRKY Proteins Regulate Vacuolar Acidification in Petunia and Hair Development in Arabidopsis. PMID:26977085
ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage. PMID:26968660
Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean. PMID:26968518
Broad taxonomic characterization of Verticillium wilt resistance genes reveals an ancient origin of the tomato Ve1 immune receptor. PMID:26946045
Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean. PMID:26935840
Identification and characterization of the Populus trichocarpa CLE family. PMID:26935217
Computational Identification Raises a Riddle for Distribution of Putative NACHT NTPases in the Genome of Early Green Plants. PMID:26930396
Transposon Tagging of a Male-Sterility, Female-Sterility Gene, St8, Revealed that the Meiotic MER3 DNA Helicase Activity Is Essential for Fertility in Soybean. PMID:26930200
Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing. PMID:26922242
Comparative Transcriptomics Indicates a Role for SHORT VEGETATIVE PHASE (SVP) Genes in Mimulus guttatus Vernalization Response. PMID:26921300
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. PMID:26911872
Comprehensive Genomic Analysis and Expression Profiling of the NOX Gene Families under Abiotic Stresses and Hormones in Plants. PMID:26907500
Cell wall-related genes studies on peach cultivars with differential susceptibility to woolliness: looking for candidates as indicators of chilling tolerance. PMID:26905727
Lipid Droplet-Associated Proteins (LDAPs) Are Required for the Dynamic Regulation of Neutral Lipid Compartmentation in Plant Cells. PMID:26896396
Using intron position conservation for homology-based gene prediction. PMID:26893356
An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom. PMID:26892257
Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens. PMID:26891798
Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. PMID:26887814
In silico analysis of Mn transporters (NRAMP1) in various plant species. PMID:26878855
Characterization of DWARF14 Genes in Populus. PMID:26875827
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform. PMID:26869702
A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes. PMID:26861168
Molecular Evolution and Functional Diversification of Replication Protein A1 in Plants. PMID:26858742
A Developmental Switch of Gene Expression in the Barley Seed Mediated by HvVP1 (Viviparous-1) and HvGAMYB Interactions. PMID:26858366
Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns. PMID:26839128
Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development. PMID:26829553
Genome-Wide Identification, Characterization and Expression Analysis of the Chalcone Synthase Family in Maize. PMID:26828478
The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots. PMID:26793216
Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies. PMID:26786939
Chimeric DCL1-Partnering Proteins Provide Insights into the MicroRNA Pathway. PMID:26779232
Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.). PMID:26771740
Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication. PMID:26770968
Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain. PMID:26734045
Dosage Sensitivity of RPL9 and Concerted Evolution of Ribosomal Protein Genes in Plants. PMID:26734020
Genome-wide identification of calcium-dependent protein kinases in soybean and analyses of their transcriptional responses to insect herbivory and drought stress. PMID:26733237
Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants. PMID:26721260
Bioinformatic landscapes for plant transcription factor system research. PMID:26719053
Laterally Transferred Gene Recruited as a Venom in Parasitoid Wasps. PMID:26715630
Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae. PMID:26714854
Physiological and transcriptional analyses of developmental stages along sugarcane leaf. PMID:26714767
Identification and Characterization of Carboxylesterases from Brachypodium distachyon Deacetylating Trichothecene Mycotoxins. PMID:26712789
A Putative Chloroplast Thylakoid Metalloprotease VIRESCENT3 Regulates Chloroplast Development in Arabidopsis thaliana. PMID:26702056
Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PMID:26698853
CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing. PMID:26697366
Evolution of Catkins: Inflorescence Morphology of Selected Salicaceae in an Evolutionary and Developmental Context. PMID:26697024
Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines. PMID:26678836
Dehydration-responsive miRNAs in foxtail millet: genome-wide identification, characterization and expression profiling. PMID:26676987
Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis. PMID:26668304
Heterotrimeric G-proteins in Picea abies and their regulation in response to Heterobasidion annosum s.l. infection. PMID:26654722
Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. PMID:26654432
Understanding Brassicaceae evolution through ancestral genome reconstruction. PMID:26653025
Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus. PMID:26649868
ALCOdb: Gene Coexpression Database for Microalgae. PMID:26644461
Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling. PMID:26635818
Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii. PMID:26633994
SIFT missense predictions for genomes. PMID:26633127
Functional testing of a PF02458 homologue of putative rice arabinoxylan feruloyl transferase genes in Brachypodium distachyon. PMID:26612070
Genome-wide expression profiles of Pyropia haitanensis in response to osmotic stress by using deep sequencing technology. PMID:26611675
Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. PMID:26607788
Genome-environment associations in sorghum landraces predict adaptive traits. PMID:26601206
Evolutionarily Dynamic, but Robust, Targeting of Resistance Genes by the miR482/2118 Gene Family in the Solanaceae. PMID:26590211
Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues. PMID:26589419
PANTHER version 10: expanded protein families and functions, and analysis tools. PMID:26578592
GREENC: a Wiki-based database of plant lncRNAs. PMID:26578586
A pathogenesis related-10 protein CaARP functions as aldo/keto reductase to scavenge cytotoxic aldehydes. PMID:26577640
Identification of the Elusive Pyruvate Reductase of Chlamydomonas reinhardtii Chloroplasts. PMID:26574578
The transcriptional landscape of insect galls: psyllid (Hemiptera) gall formation in Hawaiian Metrosideros polymorpha (Myrtaceae). PMID:26572921
Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. PMID:26572793
Comparative Genomics of NAC Transcriptional Factors in Angiosperms: Implications for the Adaptation and Diversification of Flowering Plants. PMID:26569117
Evolution of the KCS gene family in plants: the history of gene duplication, sub/neofunctionalization and redundancy. PMID:26563433
A phylogenetic approach to study the origin and evolution of the CRINKLY4 family. PMID:26557128
Molecular evolution, characterization, and expression analysis of SnRK2 gene family in Pak-choi (Brassica rapa ssp. chinensis). PMID:26557127
The WRKY transcription factor family and senescence in switchgrass. PMID:26552372
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. PMID:26546515
New insights into the interplay between codon bias determinants in plants. PMID:26546225
AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling. PMID:26538092
C4 Photosynthesis in the Rice Paddy: Insights from the Noxious Weed Echinochloa glabrescens. PMID:26527656
Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing. PMID:26523132
Construction of citrus gene coexpression networks from microarray data using random matrix theory. PMID:26504573
Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes. PMID:26504533
Transcriptomics analyses of soybean leaf and root samples during water-deficit. PMID:26484247
Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity. PMID:26472115
Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize. PMID:26470872
Evolution and divergence of SBP-box genes in land plants. PMID:26467431
Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet. PMID:26444665
Analysis of the transgenerational iron deficiency stress memory in Arabidopsis thaliana plants. PMID:26442058
Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). PMID:26442024
A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants. PMID:26438786
Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. PMID:26438416
MaizeGDB update: new tools, data and interface for the maize model organism database. PMID:26432828
Genetics and physiology of cell wall polysaccharides in the model C4 grass, Setaria viridis spp. PMID:26432387
Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean. PMID:26431031
A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq. PMID:26427366
De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform. PMID:26427005
Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom. PMID:26416765
SUVH1, a Su(var)3-9 family member, promotes the expression of genes targeted by DNA methylation. PMID:26400170
Genome-Wide Identification of the Invertase Gene Family in Populus. PMID:26393355
Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops. PMID:26391769
Two cytochromes P450 catalyze S-heterocyclizations in cabbage phytoalexin biosynthesis. PMID:26389737
The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms. PMID:26377000
Gene Co-Expression Analysis Inferring the Crosstalk of Ethylene and Gibberellin in Modulating the Transcriptional Acclimation of Cassava Root Growth in Different Seasons. PMID:26366737
Arabidopsis SEIPIN Proteins Modulate Triacylglycerol Accumulation and Influence Lipid Droplet Proliferation. PMID:26362606
Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. PMID:26362138
Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean. PMID:26348924
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing. PMID:26341416
The origin and evolution of phototropins. PMID:26322073
Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. PMID:26315624
Down-regulation of p-coumaroyl quinate/shikimate 3'-hydroxylase (C3'H) and cinnamate 4-hydroxylase (C4H) genes in the lignin biosynthetic pathway of Eucalyptus urophylla × E. grandis leads to improved sugar release. PMID:26312068
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae. PMID:26307970
Disease Resistance Gene Analogs (RGAs) in Plants. PMID:26287177
MORPHEUS, a Webtool for Transcription Factor Binding Analysis Using Position Weight Matrices with Dependency. PMID:26285209
PhenoMeter: A Metabolome Database Search Tool Using Statistical Similarity Matching of Metabolic Phenotypes for High-Confidence Detection of Functional Links. PMID:26284240
Living to Die and Dying to Live: The Survival Strategy behind Leaf Senescence. PMID:26276844
Translational genomics for plant breeding with the genome sequence explosion. PMID:26269219
Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella. PMID:26268845
Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean. PMID:26263897
Comprehensive Evolutionary and Expression Analysis of FCS-Like Zinc finger Gene Family Yields Insights into Their Origin, Expansion and Divergence. PMID:26252898
Tryptophan-Independent Indole-3-Acetic Acid Synthesis: Critical Evaluation of the Evidence. PMID:26251310
Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events. PMID:26245459
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. PMID:26243257
Comparative genomics of pectinacetylesterases: Insight on function and biology. PMID:26237162
Physiological and Molecular Responses to Excess Boron in Citrus macrophylla W. PMID:26225859
The roots of future rice harvests. PMID:26224558
Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays. PMID:26217366
Phytochrome diversity in green plants and the origin of canonical plant phytochromes. PMID:26215968
Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants. PMID:26209555
Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration. PMID:26193947
Analysis of Cell Wall-Related Genes in Organs of Medicago sativa L. under Different Abiotic Stresses. PMID:26193255
Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana. PMID:26188205
Modulation of Arabidopsis and monocot root architecture by CLAVATA3/EMBRYO SURROUNDING REGION 26 peptide. PMID:26188203
A TRP conductance modulates repolarization after sensory-dependent depolarization in Chlamydomonas reinhardtii. PMID:26186626
Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species. PMID:26185739
Genome Regions Associated with Functional Performance of Soybean Stem Fibers in Polypropylene Thermoplastic Composites. PMID:26167917
Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. PMID:26162601
Conserved regulatory mechanism controls the development of cells with rooting functions in land plants. PMID:26150509
DNA methylation and gene expression in Mimulus guttatus. PMID:26148779
Genome-wide investigation and expression analysis of Sodium/Calcium exchanger gene family in rice and Arabidopsis. PMID:26134707
Genome-wide association analysis of symbiotic nitrogen fixation in common bean. PMID:26133733
Genome-Wide Analysis of the NAC Gene Family in Physic Nut (Jatropha curcas L.). PMID:26125188
Genetical genomics of Populus leaf shape variation. PMID:26122556
Genome-wide analysis reveals phytohormone action during cassava storage root initiation. PMID:26118659
De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes. PMID:26114291
The interactome of soybean GmWRKY53 using yeast 2-hybrid library screening to saturation. PMID:26102586
The Methylome of Soybean Roots during the Compatible Interaction with the Soybean Cyst Nematode. PMID:26099268
Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures. PMID:26067253
The IDA/IDA-LIKE and PIP/PIP-LIKE gene families in Arabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide. PMID:26062745
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. PMID:26052341
Parallel subfunctionalisation of PsbO protein isoforms in angiosperms revealed by phylogenetic analysis and mapping of sequence variability onto protein structure. PMID:26051374
Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants. PMID:26046541
The maize (Zea mays ssp. mays var. B73) genome encodes 33 members of the purple acid phosphatase family. PMID:26042133
Identification of Allorecognition Loci in Neurospora crassa by Genomics and Evolutionary Approaches. PMID:26025978
Glycosyltransferase family 43 is also found in early eukaryotes and has three subfamilies in Charophycean green algae. PMID:26023931
Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii. PMID:26022256
The solute specificity profiles of nucleobase cation symporter 1 (NCS1) from Zea mays and Setaria viridis illustrate functional flexibility. PMID:26022088
Beyond the Western front: targeted proteomics and organelle abundance profiling. PMID:25999968
Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses. PMID:25999407
The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization. PMID:25992947
GraP: platform for functional genomics analysis of Gossypium raimondii. PMID:25982315
Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales. PMID:25966996
Identification and distribution of the NBS-LRR gene family in the Cassava genome. PMID:25948536
Mannans and endo-β-mannanases (MAN) in Brachypodium distachyon: expression profiling and possible role of the BdMAN genes during coleorhiza-limited seed germination. PMID:25922488
Sequences enhancing cassava mosaic disease symptoms occur in the cassava genome and are associated with South African cassava mosaic virus infection. PMID:25920485
REGULATOR OF BULB BIOGENESIS1 (RBB1) Is Involved in Vacuole Bulb Formation in Arabidopsis. PMID:25915922
Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes. PMID:25915714
Flooding impairs Fe uptake and distribution in Citrus due to the strong down-regulation of genes involved in Strategy I responses to Fe deficiency in roots. PMID:25897804
The BioMart community portal: an innovative alternative to large, centralized data repositories. PMID:25897122
An Evolutionarily Conserved DOF-CONSTANS Module Controls Plant Photoperiodic Signaling. PMID:25897001
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. PMID:25893781
Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. PMID:25888265
Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants. PMID:25887590
Genomics of Volvocine Algae. PMID:25883411
Genome-Wide Association Study on Resistance to Stalk Rot Diseases in Grain Sorghum. PMID:25882062
The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history. PMID:25881027
Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress. PMID:25874911
Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants. PMID:25859541
Beyond the thale: comparative genomics and genetics of Arabidopsis relatives. PMID:25854181
The evolution of WRKY transcription factors. PMID:25849216
Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation. PMID:25849155
Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.). PMID:25846963
Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing. PMID:25837578
PTGBase: an integrated database to study tandem duplicated genes in plants. PMID:25797062
An ontology approach to comparative phenomics in plants. PMID:25774204
Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii. PMID:25769981
Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.). PMID:25740562
Appearance and elaboration of the ethylene receptor family during land plant evolution. PMID:25682121
Distribution and evolution of the lectin family in soybean (Glycine max). PMID:25679048
Two different rickettsial bacteria invading Volvox carteri. PMID:25671568
Scanning the effects of ethyl methanesulfonate on the whole genome of Lotus japonicus using second-generation sequencing analysis. PMID:25660167
Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and transfer of the rpl32 gene to the nucleus in the ancestor of the subfamily Thalictroideae. PMID:25652741
Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance. PMID:25644024
Establishing Chlamydomonas reinhardtii as an industrial biotechnology host. PMID:25641561
Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes. PMID:25638564
A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae. PMID:25635042
Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. PMID:25634987
Evidence for active maintenance of phylotranscriptomic hourglass patterns in animal and plant embryogenesis. PMID:25631928
Molecular evolution and diversification of the Argonaute family of proteins in plants. PMID:25626325
Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys. PMID:25620112
A transient receptor potential ion channel in Chlamydomonas shares key features with sensory transduction-associated TRP channels in mammals. PMID:25595824
Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean. PMID:25566308
Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa. PMID:25552535
Soybean miR172c targets the repressive AP2 transcription factor NNC1 to activate ENOD40 expression and regulate nodule initiation. PMID:25549672
CenH3 evolution in diploids and polyploids of three angiosperm genera. PMID:25547313
Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling. PMID:25540776
Transcriptional, posttranscriptional, and posttranslational regulation of SHOOT MERISTEMLESS gene expression in Arabidopsis determines gene function in the shoot apex. PMID:25524441
Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. PMID:25505034
MOROKOSHI: transcriptome database in Sorghum bicolor. PMID:25505007
Evolutionary link between metazoan RHIM motif and prion-forming domain of fungal heterokaryon incompatibility factor HET-s/HET-s. PMID:25500536
Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. PMID:25492368
Association genetics and expression patterns of a CBF4 homolog in Populus under abiotic stress. PMID:25481715
AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants. PMID:25480687
Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. PMID:25476999
Evolution of a plant-specific copper chaperone family for chloroplast copper homeostasis. PMID:25468978
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. PMID:25435546
Plastid DNA insertions in plant nuclear genomes: the sites, abundance and ages, and a predicted promoter analysis. PMID:25433709
GenomicusPlants: a web resource to study genome evolution in flowering plants. PMID:25432975
Phylogenetic analysis reveals dynamic evolution of the poly(A)-binding protein gene family in plants. PMID:25421536
Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction. PMID:25421055
Ancient horizontal transfer of transaldolase-like protein gene and its role in plant vascular development. PMID:25420550
Genome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses. PMID:25416131
The SUPERFAMILY 1.75 database in 2014: a doubling of data. PMID:25414345
Araport: the Arabidopsis information portal. PMID:25414324
Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies. PMID:25393538
A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants. PMID:25380807
diArk--the database for eukaryotic genome and transcriptome assemblies in 2014. PMID:25378341
RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PMID:25375764
Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PMID:25369033
Loss and retention of resistance genes in five species of the Brassicaceae family. PMID:25365911
A comprehensive analysis of the Cupin gene family in soybean (Glycine max). PMID:25360675
Evolution and targeting of Omp85 homologs in the chloroplast outer envelope membrane. PMID:25352854
Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max). PMID:25348509
Expression level of a flavonoid 3'-hydroxylase gene determines pathogen-induced color variation in sorghum. PMID:25346182
Natural variation in sensitivity to a loss of chloroplast translation in Arabidopsis. PMID:25336520
Molecular evolution and transcriptional regulation of the oilseed rape proline dehydrogenase genes suggest distinct roles of proline catabolism during development. PMID:25326771
Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves. PMID:25324298
Populus tremula (European aspen) shows no evidence of sexual dimorphism. PMID:25318822
Insights into the evolution and diversification of the AT-hook Motif Nuclear Localized gene family in land plants. PMID:25311531
In silico identification, phylogenetic and bioinformatic analysis of argonaute genes in plants. PMID:25309901
Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus. PMID:25287590
PIGD: a database for intronless genes in the Poaceae. PMID:25270086
Taxonomically restricted genes of Craterostigma plantagineum are modulated in their expression during dehydration and rehydration. PMID:25262421
Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome. PMID:25260959
Plant protein peptidase inhibitors: an evolutionary overview based on comparative genomics. PMID:25253557
Phosphate concentration and arbuscular mycorrhizal colonisation influence the growth, yield and expression of twelve PHT1 family phosphate transporters in foxtail millet (Setaria italica). PMID:25251671
Nucleobase and nucleoside transport and integration into plant metabolism. PMID:25250038
Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. PMID:25239219
Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae. PMID:25232838
The contractile vacuole as a key regulator of cellular water flow in Chlamydomonas reinhardtii. PMID:25217463
Switchgrass (Panicum virgatum L) flag leaf transcriptomes reveal molecular signatures of leaf development, senescence, and mineral dynamics. PMID:25173486
Structural evolution of differential amino acid effector regulation in plant chorismate mutases. PMID:25160622
Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. PMID:25158799
Contrasting metabolism in perenniating structures of upland and lowland switchgrass plants late in the growing season. PMID:25133804
PlantCAZyme: a database for plant carbohydrate-active enzymes. PMID:25125445
sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software. PMID:25120269
The diversity of rice phytocystatins. PMID:25098420
Genome-wide comparative analysis of tonoplast intrinsic protein (TIP) genes in plants. PMID:25095751
Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in cassava. PMID:25090992
Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling. PMID:25070765
A plant-specific HUA2-LIKE (HULK) gene family in Arabidopsis thaliana is essential for development. PMID:25070081
Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane. PMID:25059596
Characterization of MORE AXILLARY GROWTH genes in Populus. PMID:25036388
A novel phylogeny and morphological reconstruction of the PIN genes and first phylogeny of the ACC-oxidases (ACOs). PMID:25018760
Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). PMID:25007843
Characterization of a proposed dichorhavirus associated with the citrus leprosis disease and analysis of the host response. PMID:25004279
A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens. PMID:24999345
HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes. PMID:24982153
Adaptive evolution and divergent expression of heat stress transcription factors in grasses. PMID:24974883
Plant genomes enclose footprints of past infections by giant virus relatives. PMID:24969138
Genome-wide analysis of the NADK gene family in plants. PMID:24968225
The BdGAMYB protein from Brachypodium distachyon interacts with BdDOF24 and regulates transcription of the BdCathB gene upon seed germination. PMID:24957701
Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides). PMID:24955773
The Chlamydomonas genome project: a decade on. PMID:24950814
Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment. PMID:24927652
Multiple isoforms of phosphoenolpyruvate carboxylase in the Orchidaceae (subtribe Oncidiinae): implications for the evolution of crassulacean acid metabolism. PMID:24913627
AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis. PMID:24902892
DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction. PMID:24901469
The transcriptome landscape of early maize meiosis. PMID:24885405
A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction. PMID:24885295
Identification of candidate genes and molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp]. PMID:24885083
Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships. PMID:24884969
Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids. PMID:24884625
Exploring the evolutionary route of the acquisition of betaine aldehyde dehydrogenase activity by plant ALDH10 enzymes: implications for the synthesis of the osmoprotectant glycine betaine. PMID:24884441
Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. PMID:24865297
Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean. PMID:24859268
Extending the model of Arabidopsis telomere length and composition across Brassicaceae. PMID:24846723
Genomewide analysis of LATERAL ORGAN BOUNDARIES Domain gene family in Zea mays. PMID:24840825
Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos. PMID:24833227
Why assembling plant genome sequences is so challenging. PMID:24832233
Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data. PMID:24832228
RNA-Seq profiling of a defective seed coat mutation in Glycine max reveals differential expression of proline-rich and other cell wall protein transcripts. PMID:24828743
Transcriptional control of ROS homeostasis by KUODA1 regulates cell expansion during leaf development. PMID:24806884
Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype. PMID:24804793
Evolution and communication of subcellular compartments: An integrated approach. PMID:24786592
Genome-wide analysis of the bZIP transcription factors in cucumber. PMID:24760072
Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. PMID:24734980
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. PMID:24733898
A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. PMID:24708035
High-Throughput Genotyping of Green Algal Mutants Reveals Random Distribution of Mutagenic Insertion Sites and Endonucleolytic Cleavage of Transforming DNA. PMID:24706510
Isopentenyltransferase-1 (IPT1) knockout in Physcomitrella together with phylogenetic analyses of IPTs provide insights into evolution of plant cytokinin biosynthesis. PMID:24692654
From plant genomes to protein families: computational tools. PMID:24688740
Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula. PMID:24675968
Phylogenetic analysis of pectin-related gene families in Physcomitrella patens and nine other plant species yields evolutionary insights into cell walls. PMID:24666997
Evidence for interactions between the mitochondrial import apparatus and respiratory chain complexes via Tim21-like proteins in Arabidopsis. PMID:24653731
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. PMID:24653211
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. PMID:24647006
Shared origins of a key enzyme during the evolution of C4 and CAM metabolism. PMID:24638902
AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae. PMID:24628857
A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation. PMID:24626287
Heterotrimeric G proteins in green algae: an early innovation in the evolution of the plant lineage. PMID:24614119
Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage. PMID:24609322
The AtCathB3 gene, encoding a cathepsin B-like protease, is expressed during germination of Arabidopsis thaliana and transcriptionally repressed by the basic leucine zipper protein GBF1. PMID:24600022
Phylogeny and molecular evolution analysis of PIN-FORMED 1 in angiosperm. PMID:24586663
Origin and evolution of metal P-type ATPases in Plantae (Archaeplastida). PMID:24575101
The histone modification H3K27me3 is retained after gene duplication and correlates with conserved noncoding sequences in Arabidopsis. PMID:24567304
Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 regulates xylem development and growth by a conserved mechanism that modulates hormone signaling. PMID:24567189
Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity. PMID:24558460
CbCBF from Capsella bursa-pastoris enhances cold tolerance and restrains growth in Nicotiana tabacum by antagonizing with gibberellin and affecting cell cycle signaling. PMID:24532380
Analysis of promoters of microRNAs from a Glycine max degradome library. PMID:24510705
Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems. PMID:24504696
Two Arabidopsis loci encode novel eukaryotic initiation factor 4E isoforms that are functionally distinct from the conserved plant eukaryotic initiation factor 4E. PMID:24501003
Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PMID:24489928
The interplay of light and oxygen in the reactive oxygen stress response of Chlamydomonas reinhardtii dissected by quantitative mass spectrometry. PMID:24482124
Transcriptome and biochemical analyses revealed a detailed proanthocyanidin biosynthesis pathway in brown cotton fiber. PMID:24466041
A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums. PMID:24456189
Evolutionary classification of ammonium, nitrate, and peptide transporters in land plants. PMID:24438197
Global changes in mineral transporters in tetraploid switchgrasses (Panicum virgatum L.). PMID:24427165
Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer. PMID:24411025
Isolation and characterization of three cassava elongation factor 1 alpha (MeEF1A) promoters. PMID:24404183
Correlations between predicted protein disorder and post-translational modifications in plants. PMID:24403539
Regulation of copper homeostasis and biotic interactions by microRNA 398b in common bean. PMID:24400089
Genome-wide identification, phylogeny, evolution and expression patterns of AP2/ERF genes and cytokinin response factors in Brassica rapa ssp. pekinensis. PMID:24386201
Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics. PMID:24380843
A single CMT methyltransferase homolog is involved in CHG DNA methylation and development of Physcomitrella patens. PMID:24370935
Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. PMID:24363285
Ancient signals: comparative genomics of green plant CDPKs. PMID:24342084
Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica. PMID:24341635
POGs2: a web portal to facilitate cross-species inferences about protein architecture and function in plants. PMID:24340041
ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants. PMID:24334350
Identification of Cassava MicroRNAs under Abiotic Stress. PMID:24328029
Enzymatic characterization of a glycoside hydrolase family 5 subfamily 7 (GH5_7) mannanase from Arabidopsis thaliana. PMID:24327260
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PMID:24324815
De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters. PMID:24324652
Snf2 family gene distribution in higher plant genomes reveals DRD1 expansion and diversification in the tomato genome. PMID:24312269
Recent achievement in gene cloning and functional genomics in soybean. PMID:24311973
Catalase and NO CATALASE ACTIVITY1 promote autophagy-dependent cell death in Arabidopsis. PMID:24285797
Extensive variation in the density and distribution of DNA polymorphism in sorghum genomes. PMID:24265758
Protein subcellular relocalization increases the retention of eukaryotic duplicate genes. PMID:24265504
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing. PMID:24225854
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. PMID:24225321
S-nitrosoglutathione reductases are low-copy number, cysteine-rich proteins in plants that control multiple developmental and defense responses in Arabidopsis. PMID:24204370
Unlocking Triticeae genomics to sustainably feed the future. PMID:24204022
Differential expression of CPKs and cytosolic Ca2+ variation in resistant and susceptible apple cultivars (Malus x domestica) in response to the pathogen Erwinia amylovora and mechanical wounding. PMID:24192013
Recovery from heat, salt and osmotic stress in Physcomitrella patens requires a functional small heat shock protein PpHsp16.4. PMID:24188413
Patterns of genomic integration of nuclear chloroplast DNA fragments in plant species. PMID:24170805
Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum). PMID:24168262
Putative DHHC-cysteine-rich domain S-acyltransferase in plants. PMID:24155879
A systems biology perspective on the role of WRKY transcription factors in drought responses in plants. PMID:24146023
Identification and annotation of small RNA genes using ShortStack. PMID:24139974
Molecular characterization of Als1, an acetohydroxyacid synthase mutation conferring resistance to sulfonylurea herbicides in soybean. PMID:24129392
Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics. PMID:24098807
Zebrafish Ciliopathy Screen Plus Human Mutational Analysis Identifies C21orf59 and CCDC65 Defects as Causing Primary Ciliary Dyskinesia. PMID:24094744
Arabidopsis thaliana AMY3 is a unique redox-regulated chloroplastic α-amylase. PMID:24089528
Nodulin 22, a novel small heat-shock protein of the endoplasmic reticulum, is linked to the unfolded protein response in common bean. PMID:24073881
Ceratopteris richardii (C-fern): a model for investigating adaptive modification of vascular plant cell walls. PMID:24065974
Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits. PMID:24048646
The unique evolution of the programmed cell death 4 protein in plants. PMID:24041411
Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PMID:24040164
High-resolution mapping of zym, a recessive gene for Zucchini yellow mosaic virus resistance in cucumber. PMID:24026172
Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PMID:24023741
gff2sequence, a new user friendly tool for the generation of genomic sequences. PMID:24020993
Species and population level molecular profiling reveals cryptic recombination and emergent asymmetry in the dimorphic mating locus of C. reinhardtii. PMID:24009520
Genome-wide characterization of the Pectate Lyase-like (PLL) genes in Brassica rapa. PMID:23999922
Evolution of plant mitochondrial intron-encoded maturases: frequent lineage-specific loss and recurrent intracellular transfer to the nucleus. PMID:23979261
Mitochondrial ferritin is a functional iron-storage protein in cucumber (Cucumis sativus) roots. PMID:23967005
GnpIS: an information system to integrate genetic and genomic data from plants and fungi. PMID:23959375
De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. PMID:23957668
A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls. PMID:23951288
Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration. PMID:23938102
A contribution to the study of plant development evolution based on gene co-expression networks. PMID:23935602
Genome-wide identification and analysis of membrane-bound O-acyltransferase (MBOAT) gene family in plants. PMID:23928653
Evaluation of genome sequencing quality in selected plant species using expressed sequence tags. PMID:23922843
Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor. PMID:23900287
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. PMID:23879659
RNA interference suppression of genes in glycosyl transferase families 43 and 47 in wheat starchy endosperm causes large decreases in arabinoxylan content. PMID:23878080
Triacylglycerol mobilization is suppressed by brefeldin A in Chlamydomonas reinhardtii. PMID:23872273
An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. PMID:23869221
The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. PMID:23855885
Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants. PMID:23834366
Different evolutionary histories of two cation/proton exchanger gene families in plants. PMID:23822194
Detailed analysis of putative genes encoding small proteins in legume genomes. PMID:23802007
Towards uncovering the roles of switchgrass peroxidases in plant processes. PMID:23802005
Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice. PMID:23800963
Open access to tree genomes: the path to a better forest. PMID:23796049
Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue. PMID:23761806
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993
Evolutionary relationship and structural characterization of the EPF/EPFL gene family. PMID:23755192
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. PMID:23749190
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. PMID:23731509
ABCC1, an ATP binding cassette protein from grape berry, transports anthocyanidin 3-O-Glucosides. PMID:23723325
Arabidopsis thaliana resistance to fusarium oxysporum 2 implicates tyrosine-sulfated peptide signaling in susceptibility and resistance to root infection. PMID:23717215
The signatures of selection for translational accuracy in plant genes. PMID:23695187
Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PMID:23691254
From manual curation to visualization of gene families and networks across Solanaceae plant species. PMID:23681907
Evolutionary, molecular and genetic analyses of Tic22 homologues in Arabidopsis thaliana chloroplasts. PMID:23675512
Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. PMID:23672450
Evolution of and horizontal gene transfer in the Endornavirus genus. PMID:23667703
Genome-wide identification, characterization and expression analysis of populus leucine-rich repeat receptor-like protein kinase genes. PMID:23663326
Kinetics and functional diversity among the five members of the NADP-malic enzyme family from Zea mays, a C4 species. PMID:23649167
Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PMID:23638091
PlantGSEA: a gene set enrichment analysis toolkit for plant community. PMID:23632162
Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max). PMID:23617936
Two common bean genotypes with contrasting response to phosphorus deficiency show variations in the microRNA 399-mediated PvPHO2 regulation within the PvPHR1 signaling pathway. PMID:23591845
RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. PMID:23590974
Structure-function analysis of a broad specificity Populus trichocarpa endo-β-glucanase reveals an evolutionary link between bacterial licheninases and plant XTH gene products. PMID:23572521
A Common histone modification code on C4 genes in maize and its conservation in Sorghum and Setaria italica. PMID:23564230
Flagellated algae protein evolution suggests the prevalence of lineage-specific rules governing evolutionary rates of eukaryotic proteins. PMID:23563973
Using RNA-Seq to profile soybean seed development from fertilization to maturity. PMID:23555009
The hybrid four-CBS-domain KINβγ subunit functions as the canonical γ subunit of the plant energy sensor SnRK1. PMID:23551663
Transcriptome-wide identification of R2R3-MYB transcription factors in barley with their boron responsive expression analysis. PMID:23539153
Transcriptome Profiling Identifies Candidate Genes Associated with the Accumulation of Distinct Sulfur γ-Glutamyl Dipeptides in Phaseolus vulgaris and Vigna mungo Seeds. PMID:23532826
Global analysis of ankyrin repeat domain C3HC4-type RING finger gene family in plants. PMID:23516424
Flying saucer1 is a transmembrane RING E3 ubiquitin ligase that regulates the degree of pectin methylesterification in Arabidopsis seed mucilage. PMID:23482858
Wheat Zapper: a flexible online tool for colinearity studies in grass genomes. PMID:23474942
AGAMOUS-Like15 promotes somatic embryogenesis in Arabidopsis and soybean in part by the control of ethylene biosynthesis and response. PMID:23457229
Evolution of land plant genes encoding L-Ala-D/L-Glu epimerases (AEEs) via horizontal gene transfer and positive selection. PMID:23452519
Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species. PMID:23425243
Common bean (Phaseolus vulgaris L.) PvTIFY orchestrates global changes in transcript profile response to jasmonate and phosphorus deficiency. PMID:23402340
Developmental and environmental regulation of Aquaporin gene expression across Populus species: divergence or redundancy? PMID:23393587
Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat. PMID:23381809
Lamin-like analogues in plants: the characterization of NMCP1 in Allium cepa. PMID:23378381
Targeted mapping of quantitative trait locus regions for rhizomatousness in chromosome SBI-01 and analysis of overwintering in a Sorghum bicolor × S. propinquum population. PMID:23316113
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PMID:23299411
Genome-wide landscape of alternative splicing events in Brachypodium distachyon. PMID:23297300
PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. PMID:23292601
Identification of putative rhamnogalacturonan-II specific glycosyltransferases in Arabidopsis using a combination of bioinformatics approaches. PMID:23272088
Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data. PMID:23265623
Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom. PMID:23230446
LSM proteins provide accurate splicing and decay of selected transcripts to ensure normal Arabidopsis development. PMID:23221597
The ARC1 E3 ligase gene is frequently deleted in self-compatible Brassicaceae species and has a conserved role in Arabidopsis lyrata self-pollen rejection. PMID:23204404
OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. PMID:23203890
Finding microRNA targets in plants: current status and perspectives. PMID:23200136
Genomicus: five genome browsers for comparative genomics in eukaryota. PMID:23193262
PGDD: a database of gene and genome duplication in plants. PMID:23180799
PIECE: a database for plant gene structure comparison and evolution. PMID:23180792
Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants. PMID:23167306
Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa. PMID:23167289
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. PMID:23161682
PMRD: a curated database for genes and mutants involved in plant male reproduction. PMID:23153247
GmDREB2A;2, a canonical DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN2-type transcription factor in soybean, is posttranslationally regulated and mediates dehydration-responsive element-dependent gene expression. PMID:23151346
The novel plant protein INAPERTURATE POLLEN1 marks distinct cellular domains and controls formation of apertures in the Arabidopsis pollen exine. PMID:23136373
Identification of positive selection in disease response genes within members of the Poaceae. PMID:23073005
The SLEEPER genes: a transposase-derived angiosperm-specific gene family. PMID:23067104
PlantRNA, a database for tRNAs of photosynthetic eukaryotes. PMID:23066098
Highly efficient isolation of Populus mesophyll protoplasts and its application in transient expression assays. PMID:23028673
Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics. PMID:23007552
Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation. PMID:23006831
Identification and characterization of orthologs of AtNHX5 and AtNHX6 in Brassica napus. PMID:22973287
A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana. PMID:22969437
Characterization of a viral synergism in the monocot Brachypodium distachyon reveals distinctly altered host molecular processes associated with disease. PMID:22961132
A transcriptomic hourglass in plant embryogenesis. PMID:22951968
Predicting and analyzing protein phosphorylation sites in plants using musite. PMID:22934099
Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. PMID:22833223
Evolution of the land plant exocyst complexes. PMID:22826714
Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison. PMID:22799003
Non-coding RNAs in the plant response to abiotic stress. PMID:22761008
Taking the next step: building an Arabidopsis information portal. PMID:22751211
Ubiquitin-mediated control of plant hormone signaling. PMID:22723083
PsRobot: a web-based plant small RNA meta-analysis toolbox. PMID:22693224
Horizontal transfer of expressed genes in a parasitic flowering plant. PMID:22681756
Divergence and Redundancy in CSLD2 and CSLD3 Function During Arabidopsis Thaliana Root Hair and Female Gametophyte Development. PMID:22661983
The CELLULOSE SYNTHASE-LIKE A and CELLULOSE SYNTHASE-LIKE C families: recent advances and future perspectives. PMID:22654891
Comparative Genomics and Molecular Characterization of the Maize PIN Family Proteins. PMID:22629275
Phylogenetic Analysis of the Thylakoid ATP/ADP Carrier Reveals New Insights into Its Function Restricted to Green Plants. PMID:22629269
The eIF4F and eIFiso4F Complexes of Plants: An Evolutionary Perspective. PMID:22611336
Reference genome sequence of the model plant Setaria. PMID:22580951
The ins and outs of algal metal transport. PMID:22569643
required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. PMID:22562610
The Cassava Genome: Current Progress, Future Directions. PMID:22523606
A beginner's guide to eukaryotic genome annotation. PMID:22510764
The Arabidopsis tetratricopeptide thioredoxin-like gene family is required for osmotic stress tolerance and male sporogenesis. PMID:22232384
Dissecting plant genomes with the PLAZA comparative genomics platform. PMID:22198273
http://dx.doi.org/10.1093/nar/GKR944

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gene
metasource: Fairsharing.org
version: None

genome
metasource: Fairsharing.org
version: None

genome visualization
metasource: Fairsharing.org
version: None

plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-09-29T11:57:30.286481

general plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-09-29T11:57:30.286481

biomart
metasource: re3data.org
version: re3data.org: Phytozome; editing status 2018-12-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38021 last accessed: 2021-09-29

genome portal
metasource: re3data.org
version: re3data.org: Phytozome; editing status 2018-12-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38021 last accessed: 2021-09-29

jbrowse
metasource: re3data.org
version: re3data.org: Phytozome; editing status 2018-12-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38021 last accessed: 2021-09-29

phytomine
metasource: re3data.org
version: re3data.org: Phytozome; editing status 2018-12-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38021 last accessed: 2021-09-29

genomics
metasource: re3data.org
version: re3data.org: Phytozome; editing status 2018-12-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38021 last accessed: 2021-09-29

metasource: bio.tools
version: extracted_at: 2021-09-29T12:14:50.614025

physiology, comparative
metasource: re3data.org
version: re3data.org: Phytozome; editing status 2018-12-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38021 last accessed: 2021-09-29

plant genomes
metasource: re3data.org
version: re3data.org: Phytozome; editing status 2018-12-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38021 last accessed: 2021-09-29

plant biology
metasource: bio.tools
version: extracted_at: 2021-09-29T12:14:50.614025

gene and protein families
metasource: bio.tools
version: extracted_at: 2021-09-29T12:14:50.614025

model organisms
metasource: bio.tools
version: extracted_at: 2021-09-29T12:14:50.614025

comparative genomics
metasource: bio.tools
version: extracted_at: 2021-09-29T12:14:50.614025

gene genome genome visualization plant plant biomart genome portal jbrowse phytomine genomics physiology, comparative plant genomes plant biology gene and protein families model organisms comparative genomics

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PhytoMine

Joint Genome Institute Data Portal

GreenPhylDB: A phylogenomic database for plant comparative genomics

JGI Genome Portal

DOE Joint Genome Institute Genome Portal

TAED - The Adaptive Evolution Database

MycoCosm

Plant repeat database

Plant Reactome

Plant Genomics and Phenomics Research Data Repository

PGDD

Plant Ontology

P3DB

Plant snoRNA DB

sRNA plant portal

PlantTribes

PPDB: Plant Proteomics Database

PHYTOPROT

PlantDHS

PlantPAN