Rice Genome Annotation Project
This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data.
Description
More detailed information about this field from each metasource.
This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data.
metasource: Fairsharing.orgversion: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Webpage:
http://rice.plantbiology.msu.edu/Webpage
More detailed information about this field from each metasource.
http://rice.plantbiology.msu.edu/
metasource: Fairsharing.orgversion: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence:
Name: Rice Genome Annotation Project Attribution requiredLicence name
More detailed information about this field from each metasource.
Rice Genome Annotation Project Attribution required
metasource: Fairsharing.orgversion: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
More detailed information about this field from each metasource.
http://rice.plantbiology.msu.edu/index.shtml
metasource: Fairsharing.orgversion: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The TIGR Rice Genome Annotation Resource: improvements and new features
PMID: 17145706
metasource: Fairsharing.org
version: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications
More detailed information about this field from each metasource.
The TIGR Rice Genome Annotation Resource: improvements and new features
PMID: 17145706
metasource: Fairsharing.org
version: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
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The TIGR Rice Genome Annotation Resource: improvements and new features
PubMed citations: 553.
553 articles citing: The TIGR Rice Genome Annotation Resource: improvements and new features
Phytohormones and Transcriptome Analyses Revealed the Dynamics Involved in Spikelet Abortion and Inflorescence Development in Rice. PMID:35887236
Current Advances and Future Prospects for Molecular Research for Agronomically Important Traits in Rice. PMID:35886876
Genome-Wide Comprehensive Survey of the Subtilisin-Like Proteases Gene Family Associated With Rice Caryopsis Development. PMID:35795345
Genomic Survey of PEBP Gene Family in Rice: Identification, Phylogenetic Analysis, and Expression Profiles in Organs and under Abiotic Stresses. PMID:35736727
Impact of Modified Atmospheres on Growth and Metabolism of Meat-Spoilage Relevant Photobacterium spp. as Predicted by Comparative Proteomics. PMID:35722325
Species-Specific Gene Expansion of the Cellulose synthase Gene Superfamily in the Orchidaceae Family and Functional Divergence of Mannan Synthesis-Related Genes in Dendrobium officinale. PMID:35720557
Assessment of Rice Sheath Blight Resistance Including Associations with Plant Architecture, as Revealed by Genome-Wide Association Studies. PMID:35716230
Gene fusion as an important mechanism to generate new genes in the genus Oryza. PMID:35706016
Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. PMID:35654976
Genome-Wide Analysis of C2H2 Zinc Finger Gene Family and Its Response to Cold and Drought Stress in Sorghum [Sorghum bicolor (L.) Moench]. PMID:35628380
Role of LOC_Os01g68450, Containing DUF2358, in Salt Tolerance Is Mediated via Adaptation of Absorbed Light Energy Dissipation. PMID:35567234
Genome-Wide Characterization of DGATs and Their Expression Diversity Analysis in Response to Abiotic Stresses in Brassica napus. PMID:35567157
Genome-Wide Identification of the NAC Gene Family in Zanthoxylum bungeanum and Their Transcriptional Responses to Drought Stress. PMID:35563160
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae. PMID:35488861
Chromosome evolution and the genetic basis of agronomically important traits in greater yam. PMID:35422045
The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions. PMID:35392808
Molecular and physiological responses to desiccation indicate the abscisic acid pathway is conserved in the peat moss, Sphagnum. PMID:35383351
Relationships Among Arsenic-Related Traits, Including Rice Grain Arsenic Concentration and Straighthead Resistance, as Revealed by Genome-Wide Association. PMID:35371188
Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62. PMID:35338132
Investigation of the JASMONATE ZIM-DOMAIN Gene Family Reveals the Canonical JA-Signaling Pathway in Pineapple. PMID:35336818
Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds. PMID:35327963
Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura). PMID:35269857
The adaptive evolution of Euryale ferox to the aquatic environment through paleo-hexaploidization. PMID:35218099
Evolutionary Significance of NHX Family and NHX1 in Salinity Stress Adaptation in the Genus Oryza. PMID:35216206
Genome-Wide Identification and Gene Expression Analysis of the OTU DUB Family in Oryza sativa. PMID:35215984
Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach. PMID:35198001
Grain dispersal mechanism in cereals arose from a genome duplication followed by changes in spatial expression of genes involved in pollen development. PMID:35192007
Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes. PMID:35172831
Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development. PMID:35093018
Using Machine Learning Approaches to Predict Target Gene Expression in Rice T-DNA Insertional Mutants. PMID:34976025
Comparative genomics of Photobacterium species from terrestrial and marine habitats. PMID:34950912
Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships. PMID:34946905
A customised target capture sequencing tool for molecular identification of Aloe vera and relatives. PMID:34934068
Genome-Wide Identification and Expression Analysis of the Plant U-Box Protein Gene Family in Phyllostachys edulis. PMID:34917124
Rice functional genomics: decades' efforts and roads ahead. PMID:34881420
Low Temperature Antioxidant Activity QTL Associate with Genomic Regions Involved in Physiological Cold Stress Tolerance Responses in Rice (Oryza sativa L.). PMID:34828305
Genome-Wide Analysis of CCT Transcript Factors to Identify Genes Contributing to Photoperiodic Flowering in Oryza rufipogon. PMID:34819938
Underwater CAM photosynthesis elucidated by Isoetes genome. PMID:34732722
Recurrent mutations promote widespread structural and functional divergence of MULE-derived genes in plants. PMID:34725701
GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. PMID:34723326
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
Identification of Candidate Genes for Self-Compatibility in Perennial Ryegrass (Lolium perenne L.). PMID:34721449
Identification, expression, and functional analysis of Hsf and Hsp20 gene families in Brachypodium distachyon under heat stress. PMID:34703676
Convergent adaptation of the genomes of woody plants at the land-sea interface. PMID:34692119
The Streptochaeta Genome and the Evolution of the Grasses. PMID:34671369
OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition. PMID:34638174
Two plastid POLLUX ion channel-like proteins are required for stress-triggered stromal Ca2+release. PMID:34618095
Papaya (Carica papaya L.) Flavour Profiling. PMID:34573398
Genome-Wide Identification and Expression Profiling of 2OGD Superfamily Genes from Three Brassica Plants. PMID:34573381
Combining Genome and Gene Co-expression Network Analyses for the Identification of Genes Potentially Regulating Salt Tolerance in Rice. PMID:34512689
A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage. PMID:34484252
A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity. PMID:34451735
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
Linkage analysis of rice bacterial blight resistance gene xa20 in XM6, a mutant line from IR24. PMID:34377062
Analysis of chromosomes and nucleotides in rice to predict gene expression through codon usage pattern. PMID:34354442
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. PMID:34354050
Malectin/Malectin-like domain-containing proteins: A repertoire of cell surface molecules with broad functional potential. PMID:34308005
A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone. PMID:34270775
A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes. PMID:34267227
Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions. PMID:34211482
Identification of stable pollen development related reference genes for accurate qRT-PCR analysis and morphological variations in autotetraploid and diploid rice. PMID:34185803
A cluster of Ankyrin and Ankyrin-TPR repeat genes is associated with panicle branching diversity in rice. PMID:34097698
Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper. PMID:34064088
The amino acid permease (AAP) genes CsAAP2A and SlAAP5A/B are required for oomycete susceptibility in cucumber and tomato. PMID:33934492
Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection. PMID:33922971
Genome-wide discovery of G-quadruplexes in barley. PMID:33846409
Identification and evolution analysis of the JAZ gene family in maize. PMID:33838665
Multimerization variants as potential drivers of neofunctionalization. PMID:33771868
Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides. PMID:33767357
EORNA, a barley gene and transcript abundance database. PMID:33767193
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture. PMID:33752605
Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System. PMID:33677700
OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species. PMID:33661371
Rice and Arabidopsis homologs of yeast CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4 commonly interact with Polycomb complexes but exert divergent regulatory functions. PMID:33647940
DCT4-A New Member of the Dicarboxylate Transporter Family in C4 Grasses. PMID:33587128
Genome-wide analysis of growth-regulating factors (GRFs) in Triticum aestivum. PMID:33552727
Genome-wide identification, evolution, expression, and alternative splicing profiles of peroxiredoxin genes in cotton. PMID:33552724
Silencing of an Ubiquitin Ligase Increases Grain Width and Weight in indica Rice. PMID:33510769
Identification and development of novel salt-responsive candidate gene based SSRs (cg-SSRs) and MIR gene based SSRs (mir-SSRs) in bread wheat (Triticum aestivum). PMID:33500485
Convergence of sphingolipid desaturation across over 500 million years of plant evolution. PMID:33495556
Cytological Observations and Bulked-Segregant Analysis Coupled Global Genome Sequencing Reveal Two Genes Associated with Pollen Fertility in Tetraploid Rice. PMID:33467721
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. PMID:33452249
RSD1 Is Essential for Stomatal Patterning and Files in Rice. PMID:33329664
Statistical Approach for Biologically Relevant Gene Selection from High-Throughput Gene Expression Data. PMID:33286973
Reproductive phasiRNAs regulate reprogramming of gene expression and meiotic progression in rice. PMID:33247135
Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses. PMID:33178241
Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations. PMID:33128049
Application of Genomic Big Data in Plant Breeding:Past, Present, and Future. PMID:33126607
Auxin apical dominance governed by the OsAsp1-OsTIF1 complex determines distinctive rice caryopses development on different branches. PMID:33108367
Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice. PMID:33066648
m6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms. PMID:33053767
Transcriptome and Gene Editing Analyses Reveal MOF1a Defect Alters the Expression of Genes Associated with Tapetum Development and Chromosome Behavior at Meiosis Stage Resulting in Low Pollen Fertility of Tetraploid Rice. PMID:33050591
SUPER STARCHY1/ONAC025 participates in rice grain filling. PMID:32995698
Comparative Cytological and Transcriptome Analysis Revealed the Normal Pollen Development Process and Up-Regulation of Fertility-Related Genes in Newly Developed Tetraploid Rice. PMID:32987934
Family-Specific Gains and Losses of Protein Domains in the Legume and Grass Plant Families. PMID:32694909
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. PMID:32683045
Sequence-based genetic mapping of Cynodon dactylon Pers. reveals new insights into genome evolution in Poaceae. PMID:32647329
Identification of novel genetic factors underlying the host-pathogen interaction between barley (Hordeum vulgare L.) and powdery mildew (Blumeria graminis f. sp. hordei). PMID:32614894
Draft genome of the famous ornamental plant Paeonia suffruticosa. PMID:32551041
Vis/NIR hyperspectral imaging distinguishes sub-population, production environment, and physicochemical grain properties in rice. PMID:32518379
What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination? PMID:32508870
Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species. PMID:32482161
Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. PMID:32427841
Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles. PMID:32295768
Biological and Cellular Functions of the Microdomain-Associated FWL/CNR Protein Family in Plants. PMID:32204387
Microbial inoculation in rice regulates antioxidative reactions and defense related genes to mitigate drought stress. PMID:32179779
Fast Track to Discover Novel Promoters in Rice. PMID:31963727
Balancing the double-edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms. PMID:31945237
GPRED-GC: a Gene PREDiction model accounting for 5 '- 3' GC gradient. PMID:31874598
Rice Stress-Resistant SNP Database. PMID:31872320
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
Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation. PMID:31857423
BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. PMID:31829136
Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84T and Silicon. PMID:31771205
ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes. PMID:31757073
A ligand-independent origin of abscisic acid perception. PMID:31744875
Stress-Activated Protein Kinase OsSAPK9 Regulates Tolerance to Salt Stress and Resistance to Bacterial Blight in Rice. PMID:31712918
A modular steroid-inducible gene expression system for use in rice. PMID:31615413
Comparison between the Transcriptomes of 'KDML105' Rice and a Salt-Tolerant Chromosome Segment Substitution Line. PMID:31554292
The Rpf84 gene, encoding a ribosomal large subunit protein, RPL22, regulates symbiotic nodulation in Robinia pseudoacacia. PMID:31485773
Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.). PMID:31399885
A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses. PMID:31396532
Different Roles of Heat Shock Proteins (70 kDa) During Abiotic Stresses in Barley (Hordeum vulgare) Genotypes. PMID:31357401
A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice. PMID:31346594
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China. PMID:31307060
Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships. PMID:31235560
Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid. PMID:31138149
Convergent Co-option of the Retroviral gag Gene during the Early Evolution of Mammals. PMID:31068420
EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches. PMID:31067213
Enhancement of vitamin B6 levels in rice expressing Arabidopsis vitamin B6 biosynthesis de novo genes. PMID:31063672
Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions. PMID:31010036
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler. PMID:30768175
Genome-wide association analysis of stalk biomass and anatomical traits in maize. PMID:30704393
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848
The genome of broomcorn millet. PMID:30683860
Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). PMID:30678298
Involving community in genes and pathway curation. PMID:30649295
Bacillus velezensis YC7010 Enhances Plant Defenses Against Brown Planthopper Through Transcriptomic and Metabolic Changes in Rice. PMID:30622550
An updated gene atlas for maize reveals organ-specific and stress-induced genes. PMID:30537259
New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics. PMID:30404601
Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae). PMID:30356408
Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs. PMID:30257650
Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes. PMID:30078073
Functional analysis of the HD-Zip transcription factor genes Oshox12 and Oshox14 in rice. PMID:30028850
An EMS-induced new sequence variant, TEMS5032, in the coding region of SRS3 gene leads to shorter grain length in rice (Oryza sativa L.). PMID:30014258
Histone Deacetylase 701 (HDT701) Induces Flowering in Rice by Modulating Expression of OsIDS1. PMID:29991671
RicyerDB: A Database For Collecting Rice Yield-related Genes with Biological Analysis. PMID:29989091
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. PMID:29931210
Genome-wide identification and characterization of the RIO atypical kinase family in plants. PMID:29892951
The Challenge of Analyzing the Sugarcane Genome. PMID:29868072
ARMOUR - A Rice miRNA: mRNA Interaction Resource. PMID:29868062
Comparative analysis of plant MKK gene family reveals novel expansion mechanism of the members and sheds new light on functional conservation. PMID:29843611
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. PMID:29843602
Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes. PMID:29673330
The Receptor-Like Cytoplasmic Kinase STRK1 Phosphorylates and Activates CatC, Thereby Regulating H2O2 Homeostasis and Improving Salt Tolerance in Rice. PMID:29581216
The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors. PMID:29543153
Characterization of OglDREB2A gene from African rice (Oryza glaberrima), comparative analysis and its transcriptional regulation under salinity stress. PMID:29430353
Statistical Approach for Gene Set Analysis with Trait Specific Quantitative Trait Loci. PMID:29402907
Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions. PMID:29359127
Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes. PMID:29346292
Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut. PMID:29321580
An Integrated "Multi-Omics" Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality. PMID:29213276
Pervasive interactions of Sa and Sb loci cause high pollen sterility and abrupt changes in gene expression during meiosis that could be overcome by double neutral genes in autotetraploid rice. PMID:29197985
Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47. PMID:29196940
Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing. PMID:29190752
Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum). PMID:29134140
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
Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes. PMID:29115926
Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles. PMID:29086189
Shaping the evolutionary tree of green plants: evidence from the GST family. PMID:29084977
Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses. PMID:29051622
Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions. PMID:29045473
Expression patterns and promoter analyses of aluminum-responsive NAC genes suggest a possible growth regulation of rice mediated by aluminum, hormones and NAC transcription factors. PMID:29023561
Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. PMID:28927400
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
Zygotic Genome Activation Occurs Shortly after Fertilization in Maize. PMID:28814645
Mining sequence variations in representative polyploid sugarcane germplasm accessions. PMID:28793856
Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode. PMID:28751896
Poaceae vs. Abiotic Stress: Focus on Drought and Salt Stress, Recent Insights and Perspectives. PMID:28744298
Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm. PMID:28713414
Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis. PMID:28588571
OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies. PMID:28491065
Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa. PMID:28453813
Genetic Architecture of a Rice Nested Association Mapping Population. PMID:28450374
Root morphogenic pathways in Eucalyptus grandis are modified by the activity of protein arginine methyltransferases. PMID:28279165
Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin-like proteins in plants. PMID:28158973
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
PceRBase: a database of plant competing endogenous RNA. PMID:28053167
Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum. PMID:27917941
Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis. PMID:27881726
Novel Genomic and Evolutionary Insight of WRKY Transcription Factors in Plant Lineage. PMID:27853303
Genome sequence and analysis of the Japanese morning glory Ipomoea nil. PMID:27824041
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. PMID:27803309
Application of rice microspore-preferred promoters to manipulate early pollen development in Arabidopsis: a heterologous system. PMID:27796586
Five novel transcription factors as potential regulators of OsNHX1 gene expression in a salt tolerant rice genotype. PMID:27766460
Monolignol ferulate conjugates are naturally incorporated into plant lignins. PMID:27757415
Tomato phyE Is Required for Shade Avoidance in the Absence of phyB1 and phyB2. PMID:27695458
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
Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles. PMID:27646307
A comparative analysis of the evolution, expression, and cis-regulatory element of polygalacturonase genes in grasses and dicots. PMID:27632199
Comparative proteomic analysis reveals alterations in development and photosynthesis-related proteins in diploid and triploid rice. PMID:27619227
The Multivesicular Bodies (MVBs)-Localized AAA ATPase LRD6-6 Inhibits Immunity and Cell Death Likely through Regulating MVBs-Mediated Vesicular Trafficking in Rice. PMID:27618555
Regulatory Cross-Talks and Cascades in Rice Hormone Biosynthesis Pathways Contribute to Stress Signaling. PMID:27617021
Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes. PMID:27540739
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure. PMID:27527578
The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. PMID:27457880
Differential Regulation of Genes Coding for Organelle and Cytosolic ClpATPases under Biotic and Abiotic Stresses in Wheat. PMID:27446158
Cross species selection scans identify components of C4 photosynthesis in the grasses. PMID:27436281
De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.). PMID:27429972
Divergent Evolutionary Pattern of Sugar Transporter Genes is Associated with the Difference in Sugar Accumulation between Grasses and Eudicots. PMID:27356489
Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. PMID:27322545
Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. PMID:27287040
Molecular mapping of the Pi2/9 allelic gene Pi2-2 conferring broad-spectrum resistance to Magnaporthe oryzae in the rice cultivar Jefferson. PMID:27234247
Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy. PMID:27177130
Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products. PMID:27100228
OsPhyA modulates rice flowering time mainly through OsGI under short days and Ghd7 under long days in the absence of phytochrome B. PMID:27039184
Analyses of Old "Prokaryotic" Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa. PMID:27014324
Rice: The First Crop Genome. PMID:27003180
Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom. PMID:26918442
Genome-Wide Identification of Mitogen-Activated Protein Kinase Gene Family across Fungal Lineage Shows Presence of Novel and Diverse Activation Loop Motifs. PMID:26918378
Dose-dependent response of Trichoderma harzianum in improving drought tolerance in rice genotypes. PMID:26898554
Ocimum sanctum leaf extract induces drought stress tolerance in rice. PMID:26890603
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform. PMID:26869702
Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. PMID:26860200
PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis. PMID:26839287
Genome-Wide Analysis of NBS-LRR Genes in Sorghum Genome Revealed Several Events Contributing to NBS-LRR Gene Evolution in Grass Species. PMID:26792976
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
Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes. PMID:26699716
De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms. PMID:26684618
Genome-wide analysis of MAPKKKs shows expansion and evolution of a new MEKK class involved in solanaceous species sexual reproduction. PMID:26645086
Functional testing of a PF02458 homologue of putative rice arabinoxylan feruloyl transferase genes in Brachypodium distachyon. PMID:26612070
OryzaGenome: Genome Diversity Database of Wild Oryza Species. PMID:26578696
GREENC: a Wiki-based database of plant lncRNAs. PMID:26578586
Mitogen Activated Protein Kinase (MPK) Interacts With Auxin Influx Carrier (OsAux/LAX1) Involved in Auxin Signaling in Plant. PMID:26526688
Information Commons for Rice (IC4R). PMID:26519466
The strigolactone biosynthesis gene DWARF27 is co-opted in rhizobium symbiosis. PMID:26503135
Genetics and physiology of cell wall polysaccharides in the model C4 grass, Setaria viridis spp. PMID:26432387
How to Isolate a Plant's Hypomethylome in One Shot. PMID:26421293
Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling. PMID:26394049
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
Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage. PMID:26369665
Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice. PMID:26362270
Functions of OsDof25 in regulation of OsC4PPDK. PMID:26337938
Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition. PMID:26327607
Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR. PMID:26319516
Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes. PMID:26272901
Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.). PMID:26230730
Identification of candidate genes associated with fertility restoration of cytoplasmic male-sterility in onion (Allium cepa L.) using a combination of bulked segregant analysis and RNA-seq. PMID:26215184
Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. PMID:26195730
Proteomic Analysis to Identify Tightly-Bound Cell Wall Protein in Rice Calli. PMID:26194822
Identification and Expression Analysis of PIN-Like (PILS) Gene Family of Rice Treated with Auxin and Cytokinin. PMID:26193322
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
Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection. PMID:26184504
Profiling the expression domains of a rice-specific microRNA under stress. PMID:26029232
Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses. PMID:25999407
Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons. PMID:25954322
Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems. PMID:25909711
Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. PMID:25888265
NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome. PMID:25849067
Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea. PMID:25774486
A classification of basic helix-loop-helix transcription factors of soybean. PMID:25763382
Advances in the understanding of cuticular waxes in Arabidopsis thaliana and crop species. PMID:25693495
The role of thionins in rice defence against root pathogens. PMID:25676661
Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants. PMID:25652661
Isolation of candidate genes for the barley Ant1 and wheat Rc genes controlling anthocyanin pigmentation in different vegetative tissues. PMID:25585663
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. PMID:25517485
Rice phenylalanine ammonia-lyase gene OsPAL4 is associated with broad spectrum disease resistance. PMID:25515696
Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. PMID:25492368
Genome re-sequencing and bioinformatics analysis of a nutraceutical rice. PMID:25492220
Regulation of MAP kinase signaling cascade by microRNAs in Oryza sativa. PMID:25482813
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. PMID:25435546
Genome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses. PMID:25416131
Genome-wide transcriptome profiles of rice hybrids and their parents. PMID:25402644
RiceVarMap: a comprehensive database of rice genomic variations. PMID:25274737
Plant protein peptidase inhibitors: an evolutionary overview based on comparative genomics. PMID:25253557
Transcriptomic dissection of the rice-Burkholderia glumae interaction. PMID:25183458
Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. PMID:25129133
Unravelling the proteomic profile of rice meiocytes during early meiosis. PMID:25104955
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. PMID:25064006
Gene response in rice plants treated with continuous fog influenced by pH, was similar to that treated with biotic stress. PMID:24987489
Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides). PMID:24955773
Mapping-by-sequencing accelerates forward genetics in barley. PMID:24917130
Identification and functional characterization of bidirectional gene pairs and their intergenic regions in maize. PMID:24886269
Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study. PMID:24884676
Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data. PMID:24832228
Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]. PMID:24608103
Global analysis of lysine acetylation suggests the involvement of protein acetylation in diverse biological processes in rice (Oryza sativa). PMID:24586658
The histone modification H3K27me3 is retained after gene duplication and correlates with conserved noncoding sequences in Arabidopsis. PMID:24567304
Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PMID:24489928
Insights into the maize pan-genome and pan-transcriptome. PMID:24488960
An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. PMID:24413664
Correlations between predicted protein disorder and post-translational modifications in plants. PMID:24403539
Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato. PMID:24399174
Molecular characterization and expression analysis of Triticum aestivum squamosa-promoter binding protein-box genes involved in ear development. PMID:24386921
POGs2: a web portal to facilitate cross-species inferences about protein architecture and function in plants. PMID:24340041
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. PMID:24280374
Narrowing down the targets for yield improvement in rice under normal and abiotic stress conditions via expression profiling of yield-related genes. PMID:24280046
The Rice Oligonucleotide Array Database: an atlas of rice gene expression. PMID:24279809
Genome-wide identification and expression analysis of the mitogen-activated protein kinase gene family from banana suggest involvement of specific members in different stages of fruit ripening. PMID:24275941
Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa. PMID:24265739
Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing. PMID:24190103
Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture. PMID:24170127
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. PMID:24163125
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. PMID:24147765
RiceWiki: a wiki-based database for community curation of rice genes. PMID:24136999
Genome-wide survey on genomic variation, expression divergence, and evolution in two contrasting rice genotypes under high salinity stress. PMID:24121498
Natural variation of the RICE FLOWERING LOCUS T 1 contributes to flowering time divergence in rice. PMID:24098411
gff2sequence, a new user friendly tool for the generation of genomic sequences. PMID:24020993
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. PMID:23986771
Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum. PMID:23923055
Evaluation of genome sequencing quality in selected plant species using expressed sequence tags. PMID:23922843
Coexpression patterns indicate that GPI-anchored non-specific lipid transfer proteins are involved in accumulation of cuticular wax, suberin and sporopollenin. PMID:23893219
A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. PMID:23874666
Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. PMID:23874343
A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis. PMID:23819624
Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and Panicoid crop species. PMID:23802002
Genome-wide expression analysis of rice aquaporin genes and development of a functional gene network mediated by aquaporin expression in roots. PMID:23801298
Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice. PMID:23800963
A computational systems biology study for understanding salt tolerance mechanism in rice. PMID:23762267
Hop-on hop-off: importin-α-guided tours to the nucleus in innate immune signaling. PMID:23734157
Strategies for vitamin B6 biofortification of plants: a dual role as a micronutrient and a stress protectant. PMID:23734155
Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function. PMID:23717514
Characterization of the phosphofructokinase gene family in rice and its expression under oxygen deficiency stress. PMID:23717315
Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid. PMID:23705659
Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes. PMID:23701735
Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice. PMID:23696832
PLANEX: the plant co-expression database. PMID:23688397
RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. PMID:23660286
dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts. PMID:23660284
PlantGSEA: a gene set enrichment analysis toolkit for plant community. PMID:23632162
Analysis of cytoplasmic effects and fine-mapping of a genic male sterile line in rice. PMID:23613915
Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. PMID:23613580
Transcriptional profiling of rice early response to Magnaporthe oryzae identified OsWRKYs as important regulators in rice blast resistance. PMID:23544090
Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array. PMID:23536906
Computational predictions provide insights into the biology of TAL effector target sites. PMID:23526890
Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. PMID:23505380
Wheat Zapper: a flexible online tool for colinearity studies in grass genomes. PMID:23474942
Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage. PMID:23437136
The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). PMID:23435089
Fine mapping of qSB-11(LE), the QTL that confers partial resistance to rice sheath blight. PMID:23423653
Massive-scale gene co-expression network construction and robustness testing using random matrix theory. PMID:23409071
Comparison of early transcriptome responses to copper and cadmium in rice roots. PMID:23400832
Locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in Arabidopsis and rice. PMID:23362157
Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. PMID:23355544
Orchidstra: an integrated orchid functional genomics database. PMID:23324169
Exploitation of interspecific diversity for monocot crop improvement. PMID:23321705
Control of transposon activity by a histone H3K4 demethylase in rice. PMID:23319643
Comparative genomics of the lipid-body-membrane proteins oleosin, caleosin and steroleosin in magnoliophyte, lycophyte and bryophyte. PMID:23317702
STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. PMID:23314754
UniVIO: a multiple omics database with hormonome and transcriptome data from rice. PMID:23314752
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PMID:23299411
Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.). PMID:23292293
Braving the attitude of altitude: Caragana jubata at work in cold desert of Himalaya. PMID:23289064
A flexible ancestral genome reconstruction method based on gapped adjacencies. PMID:23281872
Genomewide analysis of intronic microRNAs in rice and Arabidopsis. PMID:23271017
Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom. PMID:23230446
Genome-wide analysis of glutathione reductase (GR) genes from rice and Arabidopsis. PMID:23221779
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
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
RiceFREND: a platform for retrieving coexpressed gene networks in rice. PMID:23180784
RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. PMID:23180765
The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns. PMID:23167570
PMRD: a curated database for genes and mutants involved in plant male reproduction. PMID:23153247
Expression analysis of calmodulin and calmodulin-like genes from rice, Oryza sativa L. PMID:23134977
The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling. PMID:23126376
The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis. PMID:23118960
Comparative genome-wide transcriptional analysis of Al-responsive genes reveals novel Al tolerance mechanisms in rice. PMID:23110212
Genome wide analysis of Cyclophilin gene family from rice and Arabidopsis and its comparison with yeast. PMID:23073011
The SLEEPER genes: a transposase-derived angiosperm-specific gene family. PMID:23067104
Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. PMID:23050870
Alterations of mitochondrial protein assembly and jasmonic acid biosynthesis pathway in Honglian (HL)-type cytoplasmic male sterility rice. PMID:23027867
Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics. PMID:23007552
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. PMID:22992304
Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat. PMID:22989011
Transcriptomic changes and signalling pathways induced by arsenic stress in rice roots. PMID:22987115
A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa. PMID:22986792
Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background. PMID:22953761
Molecular characterization and comparative sequence analysis of defense-related gene, Oryza rufipogon receptor-like protein kinase 1. PMID:22942769
Genome-wide analysis of lectin receptor-like kinase family from Arabidopsis and rice. PMID:22936328
Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat. PMID:22935214
A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq. PMID:22935196
Brachypodium distachyon as a model for defining the allergen potential of non-prolamin proteins. PMID:22933233
Transcriptome response to nitrogen starvation in rice. PMID:22922198
Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin. PMID:22865125
AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots. PMID:22807623
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. PMID:22801500
Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. PMID:22793791
Transcriptome and methylome interactions in rice hybrids. PMID:22778444
Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.). PMID:22736259
Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize. PMID:22732243
Losing identity: structural diversity of transposable elements belonging to different classes in the genome of Anopheles gambiae. PMID:22726298
PsRobot: a web-based plant small RNA meta-analysis toolbox. PMID:22693224
Horizontal transfer of expressed genes in a parasitic flowering plant. PMID:22681756
Identification of gene modules associated with drought response in rice by network-based analysis. PMID:22662107
RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa. PMID:22645600
The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features. PMID:22639657
Transcription factor OsHsfC1b regulates salt tolerance and development in Oryza sativa ssp. japonica. PMID:22616023
New cis-regulatory elements in the Rht-D1b locus region of wheat. PMID:22592657
A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons. PMID:22544262
Transcriptional response of Medicago truncatula sulphate transporters to arbuscular mycorrhizal symbiosis with and without sulphur stress. PMID:22535379
Comprehensive gene expression analysis of the NAC gene family under normal growth conditions, hormone treatment, and drought stress conditions in rice using near-isogenic lines (NILs) generated from crossing Aday Selection (drought tolerant) and IR64. PMID:22526427
Characterization and evolution of microRNA genes derived from repetitive elements and duplication events in plants. PMID:22523544
The family of Deg/HtrA proteases in plants. PMID:22520048
A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation. PMID:22500940
Chromosomal Location of HCA1 and HCA2, Hybrid Chlorosis Genes in Rice. PMID:22500165
Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PMID:22438891
MicroRNA profiles and their control of male gametophyte development in rice. PMID:22403030
Identification of genome-wide variations among three elite restorer lines for hybrid-rice. PMID:22383984
GrameneMart: the BioMart data portal for the Gramene project. PMID:22374386
A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PMID:22359654
Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. PMID:22333298
Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots. PMID:22292855
Genome-wide analysis of syntenic gene deletion in the grasses. PMID:22275519
Identification of grass-specific enzyme that acylates monolignols with p-coumarate. PMID:22267741
Evolution and functional diversification of the small heat shock protein/α-crystallin family in higher plants. PMID:22210597
Dissecting plant genomes with the PLAZA comparative genomics platform. PMID:22198273
Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. PMID:22198147
Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes. PMID:22195734
Characteristic expression of rice pathogenesis-related proteins in rice leaves during interactions with Xanthomonas oryzae pv. oryzae. PMID:22187088
GReEn: a tool for efficient compression of genome resequencing data. PMID:22139935
Phytozome: a comparative platform for green plant genomics. PMID:22110026
Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. PMID:22102215
Identification of transcriptome profiles and signaling pathways for the allelochemical juglone in rice roots. PMID:22065257
Selection for higher gene copy number after different types of plant gene duplications. PMID:22056313
Genetic dissection of the biotic stress response using a genome-scale gene network for rice. PMID:22042862
A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PMID:22039485
Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data. PMID:21984925
Structural characterization of plant defensin protein superfamily. PMID:21947884
Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing. PMID:21935421
Leymus EST linkage maps identify 4NsL-5NsL reciprocal translocation, wheat-Leymus chromosome introgressions, and functionally important gene loci. PMID:21915709
Comparative analysis of putative pathogenesis-related gene expression in two Rhizoctonia solani pathosystems. PMID:21909999
Exploiting co-linearity among grass species to map the Aegilops ventricosa-derived Pch1 eyespot resistance in wheat and establish its relationship to Pch2. PMID:21833553
Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice. PMID:21806801
Gene coexpression network analysis as a source of functional annotation for rice genes. PMID:21799793
A major locus qS12, located in a duplicated segment of chromosome 12, causes spikelet sterility in an indica-japonica rice hybrid. PMID:21792631
Identification and validation of rice reference proteins for western blotting. PMID:21705388
Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions. PMID:21627843
Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. PMID:21606319
Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice. PMID:21598083
Evolutionary history of the GH3 family of acyl adenylases in rosids. PMID:21594748
Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues. PMID:21569431
The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. PMID:21515685
OryzaPG-DB: rice proteome database based on shotgun proteogenomics. PMID:21486466
A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PMID:21455299
Rice-Map: a new-generation rice genome browser. PMID:21450055
Exploration of plant genomes in the FLAGdb++ environment. PMID:21447150
High-resolution mapping of Rsn1, a locus controlling sensitivity of rice to a necrosis-inducing phytotoxin from Rhizoctonia solani AG1-IA. PMID:21424397
Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species. PMID:21423767
SyMAP v3.4: a turnkey synteny system with application to plant genomes. PMID:21398631
Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PMID:21390234
Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. PMID:21385395
The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles. PMID:21365258
Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. PMID:21332978
High-resolution genetic mapping and candidate gene identification of the SLP1 locus that controls glume development in rice. PMID:21327937
Fine mapping QTL for drought resistance traits in rice (Oryza sativa L.) using bulk segregant analysis. PMID:21298364
A novel compression tool for efficient storage of genome resequencing data. PMID:21266471
Genetic and molecular analysis of a purple sheath somaclonal mutant in japonica rice. PMID:21249365
Differential expression and alternative splicing of rice sulphate transporter family members regulate sulphur status during plant growth, development and stress conditions. PMID:21221698
Plant noncoding RNA gene discovery by "single-genome comparative genomics". PMID:21220549
Rice TOGO Browser: A platform to retrieve integrated information on rice functional and applied genomics. PMID:21216747
Functional genomics of rice pollen and seed development by genome-wide transcript profiling and Ds insertion mutagenesis. PMID:21209789
Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice. PMID:21205614
RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. PMID:21186176
OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. PMID:21186175
An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development. PMID:21124849
Gramene database in 2010: updates and extensions. PMID:21076153
MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. PMID:21075962
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. PMID:21037263
Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses. PMID:20941508
Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants. PMID:20932300
Twenty-first century plant biology: impacts of the Arabidopsis genome on plant biology and agriculture. PMID:20921172
RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. PMID:20860998
Arabidopsis VILLIN1 and VILLIN3 have overlapping and distinct activities in actin bundle formation and turnover. PMID:20807878
Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice. PMID:20729474
Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence. PMID:20683632
Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms. PMID:20682074
The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks. PMID:20668062
Efficient plant gene identification based on interspecies mapping of full-length cDNAs. PMID:20668003
DNA repair and recombination in higher plants: insights from comparative genomics of Arabidopsis and rice. PMID:20646326
Modeling-dependent protein characterization of the rice aldehyde dehydrogenase (ALDH) superfamily reveals distinct functional and structural features. PMID:20634950
Targeted mapping of Cdu1, a major locus regulating grain cadmium concentration in durum wheat (Triticum turgidum L. var durum). PMID:20559817
The Protein Disulfide Isomerase gene family in bread wheat (T. aestivum L.). PMID:20525253
Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes. PMID:20520764
A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block. PMID:20507561
Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. PMID:20498060
Strigolactone regulation of shoot branching in chrysanthemum (Dendranthema grandiflorum). PMID:20478970
GC3 biology in corn, rice, sorghum and other grasses. PMID:20470436
A genetic model for the female sterility barrier between Asian and African cultivated rice species. PMID:20457876
Natural and artificial mutants as valuable resources for functional genomics and molecular breeding. PMID:20440406
agriGO: a GO analysis toolkit for the agricultural community. PMID:20435677
Sequence variation and selection of small RNAs in domesticated rice. PMID:20429951
Ergatis: a web interface and scalable software system for bioinformatics workflows. PMID:20413634
Shared probe design and existing microarray reanalysis using PICKY. PMID:20406469
Genome-wide analysis of helicase gene family from rice and Arabidopsis: a comparison with yeast and human. PMID:20383562
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. PMID:20222994
RNase T2 genes from rice and the evolution of secretory ribonucleases in plants. PMID:20182746
Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. PMID:20152032
Identification and mapping of the leaf stripe resistance gene Rdg1a in Hordeum spontaneum. PMID:20041226
Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. PMID:19936069
A genome-wide characterization of microRNA genes in maize. PMID:19936050
Detailed analysis of a contiguous 22-Mb region of the maize genome. PMID:19936048
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. PMID:19892828
Integrated analyses of the rice secretome. PMID:19794859
Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. PMID:19698139
Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. PMID:19618278
Identification and characterization of pseudogenes in the rice gene complement. PMID:19607679
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. PMID:19597147
Evidence-based gene predictions in plant genomes. PMID:19541913
Expansion mechanisms and functional annotations of hypothetical genes in the rice genome. PMID:19535473
Orymold: ontology based gene expression data integration and analysis tool applied to rice. PMID:19463186
plantsUPS: a database of plants' Ubiquitin Proteasome System. PMID:19445698
Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses. PMID:19363683
The Sorghum bicolor genome and the diversification of grasses. PMID:19189423
Genomic and genetic database resources for the grasses. PMID:19126704
Comparative genomics of grasses promises a bountiful harvest. PMID:19126703
RICD: a rice indica cDNA database resource for rice functional genomics. PMID:19036133
Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes. PMID:18998058
QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR. PMID:18976492
Insights into corn genes derived from large-scale cDNA sequencing. PMID:18937034
Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PMID:18836531
Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions. PMID:18825415
The ATG autophagic conjugation system in maize: ATG transcripts and abundance of the ATG8-lipid adduct are regulated by development and nutrient availability. PMID:18790996
The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. PMID:18775973
Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. PMID:18650402
Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. PMID:18554403
Rice molecular breeding laboratories in the genomics era: Current status and future considerations. PMID:18528527
Spatial distribution of transcript changes in the maize primary root elongation zone at low water potential. PMID:18387193
Dual coding of siRNAs and miRNAs by plant transposable elements. PMID:18367716
Highly specific gene silencing by artificial miRNAs in rice. PMID:18350165
Transcriptome analysis of grain development in hexaploid wheat. PMID:18325108
Arabidopsis ribosomal proteins RPL23aA and RPL23aB are differentially targeted to the nucleolus and are disparately required for normal development. PMID:18322146
Genome-wide analysis for identification of salt-responsive genes in common wheat. PMID:18320247
A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis. PMID:18310306
Development of a novel data mining tool to find cis-elements in rice gene promoter regions. PMID:18302796
Comparative molecular biological analysis of membrane transport genes in organisms. PMID:18293089
Characterization of paralogous protein families in rice. PMID:18284697
The Rice Annotation Project Database (RAP-DB): 2008 update. PMID:18089549
PlantGDB: a resource for comparative plant genomics. PMID:18063570
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PMID:18043742
Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns. PMID:17997832
Gramene: a growing plant comparative genomics resource. PMID:17984077
EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome. PMID:17961238
Identification and characterization of lineage-specific genes within the Poaceae. PMID:17951464
A genome-wide gain-of function analysis of rice genes using the FOX-hunting system. PMID:17929174
MELOGEN: an EST database for melon functional genomics. PMID:17767721
A rice phenomics study--phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. PMID:17701278
Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence. PMID:17439966
A novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan. PMID:17351055
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chromosome
metasource: Fairsharing.org
version: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Tags
More detailed information about this field from each metasource.
chromosome
metasource: Fairsharing.orgversion: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: Rice Genome Annotation Project; Rice Genome Annotation Project; DOI: https://doi.org/10.25504/FAIRsharing.qrw6b7; Last edited: April 26, 2021, 2:41 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
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