R3N49G last accessed: 2022-11-04

Other names: Cotton Database Resources

CottonGen is a cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts.

Webpage:

https://www.cottongen.org/

Licence:

Name: other
URL: https://www.cottongen.org/disclaimer

Publications:

Publications
More detailed information about this field from each metasource.

CottonGen: a genomics, genetics and breeding database for cotton research
PMID: 24203703
metasource: Fairsharing.org
version: None

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:10.304498

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases
PMID: 31725859
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:10.304498

http://dx.doi.org/10.1093/nar/gkt1064
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

CottonGen: a genomics, genetics and breeding database for cotton research PubMed citations: 125.

125 articles citing: CottonGen: a genomics, genetics and breeding database for cotton research

AAQSP increases mapping resolution of stable QTLs through applying NGS-BSA in multiple genetic backgrounds. PMID:35904626
Gb_ANR-47 Enhances the Resistance of Gossypium barbadense to Fusarium oxysporum f. sp. vasinfectum (FOV) by Regulating the Content of Proanthocyanidins. PMID:35893607
A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants. PMID:35853967
Expression Patterns Divergence of Reciprocal F1 Hybrids Between Gossypium hirsutum and Gossypium barbadense Reveals Overdominance Mediating Interspecific Biomass Heterosis. PMID:35845678
Enhanced seedling growth by 3-n-pentadecylphenolethanolamide is mediated by fatty acid amide hydrolases in upland cotton (Gossypium hirsutum L.). PMID:35844778
Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton. PMID:35831870
Genome-wide identification and functional analysis of class III peroxidases in Gossypium hirsutum. PMID:35795174
Whole-Genome Resequencing Deciphers New Insight Into Genetic Diversity and Signatures of Resistance in Cultivated Cotton Gossypium hirsutum. PMID:35778659
Detection of Stable Elite Haplotypes and Potential Candidate Genes of Boll Weight Across Multiple Environments via GWAS in Upland Cotton. PMID:35769298
Potential Roles of 1-Aminocyclopropane-1-carboxylic Acid Synthase Genes in the Response of Gossypium Species to Abiotic Stress by Genome-Wide Identification and Expression Analysis. PMID:35684296
Analysis of the PRA1 Genes in Cotton Identifies the Role of GhPRA1.B1-1A in Verticillium dahliae Resistance. PMID:35627150
Transcriptome Analysis Reveals Differences in Anthocyanin Accumulation in Cotton (Gossypium hirsutum L.) Induced by Red and Blue Light. PMID:35432402
Comprehensive identification and expression analysis of CRY gene family in Gossypium. PMID:35331129
Genome-Wide Analysis of the GW2-Like Genes in Gossypium and Functional Characterization of the Seed Size Effect of GhGW2-2D. PMID:35330874
Genome wide study of cysteine rich receptor like proteins in Gossypium sp. PMID:35318409
A Calmodulin-Like Gene (GbCML7) for Fiber Strength and Yield Improvement Identified by Resequencing Core Accessions of a Pedigree in Gossypium barbadense. PMID:35185964
GRAND: An Integrated Genome, Transcriptome Resources, and Gene Network Database for Gossypium. PMID:35126443
Evolution and Stress Responses of CLO Genes and Potential Function of the GhCLO06 Gene in Salt Resistance of Cotton. PMID:35111180
Uncovering Novel Genomic Regions and Candidate Genes for Senescence-Related Traits by Genome-Wide Association Studies in Upland Cotton (Gossypium hirsutum L.). PMID:35069667
Biochemical and Expression Analyses Revealed the Involvement of Proanthocyanidins and/or Their Derivatives in Fiber Pigmentation of Gossypium stocksii. PMID:35055193
CottonGVD: A Comprehensive Genomic Variation Database for Cultivated Cottons. PMID:34992626
Profiling of H3K4me3 and H3K27me3 and Their Roles in Gene Subfunctionalization in Allotetraploid Cotton. PMID:34975944
Evolutionary Relationships and Divergence of KNOTTED1-Like Family Genes Involved in Salt Tolerance and Development in Cotton (Gossypium hirsutum L.). PMID:34970288
CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PMID:34961276
Silencing of GhKEA4 and GhKEA12 Revealed Their Potential Functions Under Salt and Potassium Stresses in Upland Cotton. PMID:34950173
The Evolution and Expression Profiles of EC1 Gene Family during Development in Cotton. PMID:34946950
Genome-wide analysis of the CalS gene family in cotton reveals their potential roles in fiber development and responses to stress. PMID:34909280
Phylogenetic Analysis of the Membrane Attack Complex/Perforin Domain-Containing Proteins in Gossypium and the Role of GhMACPF26 in Cotton Under Cold Stress. PMID:34868097
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. PMID:34850103
Quantitative Trait Locus Analysis and Identification of Candidate Genes for Micronaire in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense. PMID:34777444
Genome-Wide Analysis of the Phospholipase D Family in Five Cotton Species, and Potential Role of GhPLD2 in Fiber Development and Anther Dehiscence. PMID:34659294
Evolutionary Implications of the RNA N6-Methyladenosine Methylome in Plants. PMID:34633447
Genome-Wide Analysis of SRNF Genes in Gossypium hirsutum Reveals the Role of GhSRNF18 in Primary Root Growth. PMID:34630480
The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility. PMID:34549783
Genome-Wide Identification and Functional Investigation of 1-Aminocyclopropane-1-carboxylic Acid Oxidase (ACO) Genes in Cotton. PMID:34451744
Evolutionary and Characteristic Analysis of RING-DUF1117 E3 Ubiquitin Ligase Genes in Gossypium Discerning the Role of GhRDUF4D in Verticillium dahliae Resistance. PMID:34439811
Identification and Characterization of the ERF Subfamily B3 Group Revealed GhERF13.12 Improves Salt Tolerance in Upland Cotton. PMID:34434208
The Breeding Information Management System (BIMS): an online resource for crop breeding. PMID:34415997
Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress. PMID:34367198
Evolution and Characterization of Acetyl Coenzyme A: Diacylglycerol Acyltransferase Genes in Cotton Identify the Roles of GhDGAT3D in Oil Biosynthesis and Fatty Acid Composition. PMID:34356061
ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. PMID:34273949
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. PMID:34251419
Genome-Wide Comparative Analysis of Heat Shock Transcription Factors Provides Novel Insights for Evolutionary History and Expression Characterization in Cotton Diploid and Tetraploid Genomes. PMID:34168673
Molecular Traits and Functional Analysis of the CLAVATA3/Endosperm Surrounding Region-Related Small Signaling Peptides in Three Species of Gossypium Genus. PMID:34149772
Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress. PMID:34044774
Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton. PMID:34026441
pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity. PMID:33983433
POPULATION STRUCTURE AND GENETIC DIVERSITY OF THE PEE DEE COTTON BREEDING PROGRAM. PMID:33914887
Tripal MegaSearch: a tool for interactive and customizable query and download of big data. PMID:33900378
The Gossypium stocksii genome as a novel resource for cotton improvement. PMID:33871013
Characterization of cotton ARF factors and the role of GhARF2b in fiber development. PMID:33752589
Genome-Wide Mining of MYB Transcription Factors in the Anthocyanin Biosynthesis Pathway of Gossypium Hirsutum. PMID:33502632
CorkOakDB-The Cork Oak Genome Database Portal. PMID:33382885
Transcriptomic and proteomic analyses of a new cytoplasmic male sterile line with a wild Gossypium bickii genetic background. PMID:33267770
Elucidation of sequence polymorphism in fuzzless-seed cotton lines. PMID:33141290
Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding. PMID:33042184
Application of Pedimap: a pedigree visualization tool to facilitate the decisioning of rice breeding in Sri Lanka. PMID:32868819
Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.). PMID:32854609
Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium. PMID:32831017
Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum. PMID:32600247
Conservation and Divergence in Duplicated Fiber Coexpression Networks Accompanying Domestication of the Polyploid Gossypium hirsutum L. PMID:32586849
Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology. PMID:32391043
Strengthening of banana breeding through data digitalization. PMID:32283556
Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance. PMID:32268879
Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander. PMID:32257241
Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium. PMID:32185507
The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. PMID:32122962
Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family. PMID:31996127
Fiber Quality Improvement in Upland Cotton (Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application. PMID:31921240
Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.). PMID:31843806
Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. PMID:31725859
Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps. PMID:31688940
MaGenDB: a functional genomics hub for Malvaceae plants. PMID:31665439
Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton. PMID:31624240
Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum. PMID:31286851
Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton. PMID:31262248
A genomic resource derived from the integration of genome sequences, expressed transcripts and genetic markers in ramie. PMID:31185891
Cumulative and different genetic effects contributed to yield heterosis using maternal and paternal backcross populations in Upland cotton. PMID:30850683
Genome-Wide Identification, Sequence Variation, and Expression of the Glycerol-3-Phosphate Acyltransferase (GPAT) Gene Family in Gossypium. PMID:30842789
Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis. PMID:30736327
Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton. PMID:30671083
Differentially expressed genes between two groups of backcross inbred lines differing in fiber length developed from Upland × Pima cotton. PMID:30659437
Decrease of gene expression diversity during domestication of animals and plants. PMID:30634914
Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress. PMID:30514299
Genes regulating gland development in the cotton plant. PMID:30467959
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Upland Cotton (Gossypium hirsutum): Genome-Wide Identification and Expression Analysis in Fiber Development. PMID:30356782
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. PMID:30321383
Genome-Wide Analysis Elucidates the Role of CONSTANS-like Genes in Stress Responses of Cotton. PMID:30205477
Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.). PMID:30200887
Genome-wide identification and characterization of LRR-RLKs reveal functional conservation of the SIF subfamily in cotton (Gossypium hirsutum). PMID:30189845
Identification of Introgressed Alleles Conferring High Fiber Quality Derived From Gossypium barbadense L. in Secondary Mapping Populations of G. hirsutum L. PMID:30073008
Identification and Functional Characterization of a Microtubule-Associated Protein, GhCLASP2, From Upland Cotton (Gossypium hirsutum L.). PMID:29997641
Genome-Wide Study of YABBY Genes in Upland Cotton and Their Expression Patterns under Different Stresses. PMID:29467795
MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. PMID:29220435
Genome-wide recombination rate variation in a recombination map of cotton. PMID:29176878
A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton. PMID:29061116
An NAM Domain Gene, GhNAC79, Improves Resistance to Drought Stress in Upland Cotton. PMID:28993786
Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation. PMID:28831143
Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses. PMID:28683794
CottonFGD: an integrated functional genomics database for cotton. PMID:28595571
Identification of candidate genes for fiber length quantitative trait loci through RNA-Seq and linkage and physical mapping in cotton. PMID:28569138
Genome-Wide Identification and Expression Analysis of the Biotin Carboxyl Carrier Subunits of Heteromeric Acetyl-CoA Carboxylase in Gossypium. PMID:28507552
QTL analysis of cotton fiber length in advanced backcross populations derived from a cross between Gossypium hirsutum and G. mustelinum. PMID:28349176
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. PMID:28222698
Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18. PMID:28149299
blend4php: a PHP API for galaxy. PMID:28077564
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. PMID:28053168
Genome-wide identification of multifunctional laccase gene family in cotton (Gossypium spp.); expression and biochemical analysis during fiber development. PMID:27679939
High Expression of Cry1Ac Protein in Cotton (Gossypium hirsutum) by Combining Independent Transgenic Events that Target the Protein to Cytoplasm and Plastids. PMID:27391960
Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton. PMID:27342735
A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population. PMID:27256327
DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. PMID:27168520
Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects. PMID:27072350
RNA-Seq-Mediated Transcriptome Analysis of a Fiberless Mutant Cotton and Its Possible Origin Based on SNP Markers. PMID:26990639
Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. PMID:26989146
Partial Dominance, Overdominance, Epistasis and QTL by Environment Interactions Contribute to Heterosis in Two Upland Cotton Hybrids. PMID:26715091
Genome-wide mining, characterization, and development of microsatellite markers in gossypium species. PMID:26030481
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
Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. PMID:25908569
Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations. PMID:25758743
Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of Upland cotton (Gossypium hirsutum L.). PMID:25700980
A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations. PMID:25501533
The coffee genome hub: a resource for coffee genomes. PMID:25392413
Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases PubMed citations: 2.

2 articles citing: Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases

Tripal MegaSearch: a tool for interactive and customizable query and download of big data. PMID:33900378
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
http://dx.doi.org/10.1093/nar/gkt1064

Tags:

Tags
More detailed information about this field from each metasource.

genetic map
metasource: Fairsharing.org
version: None

whole genome sequencing
metasource: Fairsharing.org
version: None

plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

other plants
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

breeding
metasource: re3data.org
version: re3data.org: CottonGen; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N49G last accessed: 2022-11-04

crop science
metasource: re3data.org
version: re3data.org: CottonGen; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N49G last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: CottonGen; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N49G last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: CottonGen; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N49G last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:10.304498

gossypium
metasource: re3data.org
version: re3data.org: CottonGen; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N49G last accessed: 2022-11-04

genotype and phenotype
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:10.304498

nucleic acids
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:10.304498

mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:10.304498

sequencing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:10.304498

genetic map whole genome sequencing plant other plants breeding crop science genetics genomics gossypium genotype and phenotype nucleic acids mapping sequencing

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