CottonGen statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


CottonGen specifications


Unique identifier OMICS_04488
Name CottonGen
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes


  • person_outline Dorrie Main

Additional information

Publication for CottonGen

CottonGen citations


Evolution and Stress Responses of Gossypium hirsutum SWEET Genes

Int J Mol Sci
PMCID: 5877630
PMID: 29517986
DOI: 10.3390/ijms19030769

[…] ilable online: []. Meanwhile, the physical positions of all cotton SWEET genes on chromosomes were determined according to the genome annotation files downloaded from the CottonGen website (available online: The SWEET genes were mapped using MapInspect software [] or Circos (version 0.69) software []. Tandem duplications were analyzed on the […]


Inhibition of Heat Shock proteins HSP90 and HSP70 induce oxidative stress, suppressing cotton fiber development

Sci Rep
PMCID: 5827756
PMID: 29483524
DOI: 10.1038/s41598-018-21866-0

[…] HSP90 and HSP70 protein sequences were used as a query to perform BlastP similarity search ( against G. hirsutum proteome data available at CottonGen database. The sequences obtained were analyzed for the presence of characteristic domains of both the families using Conserved Domain Database (CDD; […]


Identification of Gossypium hirsutum long non coding RNAs (lncRNAs) under salt stress

BMC Plant Biol
PMCID: 5785843
PMID: 29370759
DOI: 10.1186/s12870-018-1238-0

[…] low-quality reads and trimming the reads whose number of N bases accounted for more than 5% (quality score, Q ≥ 30). The reference G. hirsutum genome and the annotation files were downloaded from the CottonGen database ( We built the genome index using Bowtie2 v2.2.3 [], and clean data was mapped to the G. hirsutum genome using TopHat v2.0.12 []. TopHat calls Bowtie2 for […]


Gbvdr6, a Gene Encoding a Receptor Like Protein of Cotton (Gossypium barbadense), Confers Resistance to Verticillium Wilt in Arabidopsis and Upland Cotton

Front Plant Sci
PMCID: 5776133
PMID: 29387078
DOI: 10.3389/fpls.2017.02272
call_split See protocol

[…] pro/scan.html), and SMART ( The sequences of the SSR markers that flank Verticillium wilt-resistance quantitative trait loci (QTL) in cotton were downloaded from the CottonGen ( and CottonQTLdb ( websites. The physical locations of genes and markers were determined by anchoring their sequences onto […]


QTL Mapping for Fiber Quality and Yield Traits Based on Introgression Lines Derived from Gossypium hirsutum × G. tomentosum

Int J Mol Sci
PMCID: 5796191
PMID: 29342893
DOI: 10.3390/ijms19010243
call_split See protocol

[…] reads (quality score ˂ 20 e) were first filtered out. Then, each of the high-quality reads was trimmed off by 5 bp at the terminal site []. The reference genome TM-1 sequence was downloaded from the CottonGen database ( Clean reads from each sample were achieved and mapped to the G. hirsutum TM-1 genome [] using Burrows-Wheeler-Aligner (BWA, v0.7.10) software []. The ma […]


Structural, expression and evolutionary analysis of the non specific phospholipase C gene family in Gossypium hirsutum

BMC Genomics
PMCID: 5738194
PMID: 29258435
DOI: 10.1186/s12864-017-4370-6

[…], Gossypium_hirsutum_v1.0), respectively. The G. arboretum genome (G.arboreum_BGI-A2_v1.0) and the G. raimondii genome (G.raimondii_JGI_221_v2.1) were downloaded from the CottonGen ( Then, local databases were constructed. Arabidopsis NPC sequences obtained from The Arabidopsis Information Resource (TAIR, were us […]


Looking to check out a full list of citations?

CottonGen institution(s)
Department of Horticulture, Washington State University, Pullman, WA, USA; Cotton Incorporated, Cary, NC, USA; Crop Germplasm Research Unit, USDA-ARS-SPARC, College Station, TX, USA
CottonGen funding source(s)
Supported by Cotton Incorporated; the USDA-ARS Crop Germplasm Research Unit at College Station, TX; Southern Association of Agricultural Experiment Station Directors; Bayer CropScience; Dow/Phytogen; Monsanto.

CottonGen reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CottonGen