Updates in CottonGen: An Integrated Genomics, Genetics and Breeding Database for the Cotton Research Community

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing centralized access to publicly available genomic, genetic and breeding data for cotton. Superseding CottonDB and the Cotton Marker Database, CottonGen has been built using the Tripal database infrastructure and has enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data.  CottonGen contains annotated whole genome sequences, unigene transcripts, markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community.  Major new data added in the past year includes the JGI reference genome for G. raimondii with additional annotation; a digital image library of the USDA-ARS National Cotton Germplasm Collection; 43,182 SNPs; and germplasm evaluation data from 3,027 Chinese and 848 Uzbekistan accessions. New query functionality includes an advanced marker search, gene search, publications search and a sequence retrieval tool. Data submission templates, tutorials and a frequently asked questions section have also been added. Future development will include implementation of a breeder’s toolbox, and addition of synteny, pathway, gene/genome curation tools as well as more map, marker and trait data.