New Data and Functionality in Cottongen: An Integrated Genomics, Genetics and Breeding Database for the Cotton Research Community

Established in October 2012, 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. CottonGen supersedes 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, unigene transcripts, markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Major new data 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 functionality includes an advanced marker search site, a publications search site and a sequence retrieval tool for downloading data upstream and downstream of a specific genome location or mapped feature. Data submission templates, tutorials and a frequently asked questions section have also been added. Future development will include addition of synteny, pathway, gene/genome curation tools as well as the addition of more map, marker and trait data and deployment of a breeder’s toolbox.