Working group session:
Comparative Genomics and Bioinformatics
Presentation type:
oral
Authors:
Yu, Jing; Jung, Sook; Chen, Chun-Huai; Ficklin, Stephen ; Lee, Taein ; Zheng, Ping ; Jones, Don; Percy, Richard ; Main, Dorrie
Presenter:
Yu, Jing
Correspondent:
Abstract:
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 builting 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. Since becoming publicly available in October 2012, many new data and tools have been added to CottonGen. Major data and tools include the JGI reference genome for G. raimondii with additional annotation; a digital image library of the USDA-ARS National Cotton Germplasm Collection; 39,099 CIR SNPs and 66,444 NBRI SNPs; 55467 new SSRs from CIR and NBRI; and germplasm evaluation data from 3,027 Chinese and 848 Uzbekistan accessions; the cotton metabolic pathway database (CottonCyc); the genome browser JBrowse. New querying 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, gene/genome curation tools as well as more map, marker and trait data.