Cottongen: A Central Data Repository and Analysis Resource for Cotton Community

CottonGen is a genomics, genetics and breeding database for the cotton community.  It provides a comprehensive collection of data, various analysis tools, Breeding Information Management System, and links to external resources of interest to cotton researchers.  CottonGen currently contains 28 (16 tetraploids and 12 diploids) annotated genome sequences; 1,520,001 genes, 112 genetic maps; 575,850 markers; 6,234 QTLs; 19,652 germplasm; metabolic pathways for 13 species (AD1-AD5, A, D, G, F, and kirkii); 25,150,265 SNP and 12,484 SSR genotype measurements; 529,050 phenotype measurements (mainly from RBTN and NCGC projects), 45,067 images (mainly of NCGC); and synteny data for 28 genomes with links to genes, mRNA, orthologs and function.  Analysis and visualization tools in CottonGen include genome browser JBrowse, Synteny Viewer, MapViewer, CottonCyc, BLAST+, and the Breeding Information Management System, an online system to manage and analyze private breeding data.  All the data are integrated within CottonGen and can easily be queried out through various CottonGen’s search engines.  This presentation will illustrate how to use various resources in CottonGen to find relevant information and perform further data mining.