About CottonGen.ppt

1、Updates to CottonGen the cotton community database for basic, translational and applied research,Jing Yu1, Sook Jung1, Chun-Huai Cheng1, Stephen Ficklin1, Taein Lee1, Ping Zheng1, Don Jones2, Richard Percy3, Dorrie Main1,1. Washington State University, 2. Cotton Incorporated, 3. USDA-ARS,2014 ICGI R

2、esearch Conference Wuhan, China,About CottonGen,A community database to further enable basic, translational and applied cotton research.Built using the open-source, user-friendly, Tripal database infrastructure used by several other databasesConsolidates and expands CottonDB and CMD to include trans

3、criptome, genome sequence and breeding data, and data mining tools,CottonGen Released,CottonGens 1st Year Progress,CottonDB on WSU servers,Tripal instance created,Develop ICGI website,CottonDB data in Chado,Add Tools,Web page development,Setting Queries,CottonGens 2nd Year New Features and New Data,

4、D5 genome assemblies & annotations,Trait, QTL, Publication searches,Data download, submission, FAQ, Tutorials,ARS digital images,CottonGen published in Nucl. Acids Res.,ICGI election system & website,China & UZ germplasm evaluations,New SSR and SNP markers,CottonGens 3rd Year New Tools and WGS data,

5、CottonCyc & JGI-D5 pathways,JBrowse,Getting into the Whole Genome Era,SSR marker redundancy & sequence clearification,WGS & GMAP data,50k new SSRs and 150k new SNPs,Implement genome synteny browser,Major Content,Over 265k genetic markers consisting of 3,541 RFLPs, 78,340 SSRs, 183,035 SNPs15,117 ger

6、mplasm records including 97 populations and 15,020 individual entriesOver 108k trait and QTL scores12,269 digital images of 2,016 germplasm, from USDA-ARS,Major Content (cont.),245k of Genes and UnigenesG. raimondii genome (BGI and JGI), and G. arboreum genome (BGI)Metabolic Pathways built by JGI-D5

7、 annotation v2.1 data15,155 references from journal articles, conference proceedings, patents, book chapters, and theses.,Major Tools,CMap - Comparison of various mapsGBrowse - Generic Genome BrowserJBrowse - Java based genome browser. Very fast and scales well to large datasets such as RNASeq and G

8、BSCottonCyc - Metabolic Pathways in CottonBLAST - Basic Local Alignment Search Tool,http:/www.cottongen.org/,CottonGen JBrowse,CottonCyc Current,Motablic pathways for JGI v2.0 G. raimondii (D5) genome assemblyCottonCyc JGI-D5 summary:,CottonCyc,CottonCyc - Pathway,CottonCyc cellular overview,Future

9、Work,Implement GBrowse-Syn, a GBrowse-based synteny browser.Implement more tools for genome annotation and breeder communities.Germplasm evaluation data from ARS College Station, TX Add US National Variety Trials data and make fully searchableMore QTL and QTL mapping data,Acknowledgements,Industry F

10、unding Cotton Incorporated, Bayer CropScience, Dow/Phytogen, Monsanto, Association of Agricultural Experiment Station DirectorsGovernment Funding USDA ARS USDA NIFA AFRI and SCRI programs (funding Mainlab Tripal and GenSAS Development)University Support Washington State University, Texas A&M, Clemson University Community of Cotton Researchers,Thanks for your attention Questions?,