PAG-XIX  Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA


P790: Databases

New Transcriptome Data And Tools At The Comparative Evolutionary Genomics Of Cotton Web Resource

Alan R. Gingle1 , Joshua A. Udall2 , Jordan Swanson3

1  University of Georgia, 111 Riverbend Rd., Athens, GA, 30602-6810, USA
2  Brigham Young University, Plant and Wildlife Science Dept., Provo, UT 84602, USA
3  Mechdyne Corporation, 11 East Church Street, Marshalltown, IA 50258-5011, USA

The “Comparative Evolutionary Genomics of Cotton” (CEGC) Web-database resource (http://cottonevolution.info) has been developed as one component of an NSF plant genome center (PI: J. Wendel). The resource contains search and display tools for data types ranging from BAC and genetic map through EST and gene expression. Over the past year, its transcriptome related data have grown with the addition of new gene expression, EST assembly, functional annotation and marker data. New tools for these data types include those for Cotton EST assemblies that facilitate comparative searches, based on significant BLAST sequence alignments to Arabidopsis thaliana (TAIR9) genes. These tools also facilitate searches for Cotton EST assemblies based on functional and other TAIR9 annotations. EST assemblies are displayed by a tool developed at the Udall lab and sequence alignments via the, GMOD developed, genome browser (GBrowse). Recently, new EST based SSR data have been added to the resource and the related search and display tools are being adapted to facilitate these new data. In general, data are also available as bulk downloads and, where appropriate, submitted to public repositories at NCBI. With respect to gene expression data, additional spotted oligo and NimbleGen microarray datasets have been added to the resource’s implementation of the Stanford microarray database (SMD). Data displays are in familiar formats since the growing array of transcriptome related search tools incorporate community developed and commonly used tools like GBrowse and SMD for data views and additional search functionality.