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The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max
Genomics Core-Facility, Southern Illinois University at Carbondale Carbondale, IL 62901-4415, USA 1Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M University College Station, TX 77843-2123, USA 2The Institute for Genomic Research MD, USA
*To whom correspondence should be addressed. Tel: +1 618 453 1797; Fax: +1 618 453 7457; Email: ga4082{at}siu.edu
Received July 28, 2005. Revised October 4, 2005. Accepted October 4, 2005.
Genomes that have been highly conserved following increases in ploidy (by duplication or hybridization) like Glycine max (soybean) present challenges during genome analysis. At http://soybeangenome.siu.edu the Soybean Genome Database (SoyGD) genome browser has, since 2002, integrated and served the publicly available soybean physical map, bacterial artificial chromosome (BAC) fingerprint database and genetic map associated genomic data. The browser shows both build 3 and build 4 contiguous sets of clones (contigs) of the soybean physical map. Build 4 consisted of 2854 contigs that encompassed 1.05 Gb and 404 high-quality DNA markers that anchored 742 contigs. Many DNA markers anchored sets of 2–8 different contigs. Each contig in the set represented a homologous region of related sequences. GBrowse was adapted to show sets of homologous contigs at all potential anchor points, spread laterally and prevented from overlapping. About 8064 minimum tiling path (MTP2) clones provided 13 473 BAC end sequences (BES) to decorate the physical map. Analyses of BES placed 2111 gene models, 40 marker anchors and 1053 new microsatellite markers on the map. Estimated sequence tag probes from 201 low-copy gene families located 613 paralogs. The genome browser portal showed each data type as a separate track. Tetraploid, octoploid, diploid and homologous regions are shown clearly in relation to an integrated genetic and physical map.
Present addresses: Chengcang Wu, Pioneer Hi-Bred International Inc., Johnson City, IA, USA
Kimberley Zobrist, Monsanto, Chesterfield, MO, USA
Satsuki Yaegashi, University of Tokyo, Japan Science and Technology Agency, Itabashi-Ku, Japan
Kay Shopinski, USDA, Peoria, IL, USA
M. Abdelmajid Kassem, Kean State University, NJ, USA
Khalid Meksem, Plant and Animal Genomic Laboratory, SIUC, IL, USA
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