Jayaraman, Dheepakkumaran , Shultz, Jeffry L. , Lightfoot, David A. .
Use of The Soybean Genome Database (SoyGD) For Whole Genome Annotation:.
Genomes like Glycine max (soybean) that have been highly conserved following increases in ploidy present challenges for genome analysis particularly the deconvolution of whole genome shotgun sequences (WGS). At the Soybean Genome Database (SoyGD) http://soybeangenome.siu.edu the genome browser has, since 2002, integrated and served the publicly available soybean physical map, BAC fingerprint database and genetic map associated genomic data (1). Duplicated regions have been identified and catalogued by two methods; with a-d suffix to marker anchor names; and with contig (ctg) names that communicate ploidy (ctg>8000 are tetraploid, ctg>9000 are octoploid). DNA sequence data has been used to separate DNA marker anchors from homologs of DNA marker anchors in BAC pools. About 34,840 minimum tiling path (MTP) derived BAC clones provided BAC end sequences (BES) to decorate the physical map. The BES were used to recruit contigs made from all available WGS to the linkage groups. Predicted gene models were developed for about 15% of the BES-WGS contigs. From these models candidate genes underlying disease resistance, seed yield and seed protein, oil or isoflavone content were detected and tested against fine-maps. In genome evolution analyses more than two thousand additional microsatellite marker anchors were developed for contigs, half on the map and about half still in Queue (awaiting placement). A first genome wide annotation of soybean shows gene family evolution is not random. Overabundant were unique genes, two member gene families and four member gene families. Under abundant were three, five and seven member gene families. Tetranucleotide and octonucleotide motif repeats were nearly absent. Implications for genome evolution will be discussed. NSF project #9878635 and USB 2218-6218. (1) Shultz et al., 2006. Nucleic Acids Res. D758-D765.
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1 - Southern Illinois University, Genomics and Biotechnology Facility
2 - USDA, Stoneville, MS
3 - SIUC, Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, MC4415, Carbondale, Illinois, 62901, USA
Presentation Type: Plant Biology Abstract
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM