Genomes like Glycine max (soybean) that have been highly conserved following increases in ploidy present challenges for genome analysis. At the Soybean Genome Database (SoyGD) http://soybeangenome.siu.edu the genome browser 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 with a-d suffix to marker anchor names and contig names that communicate ploidy (ctg>8000 are tetraploid, ctg>9000 are octoploid). Comparisions of BES with WGS has validated those contig assignments and provided SNPs specific to the 4 or 8 regions in each cluster. WGS sequence data has been used to separate DNA marker anchors from homologs of DNA marker anchors in BAC pools. Recently about 3,840 minimum tiling path (MTP4E) BIBAC clones added BES to decorate the physical map raising the total to 21,567. Predicted gene models were developed for about 15% of the BES. From these models candidate genes underlying disease resistance, seed yield and seed protein, oil or isoflavone content were detected and fine-mapped. In genome evolution analyses more than a thousand additional microsatellite marker anchors were developed for contigs, 353 on the map and about 700 still in Queue (awaiting placement). Linkage analysis placed one hundred of the 1,053 new microsatellite markers on the genetic map with contigs and associated features. About half of the markers mapped to regions of the genome that formed gaps in earlier maps suggesting marker clustering biases. SoyGD represents the new build 5 for the physical map with 800 contigs. Soybean genome sequence data has been added. Gene expression data has been added. NSF project #9878635 and USB 2218-6218. (1) Shultz et al., 2006. Nucleic Acids Res. D758-D765; Plant Methods 2:9-18. 2007 Theor Appl Genet 114:1081–1090;