title: 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.
abstract: 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.
authors.affiliation: Genomics Core-Facility, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA.
authors.forename: Jeffry L
authors.initials: JL
authors.lastname: Shultz
authors.forename: Deepak
authors.initials: D
authors.lastname: Kurunam
authors.forename: Kay
authors.initials: K
authors.lastname: Shopinski
authors.forename: M Javed
authors.initials: MJ
authors.lastname: Iqbal
authors.forename: Samreen
authors.initials: S
authors.lastname: Kazi
authors.forename: Kimberley
authors.initials: K
authors.lastname: Zobrist
authors.forename: Rabia
authors.initials: R
authors.lastname: Bashir
authors.forename: Satsuki
authors.initials: S
authors.lastname: Yaegashi
authors.forename: Nagajyothi
authors.initials: N
authors.lastname: Lavu
authors.forename: Ahmed J
authors.initials: AJ
authors.lastname: Afzal
authors.forename: Charles R
authors.initials: CR
authors.lastname: Yesudas
authors.forename: M Abdelmajid
authors.initials: MA
authors.lastname: Kassem
authors.forename: Chengcang
authors.initials: C
authors.lastname: Wu
authors.forename: Hong Bin
authors.initials: HB
authors.lastname: Zhang
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Khalid
authors.initials: K
authors.lastname: Meksem
authors.forename: David A
authors.initials: DA
authors.lastname: Lightfoot
mesh_terms: D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D020451:Contig Mapping; D030561:Databases, Nucleic Acid; D018745:Genome, Plant; D023281:Genomics; D020407:Internet; D018895:Microsatellite Repeats; D011123:Polyploidy; D012689:Sequence Homology, Nucleic Acid; D016324:Sequence Tagged Sites; D013025:Glycine max / Q000235:genetics*; D014584:User-Computer Interface