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.

Jeffry L. Shultz, Deepak Kurunam, Kay Shopinski, M. Javed Iqbal, Samreen Kazi, Kimberley Zobrist, Rabia Bashir, Satsuki Yaegashi, Nagajyothi Lavu, Ahmed Afzal, Charles R. Yesudas, M. Abdelmajid Kassem, Chengcang Wu, Hong Bin Zhang, Christopher D. Town, Khalid Meksem, David A. Lightfoot

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
JournalNucleic acids research
Volume34
Issue numberDatabase issue
StatePublished - Jan 1 2006

Fingerprint

Sequence Tagged Sites
Polyploidy
Soybeans
Genome
Databases
Bacterial Artificial Chromosomes
Genetic Markers
Clone Cells
Genetic Databases
Tetraploidy
Ploidies
Dermatoglyphics
Diploidy
Microsatellite Repeats
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

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. / Shultz, Jeffry L.; Kurunam, Deepak; Shopinski, Kay; Iqbal, M. Javed; Kazi, Samreen; Zobrist, Kimberley; Bashir, Rabia; Yaegashi, Satsuki; Lavu, Nagajyothi; Afzal, Ahmed; Yesudas, Charles R.; Kassem, M. Abdelmajid; Wu, Chengcang; Zhang, Hong Bin; Town, Christopher D.; Meksem, Khalid; Lightfoot, David A.

In: Nucleic acids research, Vol. 34, No. Database issue, 01.01.2006.

Research output: Contribution to journalArticle

Shultz, JL, Kurunam, D, Shopinski, K, Iqbal, MJ, Kazi, S, Zobrist, K, Bashir, R, Yaegashi, S, Lavu, N, Afzal, A, Yesudas, CR, Kassem, MA, Wu, C, Zhang, HB, Town, CD, Meksem, K & Lightfoot, DA 2006, '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.', Nucleic acids research, vol. 34, no. Database issue.
Shultz, Jeffry L. ; Kurunam, Deepak ; Shopinski, Kay ; Iqbal, M. Javed ; Kazi, Samreen ; Zobrist, Kimberley ; Bashir, Rabia ; Yaegashi, Satsuki ; Lavu, Nagajyothi ; Afzal, Ahmed ; Yesudas, Charles R. ; Kassem, M. Abdelmajid ; Wu, Chengcang ; Zhang, Hong Bin ; Town, Christopher D. ; Meksem, Khalid ; Lightfoot, David A. / 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. In: Nucleic acids research. 2006 ; Vol. 34, No. Database issue.
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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.",
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AU - Iqbal, M. Javed

AU - Kazi, Samreen

AU - Zobrist, Kimberley

AU - Bashir, Rabia

AU - Yaegashi, Satsuki

AU - Lavu, Nagajyothi

AU - Afzal, Ahmed

AU - Yesudas, Charles R.

AU - Kassem, M. Abdelmajid

AU - Wu, Chengcang

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