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 language | English (US) |
|---|---|
| Journal | Nucleic acids research |
| Volume | 34 |
| Issue number | Database issue |
| State | Published - Jan 1 2006 |
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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 journal › Article
}
TY - JOUR
T1 - The Soybean Genome Database (SoyGD)
T2 - a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max.
AU - Shultz, Jeffry L.
AU - Kurunam, Deepak
AU - Shopinski, Kay
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
AU - Zhang, Hong Bin
AU - Town, Christopher D.
AU - Meksem, Khalid
AU - Lightfoot, David A.
PY - 2006/1/1
Y1 - 2006/1/1
N2 - 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.
AB - 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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M3 - Article
VL - 34
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - Database issue
ER -