Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing
<p>Abstract</p> <p>Background</p> <p>Soybean, <it>Glycine max </it>(L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Dep...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2007-09-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/8/330 |
| _version_ | 1811296409770524672 |
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| author | Nelson Rex T Roe Bruce A O'Bleness Majesta Yi Jing Deshpande Shweta Vasylenko-Sanders Iryna F Schlueter Shannon D Lin Jer-Young Schlueter Jessica A Scheffler Brian E Jackson Scott A Shoemaker Randy C |
| author_facet | Nelson Rex T Roe Bruce A O'Bleness Majesta Yi Jing Deshpande Shweta Vasylenko-Sanders Iryna F Schlueter Shannon D Lin Jer-Young Schlueter Jessica A Scheffler Brian E Jackson Scott A Shoemaker Randy C |
| author_sort | Nelson Rex T |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Soybean, <it>Glycine max </it>(L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly.</p> <p>Results</p> <p>Seventeen BACs representing ~2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences.</p> <p>Conclusion</p> <p>This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.</p> |
| first_indexed | 2024-04-13T05:48:58Z |
| format | Article |
| id | doaj.art-e5327cfe666c43a38a08ff62ba4da5c6 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T05:48:58Z |
| publishDate | 2007-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e5327cfe666c43a38a08ff62ba4da5c62022-12-22T02:59:52ZengBMCBMC Genomics1471-21642007-09-018133010.1186/1471-2164-8-330Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencingNelson Rex TRoe Bruce AO'Bleness MajestaYi JingDeshpande ShwetaVasylenko-Sanders Iryna FSchlueter Shannon DLin Jer-YoungSchlueter Jessica AScheffler Brian EJackson Scott AShoemaker Randy C<p>Abstract</p> <p>Background</p> <p>Soybean, <it>Glycine max </it>(L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly.</p> <p>Results</p> <p>Seventeen BACs representing ~2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences.</p> <p>Conclusion</p> <p>This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.</p>http://www.biomedcentral.com/1471-2164/8/330 |
| spellingShingle | Nelson Rex T Roe Bruce A O'Bleness Majesta Yi Jing Deshpande Shweta Vasylenko-Sanders Iryna F Schlueter Shannon D Lin Jer-Young Schlueter Jessica A Scheffler Brian E Jackson Scott A Shoemaker Randy C Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing BMC Genomics |
| title | Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing |
| title_full | Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing |
| title_fullStr | Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing |
| title_full_unstemmed | Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing |
| title_short | Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing |
| title_sort | gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing |
| url | http://www.biomedcentral.com/1471-2164/8/330 |
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