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Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing
BACKGROUND: Soybean, Glycine max (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 Agr...
Autores principales: | , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077340/ https://www.ncbi.nlm.nih.gov/pubmed/17880721 http://dx.doi.org/10.1186/1471-2164-8-330 |
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author | Schlueter, Jessica A Lin, Jer-Young Schlueter, Shannon D Vasylenko-Sanders, Iryna F Deshpande, Shweta Yi, Jing O'Bleness, Majesta Roe, Bruce A Nelson, Rex T Scheffler, Brian E Jackson, Scott A Shoemaker, Randy C |
author_facet | Schlueter, Jessica A Lin, Jer-Young Schlueter, Shannon D Vasylenko-Sanders, Iryna F Deshpande, Shweta Yi, Jing O'Bleness, Majesta Roe, Bruce A Nelson, Rex T Scheffler, Brian E Jackson, Scott A Shoemaker, Randy C |
author_sort | Schlueter, Jessica A |
collection | PubMed |
description | BACKGROUND: Soybean, Glycine max (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. RESULTS: 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. CONCLUSION: 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. |
format | Text |
id | pubmed-2077340 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-20773402007-11-14 Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing Schlueter, Jessica A Lin, Jer-Young Schlueter, Shannon D Vasylenko-Sanders, Iryna F Deshpande, Shweta Yi, Jing O'Bleness, Majesta Roe, Bruce A Nelson, Rex T Scheffler, Brian E Jackson, Scott A Shoemaker, Randy C BMC Genomics Research Article BACKGROUND: Soybean, Glycine max (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. RESULTS: 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. CONCLUSION: 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. BioMed Central 2007-09-19 /pmc/articles/PMC2077340/ /pubmed/17880721 http://dx.doi.org/10.1186/1471-2164-8-330 Text en Copyright © 2007 Schlueter et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Schlueter, Jessica A Lin, Jer-Young Schlueter, Shannon D Vasylenko-Sanders, Iryna F Deshpande, Shweta Yi, Jing O'Bleness, Majesta Roe, Bruce A Nelson, Rex T Scheffler, Brian E Jackson, Scott A Shoemaker, Randy C Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing |
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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077340/ https://www.ncbi.nlm.nih.gov/pubmed/17880721 http://dx.doi.org/10.1186/1471-2164-8-330 |
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