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Open Access Research article

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

Jessica A Schlueter1, Jer-Young Lin2, Shannon D Schlueter1, Iryna F Vasylenko-Sanders3, Shweta Deshpande3, Jing Yi3, Majesta O'Bleness3, Bruce A Roe3, Rex T Nelson4, Brian E Scheffler5, Scott A Jackson1 and Randy C Shoemaker4*

Author Affiliations

1 Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA

2 Purdue Genetics Program, Purdue University, West Lafayette, IN 47907, USA

3 Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA

4 USDA-ARS, Corn Insect and Crop Genetics Research Unit, and Department of Agronomy, Iowa State University, Ames, IA 50011, USA

5 USDA-ARS-MSA Genomics Laboratory, Stoneville, MS 38776, USA

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BMC Genomics 2007, 8:330  doi:10.1186/1471-2164-8-330

Published: 19 September 2007

Abstract

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.