Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 26, 2011
Publication Date: September 13, 2011
Citation: Severin, A.J., Cannon, S.B., Graham, M.A., Grant, D.M., Shoemaker, R.C. 2011. Changes in twelve conserved soybean genomic regions following three rounds of polyploidy. The Plant Cell. 23(9):3129-3136. Interpretive Summary: The hereditary material of many important crops has been duplicated two or more times over the last hundred million years of evolution. These duplications have given rise to much of the genetic diversity breeders use to breed improved varieties and traits. Unfortunately little is known about what happens to the genes involved in the duplication events, after duplication occurs. In this study the authors took advantage of the recently completed whole-genome decoding of soybean to identify an unprecedented 12 duplicated regions derived from three separate evolutionary events. Surprisingly, the 12 regions can be directly related to three related regions on grape chromosomes. The authors questioned why the regions have been so strictly conserved over evolutionary time and discovered that the regions contain important 'housekeeping' genes involved in basic cellular machinery in the plants. This information is important to the study of crop domestication and genome evolution. The 12 regions identified in this study will provide a unique biological model of what happens to genes and chromosomes after major duplication events.
Technical Abstract: With the advent of high throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. A set of highly conserved homoeologous segments would be valuable in the exploration of the retention and evolution of genes within gene families due to the evolutionary pressures of polyploidy events and transposable elements. In this report, we provide an example of twelve surviving homoeologous genomic regions from three rounds of polyploidy that contributed to the current soybean genome: a genome triplication before the origin of the rosids (~130-240 Mya), a genome duplication early in the legumes (~59 Mya) and a duplication in the Glycine lineage (~13 Mya). These regions in soybean exhibit a much higher gene retention following polyploidy events than is seen in Arabidopsis after its polyploidy events. We also find that approximately one fourth of the transposable elements (TEs) within the twelve homoeologous segments are contained within genes, and we discuss the possible role TE insertion has on genic evolution. Finally, we hypothesize that the presence of one or several families of housekeeping-like genes may be responsible for the high level of conservation of the twelve homoeologous segments.