Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/27/2009
Publication Date: 11/1/2009
Citation: Joseph, B., Schlueter, J., Du, J., Graham, M.A., Ma, J., Shoemaker, R.C. 2009. Retrotransposons Within Syntenic Regions Between Soybean and Medicago Truncatula and Their Contribution to Local Genome Evolution. The Plant Genome. 2(3):211-223.
Interpretive Summary: Plant genome sizes are widely disparate. Yet the size of the genome is not associated with the complexity of the plant but may be associated with diversity needed for crop improvement. How genomes expand and contract is a mystery. In this paper, the authors discovered that a region of the soybean genome with few genes had been filled with transposable elements, thus expanding the region, while an evolutionarily related gene rich region had fewer of these elements and more genes. They also found evidence of regions of the genome that were undergoing contractions. They compared the regions to corresponding regions in Medicago and made similar observations. In all cases incidences of expansion and contraction ocurred at the local level of the genome and did not apply across the entire genome. This information is important to scientists who study genome evolution and may facilitate genome assembly after whole genome sequencing projects.
Technical Abstract: Comparative genome analyses have described the extent of gene level macro and microsynteny among closely related legume species. Yet the organization of the intergenic regions within syntenic blocks and the involvement of retrotransposons in the evolution of these regions have not been studied in detail. In this paper, gene-poor and gene-rich soybean homoeologous regions showing synteny with Medicago truncatula were analyzed to understand the role of retrotransposons in the evolution of homoeologous and syntenic genomic regions. A comparison of the retrotransposons in the homoelogous soybean regions indicated that the abundance and the types of retrotransposons vary in these otherwise collinear genomic regions. The gene-poor region showed an abundance of retrotransposon accumulation in soybean relative to Medicago resulting in local genome expansion in soybean. The gene-rich region on the other hand, showed minimal retrotransposon accumulation in soybean. The corresponding Medicago region however, showed retrotransposon mediated local genome expansion indicating that the local genome sizes do not always reflect the global genome size difference between soybean and Medicago. The observation of solo LTRs (Long Terminal Repeats) indicates local genome contraction events in soybean. This study also uncovered a sample of the less explored non-LTR retrotransposons in the soybean genome and their presence in the introns of genes in the genomic regions studied.