Retrotransposons within Syntenic Regions between Soybean and Medicago truncatula and Their Contribution to Local Genome Evolution

Comparative genome analyses have described the extent of macro and microsynteny among closely related legumes. 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, retrotransposon rich (gene-poor) and retrotransposon poor (gene-rich) soybean [Glycine max (L.) Merr.] regions showing synteny with Medicago truncatula Gaertn. were analyzed to understand the role of retrotransposons in the evolution of syntenic regions. The majority of the intact retroelements were inserted 2 million years ago (MYA). The abundance and the types of retrotransposons vary in homoeologous soybean regions. The retrotransposon-rich region showed local genome expansion in soybean compared to Medicago. The retrotransposon-poor region showed local genome expansion in Medicago suggesting that local genome sizes do not always reflect the global genome size difference between soybean and Medicago. One unique observation was the three-fold expansion of an ubiquitin specific protease (UBP12) gene in soybean due to multiple intronic retroelement insertions; yet a full-length transcript from the soybean UBP12 gene was confirmed. This study also uncovered a sample of the less explored non-LTR retrotransposons in soybean and their presence in the introns of genes.