The Impact of LTR-Retrotransposon Accumulation on Genome Size in Sorghum bicolor (BTx623) and its Perennial Relative S. propinquum

The impact of transposable elements on genome organization and evolution has been of great interest in the world of plant genomics.  Several studies show that variation in the rate of LTR-retrotransposon accumulation and deletion is primarily responsible for genome size differences among diverse angiosperms. Here, we present a global analysis of LTR-retrotransposon diversity and divergence between Sorghum bicolor (BTx623, domesticated), the fifth most important grain crop in the world and the second effective biofuel crop, and S. propinquum (PI653737), a wild perennial relative.  Although, S. bicolor and S. propinquum are closely related as indicated by the ease with which they hybridize and form fertile offspring, they display marked morphological diversity in addition to significant variation in genome size (S. bicolor BTx623: ~730 Mb; S. propinquum PI653737: 900 Mb).  To describe LTR-retrotransposon diversity in S. bicolor, LTR_STRUC was used to screen the BTx623 published genome sequence, and the resulting ~7,500 LTR-retrotransposons were annotated via a grass-specific repetitive database and clustered into ~50 known families based on LTR sequence similarity using RepMiner and Cytoscape. Each S. bicolor LTR-retrotransposon family contained 2-2751 (smallest to largest) copies.  Furthermore, ~470 “exemplar sequences” that best describe each of the identified S. bicolor families were mined from the total dataset in Cytoscape and queried against S. propinquum Illumina reads using Cufflinks to estimate the relative copy numbers of individual retrotransposons in terms of FPKM in the S. propinquum genome.  Our results, as they relate to genome size variation, will be discussed.