Evolution of Alternative Splicing Across Legumes Using Amborella as a Reference

Alternative splicing (AS) is the process by which a pre-mRNA can be processed into several alternate transcript isoforms. This is one of the mechanisms through which eukaryotes generate transcriptome and proteome diversity, as well regulating protein abundance. There is increasing evidence suggesting a crucial role of AS in many essential plant functions such as photosynthesis, defense response, flowering, and cereal grain quality.  Despite the important roles AS plays in angiosperms (flowering plants), the evolution and conservation of AS events across plant species is not well understood. We are interested in examining the evolutionary conservation and divergence of AS patterns in genes duplicated by independent polyploidy events during the evolutionary histories of the legumes Medicago truncatula, Glycine max, and Phaseolus vulgaris. We will , use Amborella trichopoda, a basal angiosperm with no recent lineage-specific genome duplications, as an out-group for comparison. Our study first identifies AS events in the aforementioned species using public and private transcriptome data collections generated with multiple sequencing technologies. So far we successfully developed the software pipeline to identify AS events from transcriptome data collected with multiple sequencing technologies. Our current efforts focus on defining orthologues genes with OrthoMCL, and identifying AS events conserved between orthologous genes. This work will not only provide insights into the evolution of AS in legumes, but will lay the foundation for a comprehensive AS evolution study in Angiosperms that will include multiple eudicot and monocot lineages.