Genome Wide Discovery of Alternative Splice Isoforms Across Multiple Plant Species and the Identification of Conserved Events

Alternative splicing (AS) plays important roles in many plant biological processes, but its conservation across the plant kingdom is not known. We describe a methodology to identify AS events and identify conserved AS events across large phylogenetic distances using large publicly available Illumina RNA-Seq datasets. We characterized AS genome-wide in 9 angiosperms including Amborella, the single sister species to all other extant flowering plants and 7 monocots. AS events within 40 – 70% of the expressed multi-exonic genes per species were found. Over 27,000 events were found to be conserved among two or more of the eudicot taxa studied and over 9,000 events were found to be conserved among two or more of the monocot taxa studied. While many events are species specific, many others are shared across long evolutionary distances suggesting they have functional significance. Conservation of AS event data provides an estimate of the number of ancestral AS events present at each node of the tree representing the species studied. Furthermore, the presence or absence of AS isoforms between species with different whole genome duplication (WGD) histories provides the opportunity to examine the impact of WDG on AS potential.