Alternative Splicing Landscape in Monocots: Insights from Genetic, Epigenetic and Evolutionary Perspectives

Alternative splicing (AS) plays a role in regulating mRNA levels or contributing to protein diversity. Monocots exhibit striking phenotypic and genomic variation, particularly in the grass lineage, which include the agronomical important species rice, maize, sorghum, wheat and millets. Studying AS in monocots will improve our understanding of the roles AS plays in these plants, and it will enable us to identify AS events that are conserved across the agriculturally important grass lineage, and link these events to gene function and gene structure evolution. During the course of my PhD research, I developed a pipeline to detect AS using RNA-Seq reads along with 454 and Sanger EST reads. A similar computational pipeline was applied to the Amborella genome (Amborella Genome Project 2013), but I further refined it to better filter false positive AS events, particularly the intron retention events. The refined pipeline has been applied to the maize inbred line W22 genome project. I have demonstrated the AS variations among maize inbred lines and tissues, and provide the evidence that some AS variation is regulated by cis- or trans- factors. The majority of these cis- and trans- regulated junctions can be explained by genetic polymorphisms between B73 and Mo17. This is the first research in plants that links splicing-QTL to the different types of alternative splicing events. I also demonstrate a negative correlation between gene expression levels and intron retention ratios for a subsets of genes expressed during seed development, which suggests that intron retention might play a role in regulating protein levels during maize seed development. In this dissertation, I also examined the conservation of AS across 9 species including 7 monocot, plus Arabidopsis and Amborella to identify the conserved AS across the grass lineage, monocots and the entire angiosperms. I found many important cases where AS plays a specific function role in plants. My dissertation also provides evidence that genic methylation related to AS, particular CG gene body methylation provides the most consistently reliable signal across the angiosperms. I have identified an association of genic methylation with alternatively spliced exons and alternatively retained introns. Furthermore, I demonstrate that loss of CG gene body methylation could lead to changes in AS, particularly in the context of intron retention