DISSERTATION RESEARCH: Evolutionary impact of genome duplication on alternative splicing: Genome-wide assessment in a polyploid plant (Tragopogon)

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This research will investigate the impact of whole genome duplication on genetic diversity. When an entire genome is doubled the resulting organism is said to be polyploid. Such events are of enormous economic and biological importance. Most agricultural crops are polyploid, and this duplication created much of the world's plant and animal diversity. After duplication, further changes often occur in gene number, expression, and regulation. Can such modifications generate all the genetic and ecological diversity we see? We know that when genes are translated into protein, genetic pieces can be rearranged in a process called alternative splicing. Does splicing following genome duplication further increase diversity? By studying changes in splicing patterns following duplication, this research will help determine what produces genetic diversity. This information help us understand biodiversity. It also has important economic implications for polyploid crops. Outreach to K-12 students will occur, and a new class module on agriculture for high school students will be developed. The goal of the proposed research is to address fundamental questions regarding the role and extent of RNA alternative splicing (AS) in a recently formed naturally occurring polyploid species in the flowering plant Tragopogon (goatsbeard; sunflower family). This plant genus includes two species that originated via polyploidy only 80 years ago. They serve as natural models for the study of recent and recurring Genomic Duplication (GD). This research will compare the polyploid T. miscellus to its diploid parents (T. dubius and T. pratensis). The following central questions about AS in polyploid species will be answered: (1) Are the patterns of AS in T. miscellus the average of its parents or highly divergent from the parents? (2) Do the same changes in AS occur repeatedly following GD in natural populations of independent origin? (3) Conversely, are aspects of AS highly variable and differ from one formation of this polyploid to the next? To address these questions, a nuclear genome sequence of the diploid T. dubius will be constructed and used as the reference for genome-wide AS detection. This genome will also be of potential economic value because Tragopogon is closely related to lettuce, an important crop. Functional annotation, including gene ontology enrichment analysis, will be used to examine which biological functions (e.g. photosynthesis) are closely linked to genes with changes in AS patterns after GD.