Evolution by Ancient Gene and Genome Duplication in Hexapods and Land Plants

Abstract

Gene and genome duplications have been found across the eukaryotic tree of life. Yet, many aspects of evolution by gene and genome duplications remain unclear, especially ancient duplications. In my dissertation, I focus on the incidence of ancient gene and genome duplication in different lineages of land plants and hexapods, their impact on genome evolution, and the pattern and processes of diploidization following polyploidy. In Appendix A, I use transcriptomes of gymnosperms and outgroups, and a novel phylogenetic algorithm to provide the first comprehensive study of ancient WGD in gymnosperms. In Appendix B, I use over 150 insect genomes and transcriptomes to infer ancient WGDs and other large-scale gene duplications during the evolution of hexapods. In Appendix C, I investigate ancient WGD in ferns from over 140 fern transcriptomes and test the long standing hypothesis on high chromosome number in ferns. In Appendix D, I summarize current studies on the patterns and processes of diploidization in the land plants and provide directions for testing hypotheses and understanding diploidization in the future. As a whole, this work improves our understanding of the mode and tempo of eukaryotic genome evolution and diversity.