| Summary: | The advancements of various massively parallel sequencing (MPS) methods in the last five years have enabled researchers to tackle biological problems that until recently seemed intractable. One of the most widely used MPS methods comes from Illumina®, which combines short and accurate sequencing reads with high throughput. Data generated using Illumina sequencing is used in every chapter of this thesis to characterize patterns of genome evolution using phylogenetic approaches in various plant genera. The thesis is focused on three main aspects of plant genome evolution: transposable elements (chapter 2), polyploidy (chapters 3 and 4) and plastid genomes (chapters 5 and 6). In every chapter phylogenetic hypotheses are generated from sequences assembled from Illumina reads, which I use to frame my research questions. In chapter 2 I investigated intra- and interspecific patterns of transposable element (TE) abundance in Theobroma cacao and related species. I found that reference based mapping of short sequencing reads works well to characterize TEs within the same species but is not reliable for interspecific comparison. In chapter 3 I used Illumina sequenced transcriptomes of 11 flax species, to investigate the presence of paleopolyploidy event within the genus. I discovered a previously unknown paleopolyploidy event, occurring 23 – 42 million years ago. In chapter 4 I used low coverage Illumina whole genome sequencing to test a hypothesis regarding the allopolyploid origin of a North-American Lathyrus species, L. venosus. I conclude that L. venosus is not of hybrid origin, since no incongruencies were detected between nuclear and plastid phylogenies. In chapter 5 I pinpointed the evolutionary origin of highly repetitive plastid genomes that are known to exist within the clover genus (Trifolium). I discovered that the repetitive plastomes are restricted to a single clade within Trifolium, which I estimated to be 12.4 – 13.8 million years old. In chapter 6 I investigated the pattern of gene rearrangements in the IRLC clade of legumes. While plastomes are highly rearranged in this group, I characterized certain highly conserved gene blocks that have not been rearranged internally, and argue that these blocks may represent the fundamental gene regulatory organization of the plastid. === Science, Faculty of === Botany, Department of === Graduate
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