Mechanisms of gene gain and loss in plant genome evolution

The gain and loss of genes has been, and continues to be, an ever-present feature of plant genome evolution, heavily influencing their adaptive capacity. The era of genomics has enlightened our understanding of the scale of gene content variation both between and within species, highlighting significant presence/absence variation, with plants being no exception. Deciphering the underlying mechanisms driving these processes is now possible with large comparative genomic studies encompassing a wide phylogenetic breadth of species. Nonetheless there are still multiple gaps in knowledge including the influence of human induced selection on plant gene content variation, through processes such as domestication, as well as the mechanistic basis and contribution of laterally acquired genes to the genomic repertoire of plants. In this thesis I (1) annotate the entire immune receptor gene (IRG) repertoires of crop plants and their respective wild relatives to infer how the domestication process has influenced their evolution, showing a gradual but small reduction in IRGs that positively correlates with the duration of domestication. 2) I demonstrate a novel method of inferring the donors of grass-to-grass lateral gene transfer (LGT), through the use of nuclear encoded plastid DNA, effectively identifying Eremochloa attenuata as the likely donor to a previously characterised LGT fragment. 3) I describe a repeatedly acquired LGT fragment that has been transferred to at least 11 grass species, the fragment contains a conserved set of 3 core genes and is often accompanied by variable accessory genes, from multiple other grass donors. Furthermore, the high sequence conservation and repeated acquisitions points to a potential common mechanism of transposition, providing a key target for future studies on the mechanistic basis of grass-to-grass LGT. Overall this thesis presents two distinct mechanisms of gene gain and loss in plants providing the groundwork for their future study and even potential application.