Major transitions in the plant tree of life: insights from genes, genomes and traits

The evolution of plants transformed the Earth’s surface, atmosphere and climate and enabled the colonisation of new habitats, promoting the diversity of other lineages spanning the tree of life. The evolutionary history of plants has been marked by major transitions such as multicellularity, terrestrialisation and the origin of stomata, roots and seeds. These events have been accompanied by the gain, loss, expansion and contraction of gene families. Genome sequencing has increased the potential insights from evolutionary analyses which includes comparative genomics, gene family evolution and trait evolution. The overall aim of the research presented in this thesis is to improve our understanding of genes involved in the major transitions in plant evolution, by analysing plant genome data. First, I examine the broad scale evolution of genes across the plant tree of life, identifying two bursts of gene novelty that accompanied the origin of land plants. Second, I identify the modes of genome evolution underpinning the evolution of water relations in land plants, through the morphological innovations of stomata, vascular tissue and roots. Third, I report the spread and evolution of drought tolerance across the plant phylogeny, a key stressor accompanying plant terrestrialisation. This leads to the discovery that the first land plants and vascular plants were desiccation and drought tolerant respectively. Finally, I detail an evolutionary approach for identifying uncharacterised drought tolerance genes, through incorporating trait evolution into a comparative genomics framework. Preliminary experimental analysis aims to provide support for this novel technique. This work, on the common theme of plant evolution, advances research into gene innovation and diversification as well as detailing a novel method to identify uncharacterised drought tolerance genes. Ultimately, the research presented in this thesis contributes to our understanding of the major transitions of plants via insights gained from the study of genes, genomes and traits.