Cross-kingdom transcriptomic trends in the evolution of hybrid gene expression : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, Manawatū, New Zealand

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The interbreeding of two genetically distinct parental lineages may lead to the formation of a new, reproductively isolated hybrid species. Hybridisation may occur with (allopoly-ploidisation) or without (homoploid hybridisation) a concomitant increase in chromosome number. Both allopolyploid and homoploid hybrids face a suite of near-instantaneous and longer-term biological repercussions with the potential to impede both their formation and establishment. Central to these challenges is the rewiring of gene-regulatory networks caused by the merger of the distinct genomes inherited from both parental species. Nonetheless, the success of hybrid species is well documented across the eukaryote tree of life. The applications and benefits of hybrid species drive tangible economic and cultural impacts, on both a local and global scale. Here in Aotearoa New Zealand, hybrid species permeate multiple facets of life including pastoral health and arable crop yield, long-established viticulture and microbrewery practices, and even the intrinsic nature of the land through the presence of diverse native allopolyploid flora. Despite the commonalities in hybrid formation, prior research on the evolution of hybrid gene expression has almost entirely focused on single hybrid species or a few gene families. This thesis presents the first cross-kingdom, transcriptome-wide study to explore the fates of genes following hybridisation. Each allopolyploid system (plants, animals and fungi) is paired with a closely-related homoploid hybrid to decouple the influence of increased chromosome number from genome merger on post-hybridisation expression patterns. Genome merger, not changes in chromosome number, has the greatest effect across all study systems. Across kingdoms, genes that are differentially expressed in parental species preferentially have more similar expression in hybrid descendants, likely as a consequence of regulatory cross-talk within the hybrid nucleus. Further commonalities are highlighted in the prevalence of gene loss or silencing among extremely differentially expressed genes in hybrid species. These general patterns suggest that the evolutionary process of hybridisation leads to common high-level expression outcomes, regardless of the particular species or kingdom.
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