Gene duplication fate in a genetic pathway context : an examination of the trichome initiation pathway in the allopolyploid genus Pachycladon (Brassicaceae) : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Manawatu, New Zealand
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2024-10-29
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Massey University
The following Figures were removed for copyright reasons: 1.1 (=Comai, 2005 Fig 1); 1.4 (=Joly et al., 2013 Fig 1A&B); 1.6 (=Kubista et al., 2006 Fig 3); Table A1.1 (=Bustin et al., 2009 Table 1); 3.2 (=Jones & Vandepoele, 2020 Fig 1a,b,c); 3.3 (=Gray et al., 2017 Fig 1D); 3.10 (=Birchler et al., 2007 Fig 1). Figure 2.1 is reused under a Creative Commons Attribution 2.0 Generic (CC BY 2.0) license.
The following Figures were removed for copyright reasons: 1.1 (=Comai, 2005 Fig 1); 1.4 (=Joly et al., 2013 Fig 1A&B); 1.6 (=Kubista et al., 2006 Fig 3); Table A1.1 (=Bustin et al., 2009 Table 1); 3.2 (=Jones & Vandepoele, 2020 Fig 1a,b,c); 3.3 (=Gray et al., 2017 Fig 1D); 3.10 (=Birchler et al., 2007 Fig 1). Figure 2.1 is reused under a Creative Commons Attribution 2.0 Generic (CC BY 2.0) license.
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Abstract
The evolutionary significance of polyploidy is difficult to overstate and one of the primary foci of modern polyploidy research is on the fates of duplicated genes (homeologs). The impact of gene duplication on biological evolution is strongly related to evolutionary novelty, genome architecture, and even speciation. However, current approaches to study homeolog fates are largely descriptive (e.g., whole genome scans) and lack a critical context: the genetic pathway. As a result, relatively little is known about how homeologs interactively behave within a duplicated genetic pathway to form protein-protein interactions and, how homeolog functional fates are associated with particular gene attributes such as pleiotropy and epistasis. We examined the well-characterized trichome initiation pathway in the allopolyploid Pachycladon (Brassicaceae) in this study to investigate how integrated genetic systems respond to the common phenomenon of duplication. The genus is the product of a hybridization event that took place during the Pleistocene ~0.8-1.6 mya, between two highly diverged lineages, followed by polyploidy and diversification. Considering morphological and phylogenetic diversity, four Pachycladon species, P. enysii, P. fastigiatum, P. novae-zealandiae and P. cheesemanii were selected to study the trichome initiation pathway focusing on the key genes TTG1, GL1, GL3, and EGL3.
Pachycladon’s parental origins are not known exactly yet, despite that previous studies describe that one of the parental genomes is closely related to A. thaliana. Hence, as the first step, we set out to isolate the duplicated copies (homeologs) of the four genes of interest from each of the four study species. Those sequences were then analyzed to identify the progenitor origins of each homeolog for each gene to ‘assemble’ the progenitor pathways. The gene trees resulting from phylogenetic analyses were consistent in the placements of homeologs for each gene, positioning one of the copies (Type 1) in the Camelineae lineage (lineage I) and other copy (Type 2) outside of (and typically sister to) Lineage I.
Categorization of the homeologs of each gene into progenitor Types facilitated the analysis of sequence divergence and expression studies to provide more insights into the molecular evolution of the pathway. The Type 2 copies of all genes were found to have greater variation than the Type 1 copies. Despite several mutations with likely functional effects being identified, Ka/Ks analyses suggested that both copies of most genes in most species have been under the influence of purifying selection. qPCR analyses of the relative expression of gene homeologs suggested similar gene expression patterns in four Pachycladon species and across two sample types, whole seedlings, and mature leaves. Based on the results, we assumed multiple molecular mechanisms overlap controlling the expression of the homeologs such as relative gene dosage balance, subgenome dominance, and pleiotropy. The most general finding was a trend showing preferential expression of Type 1 homeologs observed across genes and species (although there were exceptions to this pattern). Based on other studies, the Type 1 homeologs are likely to be of paternal origin, indicating a paternal bias in homeolog expression. In contrast to the other genes examined, the highly pleiotropic gene, TTG1, was found to have very similar levels of homeolog expression across all species. These results provide a detailed analysis of the molecular evolution of a genetic pathway following duplication via allopolyploidy.
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polyploidy, homeologs, genetic pathway, trichome initiation pathway, allopolyploid, Pachycladon