Comparative analyses of complete oomycete mitochondrial genome sequences : insights into structural evolution : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biological Sciences at Massey University, Manawatū, New Zealand

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2022
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Massey University
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The oomycetes, or “water molds”, are fungi-like in appearance but more closely related to algae and diatoms. This large, widespread group of pathogens infects a wide range of plant and animal hosts across habitats ranging from marine, to freshwater and terestrial. Previous studies of oomycete mitogenomes suggest that large invert repeats are common as are structural rearrangements. However, sampling has been heavily biased towards Peronosporaceae with only limited representation of the other families. This study presents comparative and phylogenetic analyses of 135 mitogenomes, including 74 newly assembled sequences, from representatives of six families in the oomycete crown group. Gene content is strongly conserved across the sampled genomes, but synteny is only weakly conserved. The present analyses identified 68 distinct synteny types and within these 26 synteny blocks ranging in size from one to 23 genes. Patterns of diversity differed between the two major crown clades, one containing Saprolegniaceae and the other the remaining families. Several types of structural change appear to have occurred with the frequency of change varying across individual genomes (e.g., conserved and variable regions). Combined with the well resolved and supported phylogenetic tree recovered from analyses of the concatenated 32 mitochondrial gene matrix these results provide insights into the structural evolution of oomycete mitocohondrial genomes. In particular, suggesting associations between the loss of the large inverted repeat and duplications of tRNA-Met and between the compactness of these genome and the relative importance of different types of structural change in specific groups (e.g., early and late diverging Peronosporaceae).
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Figure 1.1 is re-used under a Creative Commons Attribution Noncommercial License (https://creativecommons.org/licenses/by-nc/2.0). Figure 1.2 is re-used with permission.
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