Browsing by Subject "Mutation rate"

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Tempo and mode of diatom plastid genome evolution
(2017-12) Yu, Mengjie; Theriot, Edward C. (Edward Claiborne), 1953-; Jansen, Robert K., 1954-; La Claire, John W; Herrin, David L; Gutell, Robin R
Diatoms are mostly photosynthetic eukaryotes within the heterokont lineage. Their plastids were derived through secondary endosymbiosis of a red alga. Despite years of phylogenetic research, relationships among major groups of diatoms still remain uncertain. Additional plastid genome (plastome) sequences can not only provide more insight into diatom plastid evolution, but also assess phylogenetic relationships among the major lineages of diatoms. In my dissertation, I have more than doubled the available plastome sequences. My work in the plastome evolution in Thalassiosirales, one of the more comprehensively studied orders in terms of both genetics and morphology, showed highly conserved gene content and gene order within this order. I also documented the first instance of the loss of photosynthetic genes psaE, psaI and psaM in Rhizosolenia imbricata. By extensively sampling the diatoms with critical phylogenetic positions, I presented the largest genome scale phylogeny yet published for diatoms based on 103 shared plastid-coding genes from 40 diatoms and Triparma laevis as the outgroup. The most recent diatom classification posits that there are three major clades of diatoms: Coscinodiscophyceae (informally radial centrics), Mediophyceae (bi- or multipolar centrics), and Bacillariophyceae (pennates). Phylogenetic analysis of plastome data recovered the radial centric Leptocylindrus as the sister group to the remaining diatoms and recovered the polar diatoms Attheya plus Biddulphia in a clade sister to pennate diatoms. Statistical analysis comparing this optimal tree to trees constraining diatoms to the existing classification strongly rejected monophyly for the Coscinodiscophyceae and Mediophyceae. Extensive plastome rearrangements and variable gene content were observed among the 40 diatom species. Astrosyne radiata, recovered on the longest terminal branch, experienced extensive gene loss. The nucleotide substitution rates of plastid protein coding genes were estimated, and their patterns were compared across different gene categories. Relationships between substitution rates and plastome characteristics, such as indels, genome size, genome rearrangement, were examined. The analyses also revealed a strong positive correlation between sequence divergence and gene order change in diatom plastomes.