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Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales) Garrett, Natalie


PREMISE OF THE THESIS: Species in Thismiaceae can no longer photosynthesize, and instead obtain carbon from soil fungi. Here I infer Thismiaceae phylogeny using plastid genome data, and characterize the molecular evolution of this genome. METHODS: I assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. I investigated plastid genome structural changes considering locally colinear blocks (LCBs). I also characterized shifts in selection pressure in retained genes by considering changes in ω, the ratio of non-synonymous to synonymous changes. KEY RESULTS: Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses in descendent lineages. In addition to massive size reduction, plastid genomes experienced occasional inversions and two losses of the inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), but with significant and sporadic weakening or strengthening observed for several loci. The bifunctional trnE-UUC gene likely retains a role in haem biosynthesis despite repeated predicted losses of its functionality in translation. Several group IIA introns are retained despite loss of the intron maturase matK. The small single copy (SSC) region is reduced to a single bp in Thismia rodwayi. CONCLUSIONS: I inferred that most gene losses in Thismiaceae occurred early and rapidly, following an initial loss of photosynthesis in the stem lineage. As a species-rich lineage of full mycoheterotrophs, Thismiaceae provides an excellent model system for uncovering the unique and divergent ways in which heterotrophic plastid genomes may evolve.

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