Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales).

Abstract

Species in Thismiaceae can no longer photosynthesize, and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data, and also characterize the molecular evolution of this genome. We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. We investigated plastid-genome structural changes, considering locally colinear blocks (LCBs). We also characterized possible shifts in selection pressure in retained genes by considering changes in ω, the ratio of non-synonymous to synonymous changes. Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses across descendent lineages. In addition to massive size reduction, Thismiaceae plastid genomes experienced occasional inversions, and there likely were two independent losses of the plastid inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), with significant and sporadic weakening or strengthening in several instances. The bifunctional trnE-UUC gene of Thismia huangii likely retains a secondary role in heme biosynthesis, despite a probable loss of functionality in protein translation. Several cis-spliced group IIA introns are retained, despite the loss of the plastid intron maturase, matK. We infer that most gene losses in Thismiaceae occurred early and rapidly, following the initial loss of photosynthesis in its stem lineage. As a species-rich, fully mycoheterotrophic lineage, Thismiaceae provides a model system for uncovering the unique and divergent ways in which plastid genomes evolve in heterotrophic plants. This article is protected by copyright. All rights reserved.