Abstract Detail

Comparative Genomics/Transcriptomics

Garrett, Natalie (Lis) [1], Viruel, Juan [2], Klimpert, Nathaniel [1], Soto Gomez, Marybel [2], Lam, Vivienne [1], Merckx, Vincent [3], Graham, Sean [1].

Plastid phylogenomics and molecular evolution of fully mycoheterotrophic Thismiaceae.

Species in Thismiaceae can no longer photosynthesize, instead obtaining carbon from soil fungi. Here we infer Thismiaceae phylogeny and explore its molecular evolution in the broader context of Dioscoreales. We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published sequences for inference of its phylogenetic history. We investigated plastome structural changes considering locally colinear blocks (LCBs). We also characterized changes 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, followed by scattered gene losses in descendent lineages. In addition to massive size reduction, genomes experienced occasional inversions and two independent losses of its inverted repeat (IR) region. Retained genes remain under generally strong purifying selection (ω << 1), with significant but sporadic weakening or strengthening observed for several loci. The bifunctional trnE-UUC gene likely retains a role in heme biosynthesis, following multiple predicted losses of its functionality in translation. Several group IIA introns are retained, despite loss of the intron maturase matK. The short single copy (SSC) region is reduced to a single bp in Thismia rodwayi. We infer that most gene losses in Thismiaceae occurred early and rapidly, following an initial loss of photosynthesis in the family 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.

1 - University of British Columbia, Department of Botany, 6270 University Boulevard, Vancouver, BC, Canada
2 - Royal Botanic Gardens, Kew, Richmond, Surrey , TW9 3DS, UK
3 - Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands

Keywords:
Plastid genome degradation
Purifying selection
Mycoheterotrophy
Heme biosynthesis
Genome rearrangement
Gene loss.

Presentation Type: Oral Paper
Number: CGT4005
Abstract ID:883
Candidate for Awards:None