Structural Plastome Evolution in Holoparasitic Hydnoraceae with Special Focus on Inverted and Direct Repeats

Plastome condensation during adaptation to a heterotrophic lifestyle is generally well understood and lineage-independent models have been derived. However, understanding the evolutionary trajectories of comparatively old heterotrophic lineages that are on the cusp of a minimal plastome, is essential to complement and expand current knowledge. We study Hydnoraceae, one of the oldest and least investigated parasitic angiosperm lineages. Plastome comparative genomics, using seven out of eight known species of the genus Hydnora and three species of Prosopanche, reveal a high degree of structural similarity and shared gene content; contrasted by striking dissimilarities with respect to repeat content [inverted and direct repeats (DRs)]. We identified varying inverted repeat contents and positions, likely resulting from multiple, independent evolutionary events, and a DR gain in Prosopanche. Considering different evolutionary trajectories and based on a fully resolved and supported species-level phylogenetic hypothesis, we describe three possible, distinct models to explain the Hydnoraceae plastome states. For comparative purposes, we also report the first plastid genomes for the closely related autotrophic genera Lactoris (Lactoridaceae) and Thottea (Aristolochiaceae).

Automated summary

Plastome condensation during adaptation to a heterotrophic lifestyle is well understood, but studying the evolutionary trajectories of older heterotrophic lineages is crucial. This study focused on Hydnoraceae, one of the oldest and least studied parasitic angiosperm lineages. Comparative genomics revealed structural similarities and shared gene content in Hydnora and Prosopanche, but also significant differences in repeat content. Multiple independent evolutionary events likely contributed to the variations in inverted repeat content and positions, with a direct repeat gain in Prosopanche. Three distinct models were proposed to explain the Hydnoraceae plastome states, based on a resolved species-level phylogenetic hypothesis. Plastid genomes for two closely related autotrophic genera, Lactoris and Thottea, were also reported for comparative purposes.