Phylotranscriptomics provides insights into the Mesoproterozoic-Neoproterozoic origin and diversification of green...

Trebouxiophyceae, with its morphological and ecological diversity, is the ideal candidate for tracing the origin and evolution of green algae, yet its phylogeny and diversification timeline remain unresolved. Our high-density taxa and large-scale nuclear gene sampling confirm its monophyly, dividing it into the core trebouxiophyceans clade and the Chlorellales clade. We find that incomplete lineage sorting is a possible explanation for nuclear-nuclear discordance. Ancestral state reconstruction suggests that the ancestor of Trebouxiophyceae is likely a unicellular freshwater alga with vegetative reproduction. Furthermore, four calibration strategies infer the origin of Trebouxiophyceae in the late Mesoproterozoic to early Neoproterozoic. The early divergence and diversification of Trebouxiophyceae imply a potential geobiological role in changes in the ancient environments during the Mesoproterozoic-Neoproterozoic transition. This study enhances our understanding of the evolutionary history of green algae and provides insights into the diversification of ancient green plant lineages.