Using Phylotranscriptomics to Study the Evolution of the Green Algae

Abstract

The colonization of land by plants approximately 500 million years ago (Ma) is one of the most important events in the history of complex life. Land plants, hereafter referred to as “embryophytes,” comprise the ecological foundation of every major terrestrial biome, making them an essential lineage to the origin and maintenance of biodiversity in those habitats. The embryophytes form a monophyletic clade within one of the two major phyla of the green algae, the charophytes. Estimates from both fossil data and molecular clock analyses suggest that the charophytes diverged from the other main phylum of green algae, the chlorophytes, by as much as 1500 Ma. Here I present a phylogenetic analysis using transcriptomic and genomic data of 62 green algae and embryophyte operational taxonomic units, 31 of which were assembled de novo for this project. I focus on identifying the charophyte lineage that is sister to embryophytes, and show that the Zygnematophyceae have the strongest support, although the Charophyceae also have moderate support. I demonstrate that this phylogenetic tree topology is robust across different phylogenetic models and methods. Furthermore, I examine amino acid and codon usage across the tree and find that patterns in these data broadly follow the phylogenetic tree. I conclude by searching my dataset for the presence/absence of several protein domains and gene families known to be important in embryophytes, including the ethylene signaling pathway and various ion transporters. Many of these domains and genes have homologous sequences in the charophyte lineages, indicating that those green algae were particularly well-suited to the colonization of land.