Investigating the Evolution of Green Algae with a Large Transcriptomic Dataset

The colonization of land by plants, thought to have occurred approximately 450-500 million years ago (Ma) is one of the most important events in the history of life on Earth. Land plants, hereafter referred to as "embryophytes," comprise the foundation of every terrestrial biome, making them an essential lineage for the origin and maintenance of biodiversity. The embryophytes form a monophyletic clade within one of the two major phyla of the green algae, the Streptophyta. Estimates from fossil data and molecular clock analyses suggest the charophytes diverged from the other main phylum of green algae, the Chlorophyta, as much as 1500 Ma. Here we 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. We focus on identifying the charophyte lineage that is sister to embryophytes, and show that the Zygnematophyceae have the strongest support, followed by the Charophyceae. We demonstrate that this phylogenetic tree topology is robust across different phylogenetic models and methods. Furthermore, we examine amino acid and codon usage across the tree and find these data broadly follow the phylogenetic tree. We conclude by searching the dataset for 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, giving insight into the processes that underlay the colonization of the land by plants.