Inferring Relationships of Early Land Plants Using a Transcriptome-Based Approach

The origin of terrestrial plants (embryophytes) over 450 million years ago is undoubtedly one of the most consequential events in Earth’s history. Arising from a streptophytic green algal ancestor, land plants transformed the terrestrial environment and set the stage for the diversification of all life on land. Reconstructing the origin and evolution of embryophytes and their ancestors is essential for understanding how critical adaptations arose, e.g., the embryo, vascular tissue, seeds, and flowers. Well-resolved relationships for the backbone phylogeny of Viridiplantae (green plants), and within its major lineages, will significantly contribute to reconstructions of the origins of these traits. Inferring phylogenies from molecular data at this scale can be problematic. However, the use of data sampled at the genome level (phylogenomics) should significantly increase the number of characters appropriate for analyses at this breadth of taxon sampling. Recent phylogenomic reconstructions focused on the major divergences of Viridiplantae have resulted in promising, but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of generating genome-scale data. Here, I will discuss approaches to inferring the phylogeny of embryophytes and their ancestors using high-throughput transcriptome sequencing and bioinformatics. Results from both de novo transcriptome generation (the 1KP Project) and from the mining of public data will be discussed, as will comparisons with whole plastid genome phylogenies.