The Algal Tree of Life from a Genomics Perspective

Abstract

It is now widely recognized that photosynthetic eukaryotes (algae and plants) have polyphyletic origins in the eukaryotic tree of life (ETOL). The primary endosymbiosis that gave rise to the first photosynthetic organelle (plastid) occurred ca. 1.6 billion years ago via the capture and retention of a free-living cyanobacterium by a single-celled protist. This proto-alga is the ancestor of the Archaeplastida that includes the photosynthetic glaucophytes, red algae, and the green lineage. The Archaeplastida plastid spread into other protist lineages through serial endosymbiosis, giving rise to dominant marine phytoplankton such as diatoms and dinoflagellates. A significant effort has been expended on elucidating plastid origin, function, and its impacts on global primary productivity and geochemical cycles. Here we focus on the placement of algae in the ETOL, with particular emphasis on the major groups: Archaeplastida, SAR (stramenopiles, alveolates, rhizarians), haptophytes, and cryptophytes. Our approach is to rely on the analysis of ortholog groups identified in recently generated genomic and transcriptomic data to infer the ETOL, rather than using a subset of manually chosen and curated genes. We show that bioinformatic pipelines effectively, and with minimal curation recover a robust ETOL, when compared to the classical approach of utilizing “designer datasets” in multiple analyses.