Red-and-green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes

The Plantae comprising red, glaucophyte, and green algae (including land plants) is postulated to have a single common ancestor that is the founding lineage of photosynthetic eukaryotes. Recent multi-protein phylogenetic analyses have however provided little or no support for this hypothesis. These results may reflect limited genome data available from red algae, currently only the highly reduced genome of Cyanidioschyzon merolae, a reticulate gene ancestry, or significantly different gene divergence rates that mislead phylogenetic inference. Here using novel genome data from the mesophilic Porphyridium cruentum and Calliarthron tuberculosum, we increase by ca. 60,000 available red algal genes to assess support for the monophyly of the red + green (RG) algae and their extent of gene sharing with other lineages. Using a gene-by-gene approach, we find an emerging signal of RG monophyly (supported by ~50% of the examined protein phylogenies) that increases with the number of distinct phyla and terminal taxa in the analysis. A total of 1,808 phylogenies show evidence of gene sharing between Plantae and other lineages. We demonstrate that a rich, mesophilic red algal gene repertoire is crucial for testing controversial issues in eukaryote evolution and for understanding the complex patterns of protist gene inheritance.