Ortholog identification method.

<p>This diagram outlines the steps used for identifying orthologous genes for phylogenetic analysis. <b>A</b>) Unresolved phylogenetic scheme relating chlorophytes, charophytes, and embryophytes with a list of the six taxa with fully sequenced genomes used for the core ortholog determination. <b>B</b>) Core ortholog prediction from the previous six taxa. <b>C</b>) Charophyte orthog prediction. The core orthologs were then used to search for proteins in each of the eight charophyte transcriptomes. We filtered for good taxon sampling and removed orthologs with significant amino acid bias, resulting in 160 aligned proteins. These were concatenated onto one large multigene data matrix for phylogenetic analysis.