Phylogenomic and genome-based metrics analysis of Candida and related genera in the Saccharomycotina: Contributons to understand phylogenetic divergence

The yeast genus Candida includes several medically important and various biotechnologically important species of yeasts. This genus is highly polyphyletic and occurs in most lineages of Saccharomycotina. In the past two decades, more than half of the Candida species have been reassigned into existing or newly introduced genera, but the polyphyly of the genus remains. Various genera, i.e., Kuraishia, Ogataea, Wickerhamiella and Wickerhamomyces, became heterogeneous and polyphyletic with the transfer to those genera of species that were formerly classified in Candida. To fully resolve the polyphyletic feature of Candida and other genera in the Saccharomycotina, a robust phylogenomic analysis using 1 134 genomes of 1 128 species of Saccharomycotina was made. Several genome-based metrics parameters, i.e., the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP), the presence-absence patterns of orthologs (PAPO), and the relative evolutionary divergence (RED), were analyzed to address the phylogenetic relationship of all genera in the Saccharomycotina and to assess genome diversity at different taxon ranks, such as genus, family, order, and class. Fifty-five monophyletic clades and 31 single-species lineages that might be equivalent to genera were recognized based on the phylogenomic analysis, and AAI, PAPO, POCP, and RED genome-based approaches. In addition, the data suggests the presence of 24 new families, 11 new orders and four new classes. Formal taxonomic proposals based on these results will be made elsewhere.