Miao-Miao Liu, Qi-Ming Wang
The genus Candida in the Saccharomycotina has long reflected the historical practice of yeast classification based on phenotypic characteristics, retaining remnants of dual nomenclature even after its abandonment in 2011. Following this shift, many Candida species were reclassified into existing or newly proposed genera; yet, Candida itself remained heterogeneous and phylogenetically divergent. This heterogeneity is also true for genera like Ogataea, Starmerella, and Wickerhamomyces. While this heterogeneity has been demonstrated in previous studies, including several recent proposals for new genera, the inclusion of reclassified Candida species in these genera will make them more phylogenetically diverse. Despite widespread recognition of the polyphyletic nature of Candida, confusion persists due to the continued use of this single generic name for species belonging to lineages distantly related to that of the generic type species, Candida vulgaris, a current synonym under Candida tropicalis. In this study, we aim to reduce the genetic heterogeneity of the genus Candida by (i) focusing on lineages distantly related to its nomenclature type and (ii) assessing the diversity and composition of genera into which former Candida species have been reassigned. Phylogenomic analyses were conducted to determine the positions of Candida species and several genomic metrics, including average amino acid identity (AAI), percentage of conserved proteins (POCP), and presence-absence patterns of orthologs (PAPO), in order to quantify genetic divergence in genera and clades, were calculated to assist the reclassification decisions as complementary approaches. In addition to phylogenomic analyses, comprehensive phylogenetic analyses using ITS and LSU D1/D2 rDNA sequence data were performed to include species that are not represented in the genome-scale analyses and to assist species recognition in future studies. This framework led to an updated classification of Candida species and related taxa, proposing 25 new genera to accommodate reclassified species and validating 4 genera, along with 175 new combinations and 87 newly recognized species.