Taxogenomic reclassification of Candida and related genera in Saccharomycotina

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 remains heterogenous and phylogenetically divergent. This heterogeneity extended to genera like Ogataea, Starmerella, and Wickerhamomyces, which, while receiving reclassified Candida species, have also become more diverse. Despite widespread recognition of the polyphyletic nature of Candida, confusion persists due to the continued use of its name for species belonging to distant lineages. To address this, we aimed to reduce the heterogeneity of the genus 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 for reclassification. We employed several genomic metrics, including average amino acid identity (AAI), percentage of conserved proteins (POCP), and presence-absence patterns of orthologs (PAPO), to quantify genetic divergence in genera and clades, and to guide reclassification decisions. Additionally, comprehensive phylogenetic analyses using ITS and LSU D1/D2 rRNA sequence data were performed to include species not represented in the genome-scale analyses. This framework led to an updated classification of Candida species, proposing 27 new genera to accommodate reclassified species, along with 184 new combinations and 86 newly recognized species.