<b>Taxogenomic reclassification of </b><b><i>Candida</i></b><b> and related genera in Saccharomycotina</b>

The genus <i>Candida</i> 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 <i>Candida</i> species were reclassified into existing or newly proposed genera, yet <i>Candida</i> itself remains heterogenous and phylogenetically divergent. This heterogeneity extended to genera like <i>Ogataea</i>, <i>Starmerella</i>, and <i>Wickerhamomyces</i>, which, while receiving reclassified <i>Candida</i> species, have also become more diverse. Despite widespread recognition of the polyphyletic nature of <i>Candida</i>, 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 <i>Candida</i> species have been reassigned. Phylogenomic analyses were conducted to determine the positions of <i>Candida</i> 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 <i>Candida</i> species, proposing 36 new genera to accommodate reclassified species, along with 178 new combinations and 84 newly recognized species.