Phylogenomic analysis of the <i>Candida auris- Candida haemuli</i> clade and related taxa in the <i> Metschnikowiaceae,</i> and proposal of thirteen new genera, fifty-five new combinations and nine new species

<i>Candida</i> is a polyphyletic genus of asexually reproducing yeasts in the <i>Saccharomycotina</i> with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades, approximately half of the <i>Candida</i> species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. <i>Candida auris</i> is an important, globally emerging opportunistic pathogen that has caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the <i>Candida auris-Candida haemuli</i> (CAH) clade in the <i>Metschnikowiaceae</i>, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from natural environments. The clade is phylogenetically positioned remotely from the type species of the genus <i>Candida</i> that is <i>Candida vulgaris</i> (currently interpreted as a synonym of <i>Candida tropicalis</i>) and belongs to the family <i>Debaryomycetaceae</i>. Although previous phylogenetic and phylogenomic studies confirmed the position of <i>C. auris</i> in the <i>Metschnikowiaceae</i>, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera <i>Clavispora</i> and <i>Metschnikowia</i>. To resolve the position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of <i>C. auris</i> and related species in the <i>Metschnikowiaceae</i> using several metrics, such as the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). Based on those approaches, 13 new genera are proposed for various <i>Candida</i> and <i>Hyphopichia</i> species, including members of the CAH clade in the <i>Metschnikowiaceae</i>. As a result, <i>C. auris</i> and related species are reassigned to the genus <i>Candidozyma</i>. Fifty-five new combinations and nine new species are introduced and this will reduce the polyphyly of the genus <i>Candida</i>. <b>Citation</b>: Liu F, Hu Z-D, Zhao X-M, et al. 2024. Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species. Persoonia 52: 22-43. https://doi.org/10.3767/persoonia.2024.52.02 .