F. Liu, Z.-D. Hu, X.-M. Zhao, W.-N. Zhao, Z.-X. Feng, A. Yurkov, S. Alwasel, T. Boekhout, K. Bensch, F.-L. Hui, F.-Y. Bai, Q.-M. Wang
{"title":"Metschnikowiaceae 中 Candida auris- Candida haemuli 支系和相关类群的系统发生组分析,以及 13 个新属、55 个新组合和 9 个新种的提出","authors":"F. Liu, Z.-D. Hu, X.-M. Zhao, W.-N. Zhao, Z.-X. Feng, A. Yurkov, S. Alwasel, T. Boekhout, K. Bensch, F.-L. Hui, F.-Y. Bai, Q.-M. Wang","doi":"10.3767/persoonia.2024.52.02","DOIUrl":null,"url":null,"abstract":"<i>Candida</i> is a polyphyletic genus of sexually 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,\napproximately 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\ncaused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the <i>Candida auris</i> - <i>Candida haemuli</i> (CAH) clade in the <i>Metschnikowiaceae</i>, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from\nnatural 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\nphylogenetic 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\nposition 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\nof 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>\nand 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>.","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"102 1","pages":""},"PeriodicalIF":9.5000,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"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\",\"authors\":\"F. Liu, Z.-D. Hu, X.-M. Zhao, W.-N. Zhao, Z.-X. Feng, A. Yurkov, S. Alwasel, T. Boekhout, K. Bensch, F.-L. Hui, F.-Y. Bai, Q.-M. Wang\",\"doi\":\"10.3767/persoonia.2024.52.02\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<i>Candida</i> is a polyphyletic genus of sexually 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,\\napproximately 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\\ncaused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the <i>Candida auris</i> - <i>Candida haemuli</i> (CAH) clade in the <i>Metschnikowiaceae</i>, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from\\nnatural 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\\nphylogenetic 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\\nposition 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\\nof 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>\\nand 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>.\",\"PeriodicalId\":20014,\"journal\":{\"name\":\"Persoonia\",\"volume\":\"102 1\",\"pages\":\"\"},\"PeriodicalIF\":9.5000,\"publicationDate\":\"2024-06-30\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Persoonia\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.3767/persoonia.2024.52.02\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MYCOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Persoonia","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.3767/persoonia.2024.52.02","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MYCOLOGY","Score":null,"Total":0}
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
Candida is a polyphyletic genus of sexually reproducing yeasts in the Saccharomycotina 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 Candida 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. Candida auris is an important, globally emerging opportunistic pathogen that has
caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the Candida auris - Candida haemuli (CAH) clade in the Metschnikowiaceae, 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 Candida that is Candida vulgaris (currently interpreted as a synonym of Candida tropicalis) and belongs to the family Debaryomycetaceae. Although previous
phylogenetic and phylogenomic studies confirmed the position of C. auris in the Metschnikowiaceae, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera Clavispora and Metschnikowia. To resolve the
position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of C. auris and related species in the Metschnikowiaceae 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 Candida and Hyphopichia species, including members of the CAH clade in the Metschnikowiaceae. As a result, C. auris
and related species are reassigned to the genus Candidozyma. Fifty-five new combinations and nine new species are introduced, and this will reduce the polyphyly of the genus Candida.
期刊介绍:
Persoonia aspires to publish papers focusing on the molecular systematics and evolution of fungi. Additionally, it seeks to advance fungal taxonomy by employing a polythetic approach to elucidate the genuine phylogeny and relationships within the kingdom Fungi. The journal is dedicated to disseminating high-quality papers that unravel both known and novel fungal taxa at the DNA level. Moreover, it endeavors to provide fresh insights into evolutionary processes and relationships. The scope of papers considered encompasses research articles, along with topical and book reviews.