Groenewald M, Hittinger C T, Bensch K, Opulente D A, Shen X-X, Li Y, Liu C, LaBella A L, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe K H, Rosa C A, Boekhout T, Čadež N, Éter G, Sampaio J P, Lachance M-A, Yurkov A M, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A
Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The Netherlands.
Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
Stud Mycol. 2023 Jun;105:1-22. doi: 10.3114/sim.2023.105.01. Epub 2023 May 25.
The subphylum is a lineage in the fungal phylum that exhibits levels of genomic diversity similar to those of plants and animals. The consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum has much higher rates of genome sequence evolution than its sister subphylum, , it contains only one class compared to the 16 classes in . The third subphylum of , the , consists of six classes and has approximately 10 times fewer species than the . These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the contains 12 major and robustly supported phylogenetic clades; seven of these are current families (, and ), one comprises two current families ( and ), one represents the genus , and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the , including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente, A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas. M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas. M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas. Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Čadež N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum . : 1-22. doi: 10.3114/sim.2023.105.01 This study is dedicated to the memory of Cletus P. Kurtzman (1938-2017), a pioneer of yeast taxonomy.
该亚门是真菌门中的一个谱系，其基因组多样性水平与植物和动物相似。该亚门目前已知有1200多个物种，分为16个科、1个目和1个纲。该亚门中的物种在生态和代谢方面具有多样性，包括重要的人类机会性病原体，以及在生物技术应用中重要的物种。许多具有生物技术价值的性状存在于亲缘关系密切的物种中，并且通常局限于单个系统发育分支。然而，大多数酵母物种的生物技术潜力仍未得到探索。尽管该亚门的基因组序列进化速率比其姐妹亚门高得多，但它只包含1个纲，而其姐妹亚门有16个纲。该亚门的第三个亚纲，即，由6个纲组成，物种数量比少约10倍。这些数据表明，目前将所有这些酵母归为一个纲和一个目的分类方式没有充分认识到它们的多样性。我们之前的全基因组系统发育分析表明，该亚门包含12个主要且得到有力支持的系统发育分支；其中7个是当前的科（、和），1个包含2个当前的科（和），1个代表属，3个代表在CUG密码子翻译上不同的谱系（CUG-丙氨酸、CUG-丝氨酸1和CUG-丝氨酸2）。结合这些分析以及相对进化分歧和基因组内容分析，我们提出了该亚门的更新分类，包括7个纲和12个目，可通过基因组内容进行诊断。这种更新分类与该亚门内的高基因组多样性水平一致，对于使该亚门的高级分类更类似于其他真菌的分类，以及有效地交流尚未正式命名的谱系来说是必要的。M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente, A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas. M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas, M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas. M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas; M. Groenew., Hittinger, Opulente & A. Rokas. Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Čadež N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum. : 1 - 22. doi: 10.3114/sim.2023.105.01 本研究献给酵母分类学先驱Cletus P. Kurtzman（1938 - 2017）。
