Skip to main content
Home / Studies in Mycology, Volume 105, Number 1

Open Access A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

Download Article:
The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina 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 Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. 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 Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, 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 Saccharomycotina, 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 Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.

Keywords: HIGHER RANK CLASSIFICATION; NOVEL TAXA; ORTHOLOGOUS GROUPS (OGs); SACCHAROMYCOTINA; TAXONOMY; YEASTS

Document Type: Research Article

Affiliations: 1: Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The Netherlands 2: 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 3: College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China 4: Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China 5: Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte NC 28223, USA 6: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China 7: Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand 8: Microbial Diversity and Utilization Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand 9: Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal 10: Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland 11: Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil 12: College of Sciences, King Saud University, Riyadh, Saudi Arabia 13: Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; 14: National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, H-1118, Budapest, Somlói út 14-16., Hungary 15: UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal 16: Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada 17: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany 18: BCCM/MUCL, Earth and Life Institute, Mycology Laboratory, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium 19: 1Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan 20: Food Science and Technology, University of California Davis, Davis, CA, 95616, USA 21: Centro de Referencia en Levaduras y Tecnología Cervecera, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina 22: Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan 23: Laboratory of Microbiology, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo 204-8588, Japan 24: Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA

Publication date: June 1, 2023

This article was made available online on May 25, 2023 as a Fast Track article with title: "A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina".

More about this publication?
  • Studies in Mycology is an international journal which publishes systematic monographs of filamentous fungi and yeasts, and special topical issues related to all fields of mycology, biotechnology, ecology, molecular biology, pathology and systematics. The journal is Open-Access and contains monographs or topical issues (5–6 papers per issue). There are no restrictions of length, although it is generally expected that manuscripts should be at least 50 A4 pages in print.
  • Editorial Board
  • Information for Authors
  • Submit a Paper
  • Code of ethics
  • GDPR Compliance
  • Ingenta Connect is not responsible for the content or availability of external websites

Share Content

  • Access Key
  • Free content
  • Partial Free content
  • New content
  • Open access content
  • Partial Open access content
  • Subscribed content
  • Partial Subscribed content
  • Free trial content