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

  • Back
    bibtex

Document Title

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

Author

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. Gon?alves P. Robert V. Wolfe K.H. Rosa C.A. Boekhout T. ?ade? N. P?ter 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.

Affiliations

Westerdijk Fungal Biodiversity Institute Utrecht 3584 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 United States; Department of Biology Villanova University Villanova PA 19085 United States; College of Agriculture and Biotechnology Zhejiang University Hangzhou 310058 China; Institute of Marine Science and Technology Shandong University Qingdao 266237 China; Department of Bioinformatics and Genomics The University of North Carolina at Charlotte Charlotte NC 28223 United States; Guangdong Province Key Laboratory of Microbial Signals and Disease Control Integrative Microbiology Research Center South China Agricultural University Guangzhou 510642 China; Department of Microbiology Faculty of Science Kasetsart University Bangkok 10900 Thailand; 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; Associate Laboratory i4HB-Institute for Health and Bioeconomy NOVA School of Science and Technology Universidade NOVA de Lisboa Caparica Portugal; UCIBIO-Applied Molecular Biosciences Unit Department of Life Sciences NOVA School of Science and Technology Universidade NOVA de Lisboa Caparica Portugal; Conway Institute School of Medicine University College DublinDublin 4 Ireland; Departamento de Microbiologia ICB Universidade Federal de Minas Gerais C.P. 486 MG Belo Horizonte 31270-901 Brazil; College of Sciences King Saud University Riyadh Saudi Arabia; Food Science and Technology Department Biotechnical Faculty University of Ljubljana Ljubljana Slovenia; National Collection of Agricultural and Industrial Microorganisms Institute of Food Science and Technology Hungarian University of Agriculture and Life Sciences Soml?i ?t 14-16. Budapest H-1118 Hungary; UCIBIO Departamento de Ci?ncias da Vida Faculdade de Ci?ncias e Tecnologia Universidade Nova de Lisboa Caparica 2829-516 Portugal; Department of Biology University of Western Ontario London ON N6A 5B7 Canada; Leibniz Institute DSMZGerman Collection of Microorganisms and Cell Cultures Braunschweig 38124 Germany; BCCM/MUCL Earth and Life Institute Mycology Laboratory Universit? catholique de Louvain Louvain-la-Neuve 1348 Belgium; Laboratory of Yeast Systematics Tokyo NODAI Research Institute (TNRI) Tokyo University of Agriculture Sakuragaoka Setagaya Tokyo 156-8502 Japan; Food Science and Technology University of California Davis Davis CA 95616 United States; Centro de Referencia en Levaduras y Tecnolog?a Cervecera Instituto Andino Patag?nico de Tecnolog?as Biol?gicas y Geoambientales (IPATEC) Universidad Nacional del Comahue CONICET CRUB Quintral 1250 San Carlos de Bariloche R?o Negro 8400 Argentina; Laboratory of Microbiology Meiji Pharmaceutical University Kiyose Noshio Tokyo 204-8588 Japan; Department of Biological Sciences and Evolutionary Studies Initiative Vanderbilt University Nashville TN 37235 United States

Type

Article

Source Title

Studies in Mycology

ISSN

1660616

Year

2023

Volume

105

Open Access

All Open Access Green

Publisher

Westerdijk Fungal Biodiversity Institute

DOI

10.3114/sim.2023.105.01

Abstract

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. ? 2023 Westerdijk Fungal Biodiversity Institute.

Industrial Classification

N/A

Knowledge Taxonomy Level 1

Biological science

Knowledge Taxonomy Level 2

Microbiology

Knowledge Taxonomy Level 3

Applied microbiology

License

CC BY-NC-ND

Rights

Westerdijk Fungal Biodiversity Institute.

Publication Source

Scopus

Continue browsing