@article{5832ef1627c54d0dbe54855bee8523f0,
title = "A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina",
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.",
keywords = "Higher rank classification, novel taxa, orthologous groups (OGs), Saccharomycotina, taxonomy, yeasts",
author = "M. Groenewald and Hittinger, {C. T.} and K. Bensch and Opulente, {D. A.} and Shen, {X. X.} and Y. Li and C. Liu and LaBella, {A. L.} and X. Zhou and S. Limtong and S. Jindamorakot and P. Gon{\c c}alves and V. Robert and Wolfe, {K. H.} and Rosa, {C. A.} and T. Boekhout and N. {\v C}ade{\v z} and G. P{\'e}ter and Sampaio, {J. P.} and Lachance, {M. A.} and Yurkov, {A. M.} and Daniel, {H. M.} and M. Takashima and K. Boundy-Mills and D. Libkind and K. Aoki and T. Sugita and A. Rokas",
note = "Funding Information: We want to thank Barbara Roberts from the NCBI Taxonomy Team for providing the update of the current fungal names in NCBI Taxonomic database. Masako Takashima is supported by the Institution for Fermentation, Osaka (IFO). Heide-Marie Daniel is supported by the Belgian Science Policy Office grant C5/00/BCCM. Chris Todd Hittinger is supported by the National Science Foundation under Grant Nos. DEB-1442148 and DEB-2110403, the USDA National Institute of Food and Agriculture (Hatch Project 1020204), in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE–SC0018409, and an H.I. Romnes Faculty Fellowship, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. Research in Antonis Rokas{\textquoteright}s lab is supported by grants from the National Science Foundation (DEB-1442113 and DEB-2110404), the National Institutes of Health/National Institute of Allergy and Infectious Diseases (R01 AI153356), and the Burroughs Wellcome Fund. Antonis Rokas acknowledges support from a Klaus Tschira Guest Professorship from the Heidelberg Institute for Theoretical Studies and from a Visiting Research Fellowship from Merton College of the University of Oxford. Marc-Andr{\'e} Lachance acknowledges lifelong financial support from the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Carlos A. Rosa is supported by the Conselho Nacional de Desenvolvimento Cient{\'i}fico e Tecnol{\'o}gico (CNPq – Brazil, process numbers 408733/2021-7 and 406564/2022-1); Funda{\c c}{\~a}o do Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG, process numberAPQ-01525-14). Teun Boekhout is supported by the Distinguished Scientist Fellow Program of King Saud University, Ryadh, Saudi Arabia. Publisher Copyright: {\textcopyright} 2023 Westerdijk Fungal Biodiversity Institute.",
year = "2023",
doi = "10.3114/sim.2023.105.01",
language = "English",
volume = "105",
pages = "1--22",
journal = "Studies In Mycology",
issn = "0166-0616",
publisher = "Cbs Publications / Centraalbureau voor Schimmelcultures",
}