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The yeast genusTorulaspora(subphylumSaccharomycotina, familySaccharomycetaceae) is mostly known from its type species,T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains 10 species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection ofTorulasporastrains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity ofTorulaspora. We also sketch a genotype-phenotype map for the genus and show how the complex relationship between key genes and the physiological traits they control both between and within species. This remarkable increase in the number of species in the genusTorulasporahighlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomic approaches can foster the assessment of species circumscriptions in fungi. 

Ascomycota, the most speciose phylum of fungi, is a complex entity, comprising three diversesubphyla: Pezizomycotina, Saccharomycotina, and Taphrinomycotina. The largest and most diversesubphylum, Pezizomycotina, is a rich tapestry of 16 classes and 171 orders. Saccharomycotina, thesecond largest subphylum, is a diverse collection of seven classes and 12 orders, whileTaphrinomycotina, the smallest, is a unique assembly of six classes and six orders. Over the pastdecade, numerous taxonomic studies have focused on the generic, family, and class classifications ofAscomycota. These efforts, well-documented across various databases, are crucial for acomprehensive understanding of the classification. However, the study of taxonomy at the ordinallevel, a crucial tier in the taxonomic hierarchy, has been largely overlooked. In a global collaborationwith mycologists and lichenologists, this study presents the first comprehensive information on theorders within Pezizomycotina and Taphrinomycotina. The recent taxonomic classification ofSaccharomycotina has led to the exclusion of this subphylum from the present study, as an immediaterevision is not necessary. Each order is thoroughly discussed, highlighting its historical significance,current status, key identification characteristics, evolutionary relationships, ecological and economicroles, future recommendations, and updated family-level classification. Teaching diagrams for thelife cycles of several orders, viz. Asterinales, Helotiales, Hypocreales, Laboulbeniales, Meliolales,Mycosphaerellales, Ophiostomatales, Pezizales, Pleosporales, Phyllachorales, Rhytismatales,Sordariales, Venturiales, Xylariales (Pezizomycotina) and Pneumocystidales,Schizosaccharomycetales and Taphrinales (Taphrinomycotina) are provided. Each diagram is explained with a representative genus/genera of their sexual and asexual cycles of each order. WithinPezizomycotina, Dothideomycetes contains the highest number of orders, with 57, followed bySordariomycetes (52 orders), Lecanoromycetes (21 orders), Eurotiomycetes and Leotiomycetes (12orders each), Laboulbeniomycetes (3 orders), and Arthoniomycetes and Xylonomycetes (2 orderseach). Candelariomycetes, Coniocybomycetes, Geoglossomycetes, Lichinomycetes, Orbiliomycetes,Pezizomycetes, Sareomycetes, and Xylobotryomycetes each contain a single order, whileThelocarpales and Vezdaeales are treated as incertae sedis within Pezizomycotina. Notably, theclasses Candelariomycetes, Coniocybomycetes, Geoglossomycetes, Sareomycetes, andXylonomycetes, all recently grouped under Lichinomycetes, are treated as separate classes based onphylogenetic analysis and current literature. Within Lecanoromycetes, the synonymization ofSporastatiales with Rhizocarpales and Sarrameanales with Schaereriales is not supported in thephylogenetic analysis. These orders are retained separately, and the justifications are provided undereach section as well as in the discussion. Within Leotiomycetes, the order Medeolariales, which wasonce considered part of Helotiales, is treated as a distinct order based on phylogenetic evidence. Theclassification of Medeolariales may change as more data becomes available from different generegions. Lahmiales (Leotiomycetes) is not included in the phylogenetic analysis due to a lack ofmolecular data. Sareomycetes and Xylonomycetes are treated as separate classes. Spathulosporamixed with Lulworthiales and the inclusion of Spathulosporales within Lulworthiomycetidae issupported and extant molecular sampling is important to resolve the phylogenetic boundaries ofmembers of this subclass. The majority of the classes of Pezizomycotina and Taphrinomycotinaformed monophyletic clades in the phylogenetic analysis conducted based on SSU, LSU, 5.8S, TEFand RPB2 sequence data. However, Arthoniomycetes nested with the basal lineage ofDothideomycetes and formed a monophyletic clade also known as the superclass, Dothideomyceta.In Taphrinomycotina, a single order is accepted within each class. 

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.