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.

Yueomyces silvicola sp. nov., a novel ascomycetous yeast species unable to utilize ammonium, glutamate, and glutamine as sole nitrogen sources

“…Since the ITS2 sequence of strain P34-5 and the ITS1 sequence of strain OTU674 are not available for comparison, they are not included in the phylogenetic trees. | 543 from those resolved based on the whole-genome sequences (Groenewald et al, 2023;Shen et al, 2018). The present study shows that the closest relatives of the Yueomyces species are…”

“…Vanderwaltozyma and Torulaspora species with strong bootstrap supports (Figure 1). However, Shen et al (2018) and Groenewald et al (2023) showed that Y. sinensis is most closely related to Tetrapisispora blattae, followed by Vanderwaltozyma polyspora and four other Tetrapisispora species. We show here that T. blattae CBS 6284 is located in a separate branch, which is not closely related to the Yueomyces species nor to the other five Tetrapisispora species compared in this study (Figure 1).…”

“…The genus Yueomycesand the combination Yueomyces sinensis were then proposed by Wang et al (2015) to accommodate S. sinensis based on a phylogenetic analysis using multiple genes including the 18S ribosomal RNA gene (rDNA), the internal transcribed spacer (ITS) region (including the 5.8S rDNA), the D1/D2 domain of the 26S rDNA, the second largest subunit of RNA polymerase II gene (RPB2), and the translation elongation factor 1-α gene (EF1-α). The species Y. sinensis was subsequently transferred from Saccharomycodaceae to Saccharomycetaceae based on phylogenetic analyses from multiple gene and genome sequences (Groenewald et al, 2023;Wang et al, 2015).…”

Genomic and ecological factors shaping specialism and generalism across an entire subphylum

“…These distances were then clustered using standard average hierarchical clustering to visualize the raw growth rates on a heatmap built using heatmap3 in R. The phylogeny of 1,154 yeasts and fungal outgroups built from 2,408 orthologous groups of genes. Branches are colored according to their taxonomic assignment to an order of Saccharomycotina (46). The innermost rings are colored by the top-level type of isolation environment in which each specific strain was isolated.…”

Danielozyma pruni sp. nov., an asexual yeast species isolated from insect frass

“…The genome-based phylogeny obtained from sequences representing 332 yeast species demonstrated that the genus Danielozyma clustered with the genus Hyphopichia in the CUG-Ser1 clade [5]. The genus is presently classified in the family Debaryomycetaceae within the order Serinales, class Pichiomycetes, the subphylum Saccharomycotina [6].…”