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1. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

   https://doi.org/10.1126/science.adj4503  

   Opulente, Dana A; LaBella, Abigail Leavitt; Harrison, Marie-Claire; Wolters, John F; Liu, Chao; Li, Yonglin; Kominek, Jacek; Steenwyk, Jacob L; Stoneman, Hayley R; VanDenAvond, Jenna; et al (April 2024, Science)

   Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: trade-offs between performance efficiency and breadth; and the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1,154 yeast strains from 1,051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes. 

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2. The cell morphological diversity of Saccharomycotina yeasts

   https://doi.org/10.1093/femsyr/foad055  

   Chavez, Christina_M; Groenewald, Marizeth; Hulfachor, Amanda_B; Kpurubu, Gideon; Huerta, Rene; Hittinger, Chris_Todd; Rokas, Antonis (December 2023, FEMS Yeast Research)

   Abstract The ∼1 200 known species in subphylum Saccharomycotina are a highly diverse clade of unicellular fungi. During its lifecycle, a typical yeast exhibits multiple cell types with various morphologies; these morphologies vary across Saccharomycotina species. Here, we synthesize the evolutionary dimensions of variation in cellular morphology of yeasts across the subphylum, focusing on variation in cell shape, cell size, type of budding, and filament production. Examination of 332 representative species across the subphylum revealed that the most common budding cell shapes are ovoid, spherical, and ellipsoidal, and that their average length and width is 5.6 µm and 3.6 µm, respectively. 58.4% of yeast species examined can produce filamentous cells, and 87.3% of species reproduce asexually by multilateral budding, which does not require utilization of cell polarity for mitosis. Interestingly, ∼1.8% of species examined have not been observed to produce budding cells, but rather only produce filaments of septate hyphae and/or pseudohyphae. 76.9% of yeast species examined have sexual cycle descriptions, with most producing one to four ascospores that are most commonly hat-shaped (37.4%). Systematic description of yeast cellular morphological diversity and reconstruction of its evolution promises to enrich our understanding of the evolutionary cell biology of this major fungal lineage. 

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

   https://doi.org/10.3114/sim.2023.105.01  

   Groenewald, M.; Hittinger, C.T.; Bensch, K.; Opulente, D.A.; Shen, X.-X.; Li, Y.; Liu, C.; LaBella, A.L.; Zhou, X.; Limtong, S.; et al (May 2023, Studies in Mycology)

   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. 

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4. A taxogenomic view of the genus Torulaspora: an expansion from ten to twenty-two species

   https://doi.org/10.3114/persoonia.2025.54.08  

   Silva, MR; Paraíso, F; Al-Oboudi, J; Abegg, M; Aires, A; Barros, KO; Brito, PH; Jarzyna, M; Sylvester, K; Langdon, QK; et al (January 2025, Persoonia - Molecular Phylogeny and Evolution of Fungi)

   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. 

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5. Diverse signatures of convergent evolution in cactus-associated yeasts

   https://doi.org/10.1371/journal.pbio.3002832  

   Gonçalves, Carla; Harrison, Marie-Claire; Steenwyk, Jacob L; Opulente, Dana A; LaBella, Abigail L; Wolters, John F; Zhou, Xiaofan; Shen, Xing-Xing; Groenewald, Marizeth; Hittinger, Chris Todd; et al (September 2024, PLOS Biology)

   Kamoun, Sophien (Ed.)

   Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning–based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall–degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle—and perhaps more generally lifestyles favoring thermotolerance—might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity. 

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