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

Science, Год журнала: 2024, Номер 384(6694)

Опубликована: Апрель 25, 2024

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to broad (generalists). Two general paradigms have been proposed explain this variation: (i) trade-offs between performance efficiency and breadth (ii) the joint influence of extrinsic (environmental) intrinsic (genomic) factors. We assembled genomic, metabolic, data nearly all known species ancient fungal subphylum Saccharomycotina (1154 yeast strains 1051 species), grown 24 different environmental conditions, examine evolution. found that large differences carbon utilization traits yeasts stem genes encoding specific metabolic pathways, but we limited evidence for trade-offs. These comprehensive argue factors shape microbes.

Язык: Английский

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Phylogenomic analysis of the Candida auris- Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species

Persoonia - Molecular Phylogeny and Evolution of Fungi, Год журнала: 2024, Номер 52(1), С. 22 - 43

Опубликована: Апрель 7, 2024

is a polyphyletic genus of asexually reproducing yeasts in the

Язык: Английский

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Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Microbiology Spectrum, Год журнала: 2024, Номер 12(4)

Опубликована: Март 6, 2024

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale phylogenetics (phylogenomics) species and populations to reconstruct evolutionary relationships in dense data set 710 fungal genomes from the biomedically technologically important genus Aspergillus. To do so, generated novel 1,362 high-quality markers specific for Aspergillus provided profile Hidden Markov Models each, facilitating their use by others. Examining resulting phylogeny helped resolve ongoing controversies, identified new ones, revealed extensive strain misidentification (7.59% strains were previously misidentified), underscoring importance population-level sampling classification. These findings corroborated using current standard, taxonomically informative loci. suggest that phylogenomics can facilitate accurate classifications reconstructions Tree Life.IMPORTANCEIdentification relies markers. Advances genomic technologies have made it possible sequence genome any strain, making assignment (and discovery ones). We examined usefulness limitations large publicly available multiple biomedically, agriculturally, industrially Our nearly 8% misidentified. work highlights systematic biology suggests sequencing strains, including reference (e.g., type strains), will be required reduce errors public databases.

Язык: Английский

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Machine learning enables identification of an alternative yeast galactose utilization pathway

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(18)

Опубликована: Апрель 26, 2024

How genomic differences contribute to phenotypic is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources conditions 1,154 strains from 1,049 fungal species (nearly all known) the yeast subphylum Saccharomycotina provide powerful, yet complex, dataset for addressing this question. We used random forest algorithm trained these genomic, metabolic, environmental data predict several carbon with high accuracy. Known structural genes involved assimilation presence/absence other were important features contributing prediction By further examining galactose, we found that it can be predicted accuracy either (92.2%) or (82.6%) but not environment (65.6%). Prediction was even higher (93.3%) when combined data. After

Язык: Английский

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Classes and phyla of the kingdom Fungi

Fungal Diversity, Год журнала: 2024, Номер 128(1), С. 1 - 165

Опубликована: Окт. 15, 2024

Abstract Fungi are one of the most diverse groups organisms with an estimated number species in range 2–3 million. The higher-level ranking fungi has been discussed framework molecular phylogenetics since Hibbett et al., and definition higher ranks (e.g., phyla) ‘true fungi’ have revised several subsequent publications. Rapid accumulation novel genomic data advancements now facilitate a robust precise foundation for classification within kingdom. This study provides updated kingdom , drawing upon comprehensive phylogenomic analysis Holomycota which we outline well-supported nodes fungal tree explore more contentious groupings. We accept 19 phyla Fungi, viz . Aphelidiomycota Ascomycota Basidiobolomycota Basidiomycota Blastocladiomycota Calcarisporiellomycota Chytridiomycota Entomophthoromycota Entorrhizomycota Glomeromycota Kickxellomycota Monoblepharomycota Mortierellomycota Mucoromycota Neocallimastigomycota Olpidiomycota Rozellomycota Sanchytriomycota, Zoopagomycota In phylogenies, Caulochytriomycota resides ; thus, former is regarded as synonym latter, while Caulochytriomycetes viewed class provide description each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov introduced only subphylum Sanchytriomycota subclass Pneumocystomycetidae Kirk al. Pneumocystomycetes invalid thus validated. Placements fossil classes also discussed, providing examples.

Язык: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июнь 22, 2023

Abstract Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to broad (generalists). Paradigms proposed explain this either invoke trade-offs between performance efficiency and breadth or underlying intrinsic extrinsic factors. We assembled genomic (1,154 yeast strains 1,049 species), metabolic (quantitative measures of growth 843 species 24 conditions), (environmental ontology 1,088 species) data nearly all known the ancient fungal subphylum Saccharomycotina examine evolution. found large interspecific differences carbon stem genes encoding specific pathways but no evidence a limited role These comprehensive argue that factors driving microbial variation. One-Sentence Summary A complete catalog illuminates evolution their diverse ecologies metabolisms.

Язык: Английский

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Saccharomycotina yeasts defy long-standing macroecological patterns

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(10)

Опубликована: Фев. 27, 2024

The Saccharomycotina yeasts (“yeasts” hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts highly ecologically diverse, found across broad range environments in every biome continent on earth; however, little is known about what rules govern the macroecology yeast species their limits wild. Here, we trained machine learning models 12,816 terrestrial occurrence records 96 environmental variables to infer global distribution maps at ~1 km 2 resolution for 186 (~15% described from 75% orders) test drivers biogeography macroecology. We that predicted diversity hotspots occur mixed montane forests temperate climates. Diversity vegetation type topography were some greatest predictors richness, suggesting microhabitats clines key diversity. further significantly influenced by carbon niche breadth overlap with other species, specialists high-diversity exhibiting reduced geographic ranges. Finally, contravene many long-standing macroecological principles, including latitudinal gradient, temperature-dependent positive relationship between latitude size (Rapoport’s rule). These results unveil how environment governs subphylum. high-resolution distributions will facilitate prediction economically relevant emerging pathogenic under current future climate scenarios.

Язык: Английский

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Ancient origin and high diversity of zymocin-like killer toxins in the budding yeast subphylum

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(7)

Опубликована: Фев. 10, 2025

Zymocin is a well-characterized killer toxin secreted by some strains of the yeast Kluyveromyces lactis . It acts cleaving specific tRNA in sensitive recipient cells. encoded plasmid or virus-like element (VLE), which linear DNA molecule located cytosol. We hypothesized that tRNA-cleaving similar to zymocin may have caused three parallel changes nuclear genetic code occurred during evolution, codon CUG became translated as Ser Ala instead Leu. However, zymocin-like toxins are rare — both among species, and within species —and only four this type previously been discovered. Here, we identified 45 genes Saccharomycotina, budding subphylum, using bioinformatics strategy, verified many them toxic Saccharomyces cerevisiae when expressed. Some on cytosolic VLEs, whereas others VLE-derived integrated into genome. The extraordinarily diverse sequence show evidence positive selection. Toxin were found five taxonomic orders yeasts, including two reassigned codons, indicating VLEs parasites for at least 300 My their existence predates changes.

Язык: Английский

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Non-dikarya fungi share the TORC1 pathway with animals, not with Saccharomyces cerevisiae

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Фев. 18, 2025

Abstract Target of rapamycin (TOR), discovered in Saccharomyces cerevisiae , is a highly conserved serine/threonine kinase acting as regulatory hub between the cell and its environment. Like mammals, fungi, TOR complex 1 (TORC1) pathway essential for coordinating growth response to nutrient availability. The activation TORC1 similar yeast while inhibition more mammals. This divergence regulation opens question how common are mammalian variants fungal kingdom. In this work, we trace evolutionary history components throughout Our findings show that these fungi contain mammalian-specific KICSTOR inhibition. They also possess orthologs serine, arginine methionine sensors orchestrate starvation Rheb-TSC mediated was lost Saccharomycotina non-Dikarya. These indicate non-Dikarya resembles TORC1. many inhibitory evolved alternate mechanisms. Furthermore, our work highlights limitations using S. model putting forward other possible research models.

Язык: Английский

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Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces

Biotechnology for Biofuels and Bioproducts, Год журнала: 2024, Номер 17(1)

Опубликована: Фев. 7, 2024

Abstract Background Cost-effective production of biofuels from lignocellulose requires the fermentation d -xylose. Many yeast species within and closely related to genera Spathaspora Scheffersomyces (both order Serinales) natively assimilate ferment xylose. Other consume xylose inefficiently, leading extracellular accumulation xylitol. Xylitol excretion is thought be due different cofactor requirements first two steps metabolism. Xylose reductase (XR) generally uses NADPH reduce xylitol, while xylitol dehydrogenase (XDH) NAD + oxidize xylulose, creating an imbalanced redox pathway. This imbalance particularly consequential in hypoxic or anoxic environments. Results We screened growth xylose-fermenting high moderate aeration identified both ethanol producers producers. Selected were further characterized for their XR XDH preferences by enzyme assays gene expression patterns RNA-Seq. Our data revealed that metabolism more balanced some species, but it strongly affected oxygen levels. Under aeration, most switched accumulation, despite availability ample accept electrons NADH. switch was followed decreases activity genes metabolism, suggesting bottlenecks are not always preferences. Finally, we expressed XYL multiple a strain Saccharomyces cerevisiae . Recombinant S. expressing XYL1 xylosifermentans , which encodes without preference, showed improved anaerobic on as primary carbon source compared stipitis Conclusion Collectively, our do support hypothesis occurs primarily differences between dehydrogenase; instead, plays major role response have also Sc. potential can engineered into improve biofuel production.

Язык: Английский

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