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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Fermentative Yeast Diversity at the Northern Range Limit of Their Oak Tree Hosts

Environmental Microbiology Reports, Год журнала: 2025, Номер 17(3)

Опубликована: Май 23, 2025

ABSTRACT Fermentative yeasts play important roles in both ecological and industrial processes, but their distribution abundance natural environments are not well understood. We investigated the diversity of at northern range limit oak tree hosts ( Quercus spp.) Sweden, identified climatic conditions governing distribution. Yeasts were isolated from bark samples 28 forests to species level using DNA metabarcoding. Most communities dominated by Saccharomycetaceae family, especially Saccharomyces, Kluyveromyces Pichia . Each genus showed a distinct latitudinal longitudinal distribution, temperature precipitation metrics predicted significant variation abundance. Consistent with this, laboratory assays revealed effects on growth strains collected different longitudes latitudes. found that older trees harbour more diverse balanced fermentative yeast evenly distributed abundances. Communities across similar when sharing common dominant species. This work provides baseline for future studies impact climate change biodiversity temperate latitudes contributes growing collection wild isolates potential biotechnological applications.

Язык: Английский

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Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

Molecular Systems Biology, Год журнала: 2025, Номер unknown

Опубликована: Май 27, 2025

Язык: Английский

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Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(23)

Опубликована: Июнь 3, 2025

Many remarkable phenotypes have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by same underlying gene families, while other times, many different families involved. Conversely, a family may be recruited for single trait or traits. To understand general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic count in 14,785 from 993 Saccharomycotina yeasts. Using recently developed phylogenetic approach that reduces spurious correlations, found expansion contraction were significantly linked to gain loss 45/56 (80%) While 595/739 (81%) significant associated with only one trait, also identified several "keystone" up 13/56 (23%) all Strikingly, most these known encode enzymes transporters, including members industrially relevant MAL tose fermentation loci baker's yeast Saccharomyces cerevisiae. These results indicate evolution level more widespread deeper timescales than previously believed.

Язык: Английский

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Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework

Yeast, Год журнала: 2024, Номер 41(10), С. 615 - 628

Опубликована: Сен. 18, 2024

ABSTRACT Yeasts in the subphylum Saccharomycotina are found across globe disparate ecosystems. A major aim of yeast research is to understand diversity and evolution ecological traits, such as carbon metabolic breadth, insect association, cactophily. This includes studying aspects traits like genetic architecture or association with other phenotypic traits. Genomic resources have grown rapidly. Ecological data, however, still limited for many species, especially those only known from species descriptions where usually a number strains studied. Moreover, information recorded natural language format limiting high throughput computational analysis. To address these limitations, we developed an ontological framework analysis ecology. total 1,088 were added Ontology Yeast Environments (OYE) analyzed machine‐learning connect genotype flexible can be extended additional isolates, environmental sequencing data. Widespread adoption OYE would greatly aid study macroecology subphylum.

Язык: Английский

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Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 6, 2024

Abstract Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin diversification lineages. Here, we examined gene family evolution 1,154 genomes from nearly all known species in medically technologically important yeast subphylum Saccharomycotina. We found that distinct plants, animals, filamentous ascomycetes characterized by small sizes smaller numbers but larger sizes. Faster-evolving lineages (FELs) yeasts experienced significantly higher rates losses—commensurate with narrowing metabolic niche breadth—but speciation than slower-evolving sister (SELs). families most often lost those involved mRNA splicing, carbohydrate metabolism, cell division likely associated intron loss, breadth, non-canonical cycle processes. Our results highlight significant role contractions function, speciation, suggest evolutionary trajectories have differed markedly across eukaryotic

Язык: Английский

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Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 23, 2024

Many remarkable innovations have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by same underlying gene families, while other times many different families involved. Conversely, a family may be recruited for single trait or traits. To understand general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic count in 14,710 from 993 species Saccharomycotina yeasts. Using recently developed phylogenetic approach that reduces spurious correlations, discovered expansion contraction was significantly linked to gain loss 45/56 (80%) While 601/746 (81%) significant were associated with only one trait, also identified several 'keystone' up 13/56 (23%) all These results indicate yeasts governed narrow set major genetic elements mechanisms.

Язык: Английский

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Global patterns of species diversity and distribution in the biomedically and biotechnologically important fungal genusAspergillus

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 3, 2024

fungi are key producers of pharmaceuticals, enzymes, and food products exhibit diverse lifestyles, ranging from saprophytes to opportunistic pathogens. To improve understanding

Язык: Английский

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