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

Citation

D. A. Opulente et al. "Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts" Science 384:eadj4503 (2024) [DOI:10.1126/science.adj4503]

Description

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: (i) trade-offs between performance efficiency and breadth and (ii) 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 (1154 yeast strains from 1051 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 we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.

Data Access

All genome sequence assemblies and raw sequencing data have been deposited in GenBank under the accessions noted in data S1. All other data, including data on growth on different carbon and nitrogen sources and isolation environment data, have been deposited in Figshare (42). All code has been deposited in GitHub, available through Zenodo (92, 93), and is available in Figshare (42). Nearly all strains came from globally recognized yeast culture collections and may be ordered from the USDA (https://nrrl.ncaur.usda.gov for NRRL strains) or Westerdijk Fungal Biodiversity Institute (https://wi.knaw.nl for CBS strains) under their respective material transfer agreements (MTAs) for publicly deposited strains; currently, NRRL only requires an MTA for strains requiring BSL-2 precautions. Strains from the Hittinger laboratory that represent candidates for novel species that have not yet been formally described or deposited at CBS or NRRL may be obtained from C.T.H. under the Uniform Biological MTA or another mutually acceptable MTA.

Conversion
Field data
Genomics
Phylogenetic relationships