Mitochondrial genome diversity across the subphylum Saccharomycotina
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Abstract
Abstract Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae , but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae , exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
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In a subset of 340 yeast strains with good quality mitochondrial genome assemblies, 260 have at least five of the seven known mitochondrial NAD genes.
“we used a subset of 340 yeast strains from the entire dataset of 1,154, which have good quality assemblies of mitochondrial genomes available (Wolters et al. 2023), of which 260 have at least five out of the seven known mitochondrial NAD genes.”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Wolters et al. 2023
The Results (Mitochondrial Genome Sequence Rescue; page unavailable) report 353 available yeast mitochondrial genomes, many assembled as circles, and the Methods describe selecting assemblies for completeness. This supports the citation for the availability of mitochondrial assemblies, but our copy does not report the citing authors’ subset of 340 strains or the count of 260 with at least five NAD genes. (LLM, conf=0.86)
Experimental — accuracy not yet measuredLoss of mitochondrial Complex I occurred several times in evolution, most remarkably in the entire clade containing the Saccharomycetales and Saccharomycodales orders.
“The loss of mitochondrial Complex I occurred several times in evolution (Schikora-Tamarit et al. 2021; Wolters et al. 2023), most remarkably in the entire clade containing the Saccharomycetales and Saccharomycodales orders.”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Wolters et al. 2023
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Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
Opulente, D. A., LaBella, A. L., Harrison, M.-C., Wolters, J. F., Liu, C., Li, Y., Kominek, J., Steenwyk, J. L., Stoneman, H. R., VanDenAvond, J., et al. (2024) · Science · doi:10.1126/science.adj4503 · Cited by 121 · see citing works
Self-citationŁabędzka-Dmoch, K., Bui, T. H. D., Piątkowski, J., Dilling, M., Jagiełło, P., Kabza, W., & Golik, P. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag005 · Cited by 1 · see citing works
- Authors
- Wolters, J. F., LaBella, A. L., Opulente, D. A., Rokas, A., & Hittinger, C. T.
- Affiliations
- University of Wisconsin–Madison (US)
- University of North Carolina at Charlotte (US)
- Vanderbilt University (US)
- Corresponding author
- Hittinger, Chris Todd
- Venue
- Frontiers in Microbiology
- Publisher
- Frontiers Media SA
- Published
- 2023-11-23
- Volume
- 14
- Pages
- 1268944-1268944
- ISSN
- 1664-302X (ISSN-L)
- PMC
- PMC10418067
- OpenAlex
- W4388942326
- Cited by
- 17
- References
- 111
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 5
- FWCI
- 1.51
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Microbiology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- PubMed Central (submittedVersion, cc-by-nc)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (T32 HG002760-16)
- National Science Foundation (DEB-2110403, DEB-2110404)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Yeasts and Rust Fungi Studies
- Keywords
- mitochondrial genome, Saccharomycotina, yeast, Saccharomycetales, mitochondrial introns, horizontal gene transfer, homing endonucleases, GC content, mitochondrial genome size, evolutionary rates, Crabtree effect, aerobic fermentation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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