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Cited by 47Fungal and yeast genetics researchYeasts and Rust Fungi StudiesGenomics and Phylogenetic Studies

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Mitochondrial Genome Evolution in a Single Protoploid Yeast Species

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Jung, Paul P, Friedrich, Anne, Reisser, Cyrielle, Hou, Jing, Schacherer, Joseph·2012·G3 Genes|Genomes|Genetics
DOI 10.1534/g3.112.003152PMC PMC3429925
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Abstract

Mitochondria are organelles, which play a key role in some essential functions, including respiration, metabolite biosynthesis, ion homeostasis, and apoptosis. The vast numbers of mitochondrial DNA (mtDNA) sequences of various yeast species, which have recently been published, have also helped to elucidate the structural diversity of these genomes. Although a large corpus of data are now available on the diversity of yeast species, little is known so far about the mtDNA diversity in single yeast species. To study the genetic variations occurring in the mtDNA of wild yeast isolates, we performed a genome-wide polymorphism survey on the mtDNA of 18 Lachancea kluyveri (formerly Saccharomyces kluyveri) strains. We determined the complete mt genome sequences of strains isolated from various geographical locations (in North America, Asia, and Europe) and ecological niches (Drosophila, tree exudates, soil). The mt genome of the NCYC 543 reference strain is 51,525 bp long. It contains the same core of genes as Lachancea thermotolerans, the nearest relative to L. kluyveri. To explore the mt genome variations in a single yeast species, we compared the mtDNAs of the 18 isolates. The phylogeny and population structure of L. kluyveri provide clear-cut evidence for the existence of well-defined geographically isolated lineages. Although these genomes are completely syntenic, their size and the intron content were found to vary among the isolates studied. These genomes are highly polymorphic, showing an average diversity of 28.5 SNPs/kb and 6.6 indels/kb. Analysis of the SNP and indel patterns showed the existence of a particularly high overall level of polymorphism in the intergenic regions. The dN/dS ratios obtained are consistent with purifying selection in all these genes, with the noteworthy exception of the VAR1 gene, which gave a very high ratio. These data suggest that the intergenic regions have evolved very fast in yeast mitochondrial genomes.

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Metadata

Authors
Jung, P. P., Friedrich, A., Reisser, C., Hou, J., & Schacherer, J.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Schacherer, Joseph
ORCID
Venue
G3 Genes|Genomes|Genetics
Publisher
Oxford University Press (OUP)
Published
2012-09-01
Volume
2
Issue
9
Pages
1103-1111
ISSN
2160-1836 (ISSN-L)
DOI
10.1534/g3.112.003152
PMC
PMC3429925
OpenAlex
W2141324919
Cited by
47
References
1
Citations by year
2026: 1 · 2025: 2 · 2023: 1 · 2021: 2 · 2020: 3 · 2019: 6 · 2018: 5 · 2017: 7 · 2016: 7 · 2015: 9 · 2014: 3 · 2012: 1
FWCI
1.67
Type
journal article
Language
en
Open access
Licence
Locations
  • G3 Genes Genomes Genetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
Funders
  • Agence Nationale de la Recherche (ANR-10-BLAN-1606, 2011-JSV6-004-01)
  • Centre National de la Recherche Scientifique
  • Conseil Régional d'Alsace
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Immunology and Microbiology › Microbiology › Yeasts and Rust Fungi Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
mitochondrial genome evolution, Lachancea kluyveri, Saccharomyces kluyveri, mitochondrial DNA polymorphism, purifying selection, tree exudates, soil yeasts
MeSH terms
DNA, Mitochondrial, Introns, Phylogeny, Saccharomyces, Genetic Variation, Open Reading Frames, Evolution, Molecular, Polymorphism, Single Nucleotide, Genome, Mitochondrial

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