Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Mitochondrial genome diversity across the subphylum Saccharomycotina

Journal Article · · Frontiers in Microbiology
 [1];  [2];  [3];  [4];  [5]
  1. University of Wisconsin-Madison, WI (United States); University of Wisconsin-Madison Laboratory of Genetics
  2. University of North Carolina at Charlotte, NC (United States); Vanderbilt University, Nashville, TN (United States)
  3. University of Wisconsin-Madison, WI (United States); Villanova University, PA (United States)
  4. Vanderbilt University, Nashville, TN (United States)
  5. University of Wisconsin-Madison, WI (United States)

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.

Research Organization:
Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF)
Grant/Contract Number:
SC0018409
OSTI ID:
2294089
Journal Information:
Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 14; ISSN 1664-302X
Publisher:
Frontiers Research FoundationCopyright Statement
Country of Publication:
United States
Language:
English

References (104)

Rolling circle replication of DNA in yeast mitochondria. journal December 1991
The Wickerhamiella/Starmerella clade—A treasure trove for the study of the evolution of yeast metabolism journal April 2020
Linear mitochondrial DNAs from yeasts: telomeres with large tandem repetitions journal January 1995
Fungal mitochondrial genomes and genetic polymorphisms journal September 2018
Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy journal July 2003
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum journal November 2018
Diversity and origin of alternative NADH:ubiquinone oxidoreductases journal August 2000
The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae journal December 1998
A novel motif for identifying Rps3 homologs in fungal mitochondrial genomes journal August 2000
Evolution of mitochondrial gene content: gene loss and transfer to the nucleus journal December 2003
Maintenance and expression of the S. cerevisiae mitochondrial genome—From genetics to evolution and systems biology journal June 2010
The Warburg and Crabtree effects: On the origin of cancer cell energy metabolism and of yeast glucose repression journal June 2011
The Crabtree and Warburg effects: Do metabolite-induced regulations participate in their induction? journal August 2016
The plant mitochondrial genome: Dynamics and maintenance journal May 2014
Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention journal February 2016
Ancient Homology of the Mitochondrial Contact Site and Cristae Organizing System Points to an Endosymbiotic Origin of Mitochondrial Cristae journal June 2015
The Origin and Diversification of Mitochondria journal November 2017
The strange mitochondrial genomes of Metschnikowia yeasts journal July 2020
Genomics and the making of yeast biodiversity journal December 2015
Mitonuclear interplay in yeast: from speciation to phenotypic adaptation journal October 2022
Strand Invasion Structures in the Inverted Repeat of Candida albicans Mitochondrial DNA Reveal a Role for Homologous Recombination in Replication journal September 2010
Mitochondrial introns: a critical view journal March 2007
Saccharomyces diversity and evolution: a budding model genus journal May 2013
Mitochondrial inheritance in budding yeasts: towards an integrated understanding journal November 2010
Mt-rps3 is an ancient gene which provides insight into the evolution of fungal mitochondrial genomes journal October 2018
Evolution of pathogenicity and sexual reproduction in eight Candida genomes journal May 2009
Parallel evolution of the make–accumulate–consume strategy in Saccharomyces and Dekkera yeasts journal May 2011
Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus journal July 2018
Massive programmed translational jumping in mitochondria journal April 2014
The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast journal May 2018
The Saccharomyces cerevisiae NDE1 and NDE2 Genes Encode Separate Mitochondrial NADH Dehydrogenases Catalyzing the Oxidation of Cytosolic NADH journal September 1998
Fast unfolding of communities in large networks journal October 2008
Evolution of a Record-Setting AT-Rich Genome: Indel Mutation, Recombination, and Substitution Bias journal September 2020
Repeated horizontal gene transfer of GAL actose metabolism genes violates Dollo’s law of irreversible loss journal November 2020
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses journal June 2009
plasmidSPAdes: assembling plasmids from whole genome sequencing data journal July 2016
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes journal June 2017
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R journal July 2018
Mitochondrial genome evolution in yeasts: an all-encompassing view journal May 2015
The complete mitochondrial DNA sequence from Kazachstania sinensis reveals a general +1C frameshift mechanism in CTGY codons journal March 2018
Mitogenomics and mitochondrial gene phylogeny decipher the evolution ofSaccharomycotinayeasts journal May 2022
Population Genomic Analysis Reveals Highly Conserved Mitochondrial Genomes in the Yeast Species Lachancea thermotolerans journal September 2014
Genetic Drift and Indel Mutation in the Evolution of Yeast Mitochondrial Genome Size journal November 2017
Evolutionary genetics of the mitochondrial genome: insights fromDrosophila journal May 2023
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era journal February 2020
Evolutionary Trajectories are Contingent on Mitonuclear Interactions journal March 2023
PAML 4: Phylogenetic Analysis by Maximum Likelihood journal April 2007
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability journal January 2013
Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast journal May 2015
Cellular and population level processes influence the rate, accumulation and observed frequency of inherited and somatic mtDNA mutations journal March 2017
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation journal April 2021
Evolution of linear chromosomes and multipartite genomes in yeast mitochondria journal January 2011
Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria journal September 2013
NOVOPlasty: de novo assembly of organelle genomes from whole genome data journal October 2016
Hyaloraphidium curvatum: A Linear Mitochondrial Genome, tRNA Editing, and an Evolutionary Link to Lower Fungi journal March 2002
Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi journal April 2021
Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species preprint November 2016
Relaxation of yeast mitochondrial functions after whole-genome duplication journal July 2008
The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen journal April 2015
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation journal March 2017
Mitochondrial‐encoded endonucleases drive recombination of protein‐coding genes in yeast journal September 2019
Why, when, and how did yeast evolve alcoholic fermentation? journal June 2014
A review of long-branch attraction journal April 2005
Temperature-Specific Outcomes of Cytoplasmic-Nuclear Interactions on Egg-To-Adult Development time in seed Beetles journal January 2007
The mitochondrial genome of the wine yeast Hanseniaspora uvarum : a unique genome organization among yeast/fungal counterparts journal January 2006
Fermentative lifestyle in yeasts belonging to the Saccharomyces complex : Fermentative lifestyle in yeasts journal January 2007
A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities? journal September 2012
Glycolytic Functions Are Conserved in the Genome of the Wine Yeast Hanseniaspora uvarum, and Pyruvate Kinase Limits Its Capacity for Alcoholic Fermentation journal September 2017
Draft Genome Sequence of the Yeast Nadsonia starkeyi-henricii UCD142, Isolated from Forest Soil in Ireland journal June 2018
Linear mitochondrial DNAs of yeasts: closed-loop structure of the termini and possible linear-circular conversion mechanisms. journal April 1993
Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation journal April 2017
Characterizing and measuring bias in sequence data journal January 2013
The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen journal September 2018
Mitochondrial-nuclear coadaptation revealed through mtDNA replacements in Saccharomyces cerevisiae journal September 2020
Population structure of mitochondrial genomes in Saccharomyces cerevisiae journal June 2015
Factors driving metabolic diversity in the budding yeast subphylum journal March 2018
Discordant evolution of mitochondrial and nuclear yeast genomes at population level journal May 2020
Breath-giving cooperation: critical review of origin of mitochondria hypotheses: Major unanswered questions point to the importance of early ecology journal August 2017
Benchmarking of long-read assemblers for prokaryote whole genome sequencing journal December 2019
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage journal August 2015
Origin of the Yeast Whole-Genome Duplication journal August 2015
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts journal May 2019
Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes journal February 2010
Mapping mitonuclear epistasis using a novel recombinant yeast population journal March 2023
Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly journal April 2013
Yeast “Make-Accumulate-Consume” Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication journal July 2013
A Study on the Fundamental Mechanism and the Evolutionary Driving Forces behind Aerobic Fermentation in Yeast journal January 2015
Variability of the mitochondrial genome in mammals at the inter-species/intra-species boundary journal August 2007
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus journal June 2011
Horizontal Transfer and Gene Conversion as an Important Driving Force in Shaping the Landscape of Mitochondrial Introns journal February 2014
Mitochondrial-Nuclear Epistasis Contributes to Phenotypic Variation and Coadaptation in Natural Isolates of Saccharomyces cerevisiae journal August 2014
Mitonuclear Epistasis for Development Time and Its Modification by Diet in Drosophila journal May 2016
Mobile Introns Shape the Genetic Diversity of Their Host Genes journal April 2017
Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection journal May 2020
A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina journal June 2023
From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes? journal January 2022
An evolutionary perspective on the Crabtree effect journal October 2014
The Mighty NUMT: Mitochondrial DNA Flexing Its Code in the Nuclear Genome journal April 2023
Organellar Introns in Fungi, Algae, and Plants journal August 2021
A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina dataset January 2023
Factors driving metabolic diversity in the budding yeast subphylum [Supplemental Data] collection March 2018
Discordant evolution of mitochondrial and nuclear yeast genomes at population level collection January 2020
A computational screen for alternative genetic codes in over 250,000 genomes journal November 2021
Contingency and selection in mitochondrial genome dynamics journal April 2022

Figures / Tables (6)


Similar Records

Budding yeasts in the subphylum Saccharomycotina Genome sequencing and assembly
Dataset · Tue Jul 25 00:00:00 EDT 2023 · OSTI ID:3003520

Data for Mitochondrial Genome Diversity across the Subphylum Saccharomycotina
Dataset · Sun Nov 05 00:00:00 EDT 2023 · OSTI ID:3003521

The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum
Journal Article · Sun Jan 18 19:00:00 EST 2026 · FEMS Yeast Research · OSTI ID:3013686