Population structure of mitochondrial genomes in Saccharomyces cerevisiae

Abstract

BackgroundRigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences.ResultsTo address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae.ConclusionsOur results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1664-4) contains supplementary material, which is available to authorized users.

Discordant evolution of mitochondrial and nuclear yeast genomes at population level

“…The release of mitochondrial genomes of several isolates (Bergström et al 2014;Strope et al 2015) offered an opportunity for mitochondrial population surveys (Wolters et al 2015). We recently released high coverage genome sequence for a panel of 1,011 natural strains, isolated from both anthropic and wild niches (Peter et al 2018).…”

“…We could retrieve the complete CDSs set for two of them (CQS and YCL), while the third (ADE) is incomplete but very close to YCL. The mitochondria introgression in YCL (YJM1399) strain was already reported, but no further analyses were presented (Wolters et al 2015). We generated a set of polymorphic markers (methods), to accurately identify the introgression boundaries.…”

Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data

“…This pipeline pre-selects the best 20X coverage reads using BLAST searches [10], then corrects and assembles them using CA. PacBio sequencing and OLC assemblers have been successfully applied to the sequencing of yeast mitochondrial genomes [11] and chloroplast genomes such as those of Potentilla micrantha [12], Nelumbo nucifera [13], and sugar beet ( Beta vulgaris ) [14]. …”

Draft Genome Sequence of the Yeast Saccharomyces cerevisiae GUJ105 From Gujarat, India

“…S. cerevisiae has been studied extensively for decades as a model organism for the following reasons: (i) it is used as a host for recombinant protein production (2), (ii) it is tolerant of a wide range of physiological stresses, such as low pH, high ethanol, and osmotic pressure (3, 4), (iii) it is used in the baking industry and in fermentations of food-grade alcohol production (5, 6), (iv) it is used as a model for biofuel production (7), (v) it is used as a model system for evolutionary biology (8), and (vi) it is used as a model for population and quantitative genetics. S. cerevisiae is found in multiple environments, one of which is the human body as an opportunistic pathogen (9, 10).…”