Mitochondrial Genome Evolution in a Single Protoploid Yeast Species

Department of Genetics, Genomics and Microbiology, University of Strasbourg/Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7156, Strasbourg, France.
G3-Genes Genomes Genetics (Impact Factor: 3.2). 09/2012; 2(9):1103-11. DOI: 10.1534/g3.112.003152
Source: PubMed


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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    • "The assembled mitochondrial contigs of six unique V. nonalfalfae strains were compared to reveal a possible pattern of variation. A similar approach was used by [59] to distinguish among 18 strains of Lachancea kluyveri, which had been isolated from various geographical locations and ecological niches. They found great diversity in the intergenic regions, with variants and indels, and also highly conserved coding regions in the mitochondrial genomes. "
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    • "Ultimately, we procured a valuable group of sequences for the expansion of intraspecies mt genome comparisons among clades of the Lachancea genus. A Model System for the Analysis of Inter and Intraspecific Diversity: Sister Species of the Lachancea Genus Previous to this work, only one study assessed the intraspecies mt diversity within a single yeast lineage, specifically, among 18 isolates of L. kluyveri (Jung et al. 2012). This species is most closely related to L. thermotolerans and the mt genomes share a variety of features (Talla et al. 2005). "
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    ABSTRACT: The increasing availability of mitochondrial (mt) sequence data from various yeasts provides a tool to study genomic evolution within and between different species. While the genomes from a range of lineages are available, there is a lack of information concerning intraspecific mtDNA diversity. Here, we analyzed the mt genomes of 50 strains from Lachancea thermotolerans, a protoploid yeast species that has been isolated from several locations (Europe, Asia, Australia, South Africa, and North / South America) and ecological sources (fruit, tree exudate, plant material, and grape and agave fermentations). Protein-coding genes from the mtDNA were used to construct a phylogeny, which reflected a similar, yet less resolved topology than the phylogenetic tree of 50 nuclear genes. In comparison to its sister species Lachancea kluyveri, L. thermotolerans has a smaller mt genome. This is due to shorter intergenic regions and fewer introns, of which the latter are only found in COX1. We revealed that L. kluyveri and L. thermotolerans share similar levels of intraspecific divergence concerning the nuclear genomes. However, L. thermotolerans has a more highly conserved mt genome with the coding regions characterized by low rates of nonsynonymous substitution. Thus, in the mt genomes of L. thermotolerans, stronger purifying selection and lower mutation rates potentially shape genome diversity in contract to what was found for L. kluyveri, demonstrating that the factors driving mt genome evolution are different even between closely related species.
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    • "To obtain a global view of the genetic variations occurring in the mtDNA within a species, we recently performed a genome-wide polymorphism survey on the mt genome of 18 Lachancea kluyveri (formerly known as Saccharomyces kluyveri) isolates [2]. We generated a comprehensive view of mitochondrial sequence polymorphism in this single species. "
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