The Baker's Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and Meiosis

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
PLoS Genetics (Impact Factor: 7.53). 09/2010; 6(9). DOI: 10.1371/journal.pgen.1001109
Source: PubMed


Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness. We used whole-genome DNA sequencing, pulse-field gel electrophoresis, and comparative genome hybridization to determine mutation rates in diploid vegetative and meiotic mutation accumulation lines of Saccharomyces cerevisiae. The vegetative lines underwent only mitotic divisions while the meiotic lines underwent a meiotic cycle every ∼20 vegetative divisions. Similar base substitution rates were estimated for both lines. Given our experimental design, these measures indicated that the meiotic mutation rate is within the range of being equal to zero to being 55-fold higher than the vegetative rate. Mutations detected in vegetative lines were all heterozygous while those in meiotic lines were homozygous. A quantitative analysis of intra-tetrad mating events in the meiotic lines showed that inter-spore mating is primarily responsible for rapidly fixing mutations to homozygosity as well as for removing mutations. We did not observe 1-2 nt insertion/deletion (in-del) mutations in any of the sequenced lines and only one structural variant in a non-telomeric location was found. However, a large number of structural variations in subtelomeric sequences were seen in both vegetative and meiotic lines that did not affect viability. Our results indicate that the diploid yeast nuclear genome is remarkably stable during the vegetative and meiotic cell cycles and support the hypothesis that peripheral regions of chromosomes are more dynamic than gene-rich central sections where structural rearrangements could be deleterious. This work also provides an improved estimate for the mutational load carried by diploid organisms.

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    • "lists the 93 S. cerevisiae strains sequenced in this study and seven strains that are isogenic with strains sequenced in other studies (Goffeau et al. 1996; RM11 2004; Wei et al. 2007; Doniger et al. 2008; Dowell et al. 2010; Nishant et al. 2010). All sequence-based analyses in this study are on the genomes of the 93 sequenced strains, as well as the reference S288c genome; all phenotypic and association analyses include all 100 strains, unless otherwise noted. "
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    ABSTRACT: Saccharomyces cerevisiae, a well-established model for species as diverse as humans and pathogenic fungi, is more recently 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. To aid in the understanding of the S. cerevisiae population and quantitative genetics, as well as its emergence as an opportunistic pathogen, we sequenced, de novo assembled, and extensively manually edited and annotated the genomes of 93 S. cerevisiae strains from multiple geographic and environmental origins, including many clinical origin strains. These 93 S. cerevisiae strains, the genomes of which are near-reference quality, together with seven previously sequenced strains, constitute a novel genetic resource, the "100-genomes" strains. Our sequencing coverage, high-quality assemblies, and annotation provide unprecedented opportunities for detailed interrogation of complex genomic loci, examples of which we demonstrate. We found most phenotypic variation to be quantitative and identified population, genotype, and phenotype associations. Importantly, we identified clinical origin associations. For example, we found that an introgressed PDR5 was present exclusively in clinical origin mosaic group strains; that the mosaic group was significantly enriched for clinical origin strains; and that clinical origin strains were much more copper resistant, suggesting that copper resistance contributes to fitness in the human host. The 100-genomes strains are a novel, multipurpose resource to advance the study of S. cerevisiae population genetics, quantitative genetics, and the emergence of an opportunistic pathogen. © 2015 Strope et al.; Published by Cold Spring Harbor Laboratory Press.
    Genome Research 04/2015; 25(5). DOI:10.1101/gr.185538.114 · 14.63 Impact Factor
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    • "The average rate of mutation for the msh2-null strains was 7.4 · 10 28 mutations per base pair per generation (Table 2). This rate is two orders of magnitude greater than the estimate of 3 · 10 210 mutations per base pair per generation for wild-type yeast strains (Lynch et al. 2008; Nishant et al. 2010); the genomic wild-type strain accumulated only a single mutation over the 170 generations, consistent with a wild-type per-base pair per-generation mutation rate of ~10 210 mutations per base pair per generation. In the absence of mismatch repair, the mutation rate for single-base pair substitutions was 4.8 · 10 29 mutations per base pair per generation, and for insertions or deletions at mono-, di-, and trinucleotide repeats was 7.0 · 10 28 mutations per base pair per generation. "
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    ABSTRACT: DNA mismatch repair is a highly conserved DNA repair pathway. In humans, germline mutations in hMSH2 or hMLH1, key components mismatch repair, have been associated with Lynch Syndrome, a leading cause of inherited cancer mortality. Current estimates of the mutation rate and the mutational spectra in mismatch repair defective cells are primarily limited to a small number of individual reporter loci. Here we use the yeast Saccharomyces cerevisiae to generate a genome-wide view of the rates, spectra, and distribution of mutation in the absence of mismatch repair. We performed mutation accumulation assays and next generation sequencing on 19 strains, including 16 msh2 missense variants implicated in Lynch Cancer Syndrome. The mutation rate for DNA mismatch repair null strains was ~1 mutation per genome per generation, 225-fold higher than the wild-type rate. The mutations were distributed randomly throughout the genome, independent of replication timing. The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%). Additionally, repeat regions with proximal repeats are more likely to be mutated. A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites. Interestingly, 5% of the single base pair substitutions might represent double slippage events that occurred at the junction of immediately adjacent repeats, resulting in a shift in the repeat boundary. These data suggest a closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells.
    G3-Genes Genomes Genetics 07/2013; 3(9). DOI:10.1534/g3.113.006429 · 3.20 Impact Factor
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    • "One lineage within the Saccharomycotina (Saccharomyces) has also experienced duplicate gene loss and genome compaction following whole-genome duplications (Dujon et al. 2004). These reductive trends do not parallel the drift-associated genome degradation observed in endosymbiotic bacteria and nucleomorphs in that these fungi have large effective population sizes (estimated to be ;107 for Saccharomyces cerevisiae), a lack of a deletional bias and strong purifying selection of intron splice sequences (Skelly et al. 2009; Nishant et al. 2010). Instead, such trends suggest these genomes have contracted due to selection. "
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    ABSTRACT: Fungi display a large diversity in genome size and complexity, variation that is often considered to be adaptive. But because nonadaptive processes can also have important consequences on the features of genomes, we investigated the relationship of genetic drift and genome size in the phylum Ascomycota using multiple indicators of genetic drift. We detected a complex relationship between genetic drift and genome size in fungi: genetic drift is associated with genome expansion on broad evolutionary timescales, as hypothesized for other eukaryotes; but within subphyla over smaller timescales, the opposite trend is observed. Moreover, fungi and bacteria display similar patterns of genome degradation that are associated with initial effects of genetic drift. We conclude that changes in genome size within Ascomycota have occurred using two different routes: large-scale genome expansions are catalyzed by increasing drift as predicted by the mutation-hazard model of genome evolution and small-scale modifications in genome size are independent of drift.
    Genome Biology and Evolution 11/2011; 4(1):13-23. DOI:10.1093/gbe/evr124 · 4.23 Impact Factor
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