Population genomics of domestic and wild yeasts

Liti, Gianni; Carter, David M.; Moses, Alan M.; Warringer, Jonas; Parts, Leopold; James, Stephen A.; Davey, Robert P.; Roberts, Ian N.; Burt, Austin; Koufopanou, Vassiliki; Tsai, Isheng Jason; Bergman, Casey M.; Bensasson, Douda; O’Kelly, Michael; Oudenaarden, Alexander van; Barton, David B. H.; Bailes, Elizabeth; Nguyen, Alex N.; Jones, Matthew C.; Quail, Michael A.; Goodhead, Ian; Sims, Sarah; Smith, Frances J.D.; Durbin, Richard; Louis, Edward J.

doi:10.1038/nature07743

Cited by 1,317 publications

(2,265 citation statements)

References 28 publications

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“…The phylogeny of our strain subset matches that of a larger reported and discussed collection (Liti et al, 2009). In our strain phylogeny, there were three clusters, North American, Malaysian and European/ North American, each containing genetically similar strains that probably did not hybridize in nature to strains from other clusters and therefore have pure genomes.…”

Section: Genetic Distance Between Parents and Heterosis In Their Hybridssupporting

confidence: 57%

“…Sixteen wild strains were selected for this study (Supplementary Table S2) from the larger collection of fully sequenced strains previously described by Liti et al (2009). The stages of strain-collection construction are detailed in Supplementary Figure S1.…”

Section: Hybrid-collection Constructionmentioning

confidence: 99%

“…Vegetative growth rate correlates with the yeast's fitness (St Onge et al, 2007;Hillenmeyer et al, 2010), and as heterosis is more often found in fitness-related traits, growth under multiple conditions is suitable for studying heterosis. In addition, evidence from genome sequencing has suggested that in nature yeast propagates mainly by asexual reproduction, and thus yeast isolates can often be regarded as distantly related inbred populations, each adapted to its ecological niche (Schacherer et al, 2007;Liti et al, 2009;Warringer et al, 2011). Hybrids between such isolates provide a good opportunity to study heterosis and can illustrate the relative importance of the different genetic mechanisms governing this complex phenotypic phenomenon.…”

Section: Introductionmentioning

confidence: 99%

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Extensive heterosis in growth of yeast hybrids is explained by a combination of genetic models

et al. 2014

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Heterosis, also known as hybrid vigor, is the superior performance of a heterozygous hybrid relative to its homozygous parents. Despite the scientific curiosity of this phenotypic phenomenon and its significance for food production in agriculture, its genetic basis is insufficiently understood. Studying heterosis in yeast can potentially yield insights into its genetic basis, can allow one to test the different hypotheses that have been proposed to explain the phenomenon and allows better understanding of how to take advantage of this phenomenon to enhance food production. We therefore crossed 16 parental yeast strains to form 120 yeast hybrids, and measured their growth rates under five environmental conditions. A considerable amount of dominant genetic variation was found in growth performance, and heterosis was measured in 35% of the hybrid-condition combinations. Despite previous reports of correlations between heterosis and measures of sequence divergence between parents, we detected no such relationship. We used several analyses to examine which genetic model might explain heterosis. We found that dominance complementation of recessive alleles, overdominant interactions within loci and epistatic interactions among loci each contribute to heterosis. We concluded that in yeast heterosis is a complex phenotype created by the combined contribution of different genetic interactions.

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Section: Genetic Distance Between Parents and Heterosis In Their Hybridssupporting

confidence: 57%

Section: Hybrid-collection Constructionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Extensive heterosis in growth of yeast hybrids is explained by a combination of genetic models

et al. 2014

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“…Diploid S. cerevisiae strains from publicly available (Liti et al., 2009; Strope et al., 2015) and personal collections were screened using the classification system of Granek and Magwene (2010) (Table S1). Smooth strains and biofilm‐forming strains with distinct colony morphologies and from different ecological niches were identified.…”

Section: Methodsmentioning

confidence: 99%

Biofilm formation and toxin production provide a fitness advantage in mixed colonies of environmental yeast isolates

Deschaine

Heysel

Lenhart

et al. 2018

Ecology and Evolution

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Microbes can engage in social interactions ranging from cooperation to warfare. Biofilms are structured, cooperative microbial communities. Like all cooperative communities, they are susceptible to invasion by selfish individuals who benefit without contributing. However, biofilms are pervasive and ancient, representing the first fossilized life. One hypothesis for the stability of biofilms is spatial structure: Segregated patches of related cooperative cells are able to outcompete unrelated cells. These dynamics have been explored computationally and in bacteria; however, their relevance to eukaryotic microbes remains an open question. The complexity of eukaryotic cell signaling and communication suggests the possibility of different social dynamics. Using the tractable model yeast, Saccharomyces cerevisiae, which can form biofilms, we investigate the interactions of environmental isolates with different social phenotypes. We find that biofilm strains spatially exclude nonbiofilm strains and that biofilm spatial structure confers a consistent and robust fitness advantage in direct competition. Furthermore, biofilms may protect against killer toxin, a warfare phenotype. During biofilm formation, cells are susceptible to toxin from nearby competitors; however, increased spatial use may provide an escape from toxin producers. Our results suggest that yeast biofilms represent a competitive strategy and that principles elucidated for the evolution and stability of bacterial biofilms may apply to more complex eukaryotes.

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“…The tiling array data indicate the presence of an unknown weakly expressed SUT-type antisense transcript that overlaps IWR1; however, the function of this transcript, if it has any at all, is presently unclear. High-throughput data for mIWR1, IWR1 and YDL114W obtained with SK1 are reproduced by RT-PCR assays using samples from the distantly related strain JHY222 (which is derived from the standard background S288C 9,28 ), indicating that the phenomenon is not strain-specific but generally occurs in budding yeast (Fig. S2B).…”

Section: Divergent Promoters Driving Isoforms Pair Them With Ubiquitomentioning

confidence: 99%

Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae

Xie

Horecka²,

Chu³

et al. 2016

RNA Biology

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The origin of replication complex subunit ORC1 is important for DNA replication. The gene is known to encode a meiotic transcript isoform (mORC1) with an extended 5 0 -untranslated region (5 0 -UTR), which was predicted to inhibit protein translation. However, the regulatory mechanism that controls the mORC1 transcript isoform is unknown and no molecular biological evidence for a role of mORC1 in negatively regulating Orc1 protein during gametogenesis is available. By interpreting RNA profiling data obtained with growing and sporulating diploid cells, mitotic haploid cells, and a starving diploid control strain, we determined that mORC1 is a middle meiotic transcript isoform. Regulatory motif predictions and genetic experiments reveal that the activator Ndt80 and its middle sporulation element (MSE) target motif are required for the full induction of mORC1 and the divergently transcribed meiotic SMA2 locus. Furthermore, we find that the MSE-binding negative regulator Sum1 represses both mORC1 and SMA2 during mitotic growth. Finally, we demonstrate that an MSE deletion strain, which cannot induce mORC1, contains abnormally high Orc1 levels during post-meiotic stages of gametogenesis. Our results reveal the regulatory mechanism that controls mORC1, highlighting a novel developmental stage-specific role for the MSE element in bi-directional mORC1/SMA2 gene activation, and correlating mORC1 induction with declining Orc1 protein levels. Because eukaryotic genes frequently encode multiple transcripts possessing 5 0 -UTRs of variable length, our results are likely relevant for gene expression during development and disease in higher eukaryotes.

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Population genomics of domestic and wild yeasts

Cited by 1,317 publications

References 28 publications

Extensive heterosis in growth of yeast hybrids is explained by a combination of genetic models

Extensive heterosis in growth of yeast hybrids is explained by a combination of genetic models

Biofilm formation and toxin production provide a fitness advantage in mixed colonies of environmental yeast isolates

Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae

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