1
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Legrand S, Saifudeen A, Bordelet H, Vernerey J, Guille A, Bignaud A, Thierry A, Acquaviva L, Gaudin M, Sanchez A, Johnson D, Friedrich A, Schacherer J, Neale MJ, Borde V, Koszul R, Llorente B. Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri. Proc Natl Acad Sci U S A 2024; 121:e2312820121. [PMID: 38478689 PMCID: PMC10962940 DOI: 10.1073/pnas.2312820121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/24/2024] [Indexed: 03/27/2024] Open
Abstract
Meiotic recombination shows broad variations across species and along chromosomes and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here, we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence of recruitment of the two chromosome axis proteins Red1 and Hop1, essential for proper Spo11-DSBs formation. Furthermore, cytological observation of spread pachytene meiotic chromosomes reveals that Lakl0C-left does not undergo synapsis. However, we show that the behavior of Lakl0C-left is independent of its particularly early replication timing and is not accompanied by any peculiar chromosome structure as detectable by Hi-C in this yet poorly studied yeast. Finally, we observed an accumulation of heterozygous mutations on Lakl0C-left and a sexual dimorphism of the haploid meiotic offspring, supporting a direct effect of this absence of meiotic recombination on L. kluyveri genome evolution and fitness. Because suppression of meiotic recombination on sex chromosomes is widely observed across eukaryotes, the mechanism for recombination suppression described here may apply to other species, with the potential to impact sex chromosome evolution.
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Affiliation(s)
- Sylvain Legrand
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Asma Saifudeen
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Hélène Bordelet
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Julien Vernerey
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Arnaud Guille
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Laurent Acquaviva
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Maxime Gaudin
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Aurore Sanchez
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris75005, France
| | - Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BrightonBN1 9RH, United Kingdom
| | - Anne Friedrich
- Université de Strasbourg, CNRS, Génétique moléculaire, génomique, microbiologie UMR 7156, Strasbourg67000, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, Génétique moléculaire, génomique, microbiologie UMR 7156, Strasbourg67000, France
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BrightonBN1 9RH, United Kingdom
| | - Valérie Borde
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris75005, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Bertrand Llorente
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
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2
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Friedrich A, Gounot JS, Tsouris A, Bleykasten C, Freel K, Caradec C, Schacherer J. Contrasting Genomic Evolution Between Domesticated and Wild Kluyveromyces lactis Yeast Populations. Genome Biol Evol 2023; 15:6986421. [PMID: 36634937 PMCID: PMC9897184 DOI: 10.1093/gbe/evad004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/20/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
The process of domestication has variable consequences on genome evolution leading to different phenotypic signatures. Access to the complete genome sequences of a large number of individuals makes it possible to explore the different facets of this domestication process. Here, we sought to explore the genome evolution of Kluyveromyces lactis, a yeast species well known for its involvement in dairy processes and also present in natural environments. Using a combination of short- and long-read sequencing strategies, we investigated the genomic variability of 41 K. lactis isolates and found that the overall genetic diversity of this species is very high (θw = 3.3 × 10-2) compared with other species such as Saccharomyces cerevisiae (θw = 1.6 × 10-2). However, the domesticated dairy population shows a reduced level of diversity (θw = 1 × 10-3), probably due to a domestication bottleneck. In addition, this entire population is characterized by the introgression of the LAC4 and LAC12 genes, responsible for lactose fermentation and coming from the closely related species, Kluyveromyces marxianus, as previously described. Our results highlighted that the LAC4/LAC12 gene cluster was acquired through multiple and independent introgression events. Finally, we also identified several genes that could play a role in adaptation to dairy environments through copy number variation. These genes are involved in sugar consumption, flocculation, and drug resistance, and may play a role in dairy processes. Overall, our study illustrates contrasting genomic evolution and sheds new light on the impact of domestication processes on it.
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Affiliation(s)
| | | | - Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | | | - Kelle Freel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
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3
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Bigey F, Pasteur E, Połomska X, Thomas S, Crutz-Le Coq AM, Devillers H, Neuvéglise C. Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica. J Fungi (Basel) 2023; 9:jof9010076. [PMID: 36675897 PMCID: PMC9865632 DOI: 10.3390/jof9010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.
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Affiliation(s)
- Frédéric Bigey
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
| | - Emilie Pasteur
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Xymena Połomska
- Department of Biotechnology & Food Microbiology, Wroclaw University of Environmental and Life Sciences (WUELS), 50-375 Wroclaw, Poland
| | - Stéphane Thomas
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- IJPB, INRAE, 78000 Versailles, France
| | - Hugo Devillers
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- Correspondence:
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4
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Villarreal P, Villarroel CA, O'Donnell S, Agier N, Quintero-Galvis JF, Peña TA, Nespolo RF, Fischer G, Varela C, Cubillos FA. Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri. Environ Microbiol 2022; 24:5615-5629. [PMID: 35769023 DOI: 10.1111/1462-2920.16103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 01/12/2023]
Abstract
Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles. Lachancea cidri is an ideal yeast model for exploring the interplay between genetics, ecological function and evolution. Lachancea cidri diverged from the Saccharomyces lineage before the whole-genome duplication and is distributed across the South Hemisphere, displaying an important ecological success. We applied phylogenomics to investigate the genetic variation of L. cidri isolates obtained from Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggests that SoAm and Aus lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA). Interestingly, we found that the French reference strain is closely related to the Australian strains, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, we identified different lineages within the South American population, revealing that Patagonia contains a similar genetic diversity comparable to that of other lineages in S. cerevisiae. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favoured the extensive distribution of L. cidri in Patagonia.
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Affiliation(s)
- Pablo Villarreal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Carlos A Villarroel
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile
| | - Sam O'Donnell
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Julian F Quintero-Galvis
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Tomas A Peña
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Roberto F Nespolo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago, Chile.,Millenium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Cristian Varela
- The Australian Wine Research Institute, Glen Osmond, Adelaide, South Australia, Australia.,Department of Wine and Food Science, University of Adelaide, Glen Osmond, Adelaide, South Australia, Australia
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Millenium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
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5
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Cope AL, Shah P. Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage. PLoS Genet 2022; 18:e1010256. [PMID: 35714134 PMCID: PMC9246145 DOI: 10.1371/journal.pgen.1010256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 06/30/2022] [Accepted: 05/13/2022] [Indexed: 11/20/2022] Open
Abstract
Patterns of non-uniform usage of synonymous codons vary across genes in an organism and between species across all domains of life. This codon usage bias (CUB) is due to a combination of non-adaptive (e.g. mutation biases) and adaptive (e.g. natural selection for translation efficiency/accuracy) evolutionary forces. Most models quantify the effects of mutation bias and selection on CUB assuming uniform mutational and other non-adaptive forces across the genome. However, non-adaptive nucleotide biases can vary within a genome due to processes such as biased gene conversion (BGC), potentially obfuscating signals of selection on codon usage. Moreover, genome-wide estimates of non-adaptive nucleotide biases are lacking for non-model organisms. We combine an unsupervised learning method with a population genetics model of synonymous coding sequence evolution to assess the impact of intragenomic variation in non-adaptive nucleotide bias on quantification of natural selection on synonymous codon usage across 49 Saccharomycotina yeasts. We find that in the absence of a priori information, unsupervised learning can be used to identify genes evolving under different non-adaptive nucleotide biases. We find that the impact of intragenomic variation in non-adaptive nucleotide bias varies widely, even among closely-related species. We show that the overall strength and direction of translational selection can be underestimated by failing to account for intragenomic variation in non-adaptive nucleotide biases. Interestingly, genes falling into clusters identified by machine learning are also physically clustered across chromosomes. Our results indicate the need for more nuanced models of sequence evolution that systematically incorporate the effects of variable non-adaptive nucleotide biases on codon frequencies.
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Affiliation(s)
- Alexander L. Cope
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
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6
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Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Riffo FC, Dashko S, Dimitrov R, Fisher KJ, Gibson BR, Gouliamova D, Greig D, Heistinger L, Hittinger CT, Jecmenica M, Koufopanou V, Landry CR, Mašínová T, Naumova ES, Opulente D, Peña JJ, Petrovič U, Tsai IJ, Turchetti B, Villarreal P, Yurkov A, Liti G, Boynton P. Yeasts from temperate forests. Yeast 2022; 39:4-24. [PMID: 35146791 DOI: 10.1002/yea.3699] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.
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Affiliation(s)
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Graham Bell
- Biology Department and Redpath Museum, McGill University, Québec, Canada
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Neža Čadež
- Biotechnical Faculty, Food Science and Technology Department, University of Ljubljana, Ljubljana, Slovenia
| | - Francisco Cubillos Riffo
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sofia Dashko
- DSM Food Specialties, Center for Food Innovation, AX, Delft, The Netherlands
| | - Roumen Dimitrov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kaitlin J Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian R Gibson
- Technische Universität Berlin, Institute of Food Technology and Food Chemistry, Chair of Brewing and Beverage Technology, Berlin, Germany
| | - Dilnora Gouliamova
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Duncan Greig
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Lina Heistinger
- ETH Zurich, Department of Biology, Institute of Biochemistry, Switzerland
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Canada.,PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Canada.,Centre de Recherche sur les Données Massives, Université Laval, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Canada
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dana Opulente
- Department of Biology, Villanova University, Villanova, Pennsylvania, USA
| | | | - Uroš Petrovič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia.,Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Ljubljana, Slovenia
| | | | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Pablo Villarreal
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
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7
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Papaioannou IA, Dutreux F, Peltier FA, Maekawa H, Delhomme N, Bardhan A, Friedrich A, Schacherer J, Knop M. Sex without crossing over in the yeast Saccharomycodes ludwigii. Genome Biol 2021; 22:303. [PMID: 34732243 PMCID: PMC8567612 DOI: 10.1186/s13059-021-02521-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution. Previous studies of the budding yeast species Saccharomycodes ludwigii suggested that meiotic crossing over might be absent from its sexual life cycle, which is predominated by fertilization within the meiotic tetrad. RESULTS We demonstrate that recombination is extremely suppressed during meiosis in Sd. ludwigii. DNA double-strand break formation by the conserved transesterase Spo11, processing and repair involving interhomolog interactions are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers in its genome. A strong AT bias of spontaneous mutations and the absence of recombination are likely responsible for its unusually low genomic GC level. CONCLUSIONS Sd. ludwigii has followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent mating between products of the same meiotic event with the extreme suppression of meiotic recombination. This life style ensures preservation of heterozygosity throughout its genome and may enable the species to adapt to its environment and survive with only minimal levels of rare meiotic recombination. We propose Sd. ludwigii as an excellent natural forum for the study of genome evolution and recombination rates.
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Affiliation(s)
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - France A. Peltier
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Hiromi Maekawa
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Current affiliation: Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Amit Bardhan
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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8
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Binati RL, Salvetti E, Bzducha-Wróbel A, Bašinskienė L, Čižeikienė D, Bolzonella D, Felis GE. Non-conventional yeasts for food and additives production in a circular economy perspective. FEMS Yeast Res 2021; 21:6380488. [PMID: 34601574 DOI: 10.1093/femsyr/foab052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/27/2021] [Indexed: 12/18/2022] Open
Abstract
Yeast species have been spontaneously participating in food production for millennia, but the scope of applications was greatly expanded since their key role in beer and wine fermentations was clearly acknowledged. The workhorse for industry and scientific research has always been Saccharomyces cerevisiae. It occupies the largest share of the dynamic yeast market, that could further increase thanks to the better exploitation of other yeast species. Food-related 'non-conventional' yeasts (NCY) represent a treasure trove for bioprospecting, with their huge untapped potential related to a great diversity of metabolic capabilities linked to niche adaptations. They are at the crossroad of bioprocesses and biorefineries, characterized by low biosafety risk and produce food and additives, being also able to contribute to production of building blocks and energy recovered from the generated waste and by-products. Considering that the usual pattern for bioprocess development focuses on single strains or species, in this review we suggest that bioprospecting at the genus level could be very promising. Candida, Starmerella, Kluyveromyces and Lachancea were briefly reviewed as case studies, showing that a taxonomy- and genome-based rationale could open multiple possibilities to unlock the biotechnological potential of NCY bioresources.
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Affiliation(s)
- Renato L Binati
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Elisa Salvetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Anna Bzducha-Wróbel
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159c St., 02-776 Warsaw, Poland
| | - Loreta Bašinskienė
- Department of Food Science and Technology, Kaunas University of Technology, Radvilėnų St. 19A, 44249 Kaunas, Lithuania
| | - Dalia Čižeikienė
- Department of Food Science and Technology, Kaunas University of Technology, Radvilėnų St. 19A, 44249 Kaunas, Lithuania
| | - David Bolzonella
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
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9
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Hanson SJ, Cinnéide EÓ, Salzberg LI, Wolfe KH, McGowan J, Fitzpatrick DA, Matlin K. Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex. G3 (BETHESDA, MD.) 2021; 11:jkab211. [PMID: 34849824 PMCID: PMC8496258 DOI: 10.1093/g3journal/jkab211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022]
Abstract
The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.
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Affiliation(s)
- Sara J Hanson
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Eoin Ó Cinnéide
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Letal I Salzberg
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Kate Matlin
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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10
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Gounot JS, Neuvéglise C, Freel KC, Devillers H, Piškur J, Friedrich A, Schacherer J. High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population. Genome Biol Evol 2021; 12:795-807. [PMID: 32302403 PMCID: PMC7313668 DOI: 10.1093/gbe/evaa077] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype–phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to characterize at the population level the Brettanomyces bruxellensis yeast species, which is a major cause of wine spoilage and can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.
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Affiliation(s)
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Kelle C Freel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jure Piškur
- Department of Biology, Lund University, Sweden
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF)
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11
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Brion C, Caradec C, Pflieger D, Friedrich A, Schacherer J. Pervasive Phenotypic Impact of a Large Nonrecombining Introgressed Region in Yeast. Mol Biol Evol 2021; 37:2520-2530. [PMID: 32359150 PMCID: PMC7475044 DOI: 10.1093/molbev/msaa101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To explore the origin of the diversity observed in natural populations, many studies have investigated the relationship between genotype and phenotype. In yeast species, especially in Saccharomyces cerevisiae, these studies are mainly conducted using recombinant offspring derived from two genetically diverse isolates, allowing to define the phenotypic effect of genetic variants. However, large genomic variants such as interspecies introgressions are usually overlooked even if they are known to modify the genotype–phenotype relationship. To have a better insight into the overall phenotypic impact of introgressions, we took advantage of the presence of a 1-Mb introgressed region, which lacks recombination and contains the mating-type determinant in the Lachancea kluyveri budding yeast. By performing linkage mapping analyses in this species, we identified a total of 89 loci affecting growth fitness in a large number of conditions and 2,187 loci affecting gene expression mostly grouped into two major hotspots, one being the introgressed region carrying the mating-type locus. Because of the absence of recombination, our results highlight the presence of a sexual dimorphism in a budding yeast for the first time. Overall, by describing the phenotype–genotype relationship in the Lachancea kluyveri species, we expanded our knowledge on how genetic characteristics of large introgression events can affect the phenotypic landscape.
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Affiliation(s)
- Christian Brion
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - David Pflieger
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
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12
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Hartmann FE, Duhamel M, Carpentier F, Hood ME, Foulongne‐Oriol M, Silar P, Malagnac F, Grognet P, Giraud T. Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes. THE NEW PHYTOLOGIST 2021; 229:2470-2491. [PMID: 33113229 PMCID: PMC7898863 DOI: 10.1111/nph.17039] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/03/2020] [Indexed: 05/08/2023]
Abstract
Genomic regions determining sexual compatibility often display recombination suppression, as occurs in sex chromosomes, plant self-incompatibility loci and fungal mating-type loci. Regions lacking recombination can extend beyond the genes determining sexes or mating types, by several successive steps of recombination suppression. Here we review the evidence for recombination suppression around mating-type loci in fungi, sometimes encompassing vast regions of the mating-type chromosomes. The suppression of recombination at mating-type loci in fungi has long been recognized and maintains the multiallelic combinations required for correct compatibility determination. We review more recent evidence for expansions of recombination suppression beyond mating-type genes in fungi ('evolutionary strata'), which have been little studied and may be more pervasive than commonly thought. We discuss testable hypotheses for the ultimate (evolutionary) and proximate (mechanistic) causes for such expansions of recombination suppression, including (1) antagonistic selection, (2) association of additional functions to mating-type, such as uniparental mitochondria inheritance, (3) accumulation in the margin of nonrecombining regions of various factors, including deleterious mutations or transposable elements resulting from relaxed selection, or neutral rearrangements resulting from genetic drift. The study of recombination suppression in fungi could thus contribute to our understanding of recombination suppression expansion across a broader range of organisms.
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Affiliation(s)
- Fanny E. Hartmann
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
| | - Marine Duhamel
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
- Ruhr‐Universität Bochum, Evolution of Plants and Fungi ‐ Gebäude ND 03/174Universitätsstraße150, 44801 BochumGermany
| | - Fantin Carpentier
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
| | - Michael E. Hood
- Biology Department, Science CentreAmherst CollegeAmherstMA01002USA
| | | | - Philippe Silar
- Lab Interdisciplinaire Energies DemainUniv Paris DiderotSorbonne Paris CiteParis 13F‐75205France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐Yvette91198France
| | - Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐Yvette91198France
| | - Tatiana Giraud
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
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13
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Landerer C, O'Meara BC, Zaretzki R, Gilchrist MA. Unlocking a signal of introgression from codons in Lachancea kluyveri using a mutation-selection model. BMC Evol Biol 2020; 20:109. [PMID: 32842959 PMCID: PMC7449078 DOI: 10.1186/s12862-020-01649-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 07/01/2020] [Indexed: 11/18/2022] Open
Abstract
Background For decades, codon usage has been used as a measure of adaptation for translational efficiency and translation accuracy of a gene’s coding sequence. These patterns of codon usage reflect both the selective and mutational environment in which the coding sequences evolved. Over this same period, gene transfer between lineages has become widely recognized as an important biological phenomenon. Nevertheless, most studies of codon usage implicitly assume that all genes within a genome evolved under the same selective and mutational environment, an assumption violated when introgression occurs. In order to better understand the effects of introgression on codon usage patterns and vice versa, we examine the patterns of codon usage in Lachancea kluyveri, a yeast which has experienced a large introgression. We quantify the effects of mutation bias and selection for translation efficiency on the codon usage pattern of the endogenous and introgressed exogenous genes using a Bayesian mixture model, ROC SEMPPR, which is built on mechanistic assumptions about protein synthesis and grounded in population genetics. Results We find substantial differences in codon usage between the endogenous and exogenous genes, and show that these differences can be largely attributed to differences in mutation bias favoring A/T ending codons in the endogenous genes while favoring C/G ending codons in the exogenous genes. Recognizing the two different signatures of mutation bias and selection improves our ability to predict protein synthesis rate by 42% and allowed us to accurately assess the decaying signal of endogenous codon mutation and preferences. In addition, using our estimates of mutation bias and selection, we identify Eremothecium gossypii as the closest relative to the exogenous genes, providing an alternative hypothesis about the origin of the exogenous genes, estimate that the introgression occurred ∼6×108 generation ago, and estimate its historic and current selection against mismatched codon usage. Conclusions Our work illustrates how mechanistic, population genetic models like ROC SEMPPR can separate the effects of mutation and selection on codon usage and provide quantitative estimates from sequence data.
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Affiliation(s)
- Cedric Landerer
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, 37996, TN, USA. .,National Institute for Mathematical and Biological Synthesis, Knoxville, 37996, TN, USA. .,Max-Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, 01307, Germany.
| | - Brian C O'Meara
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, 37996, TN, USA.,National Institute for Mathematical and Biological Synthesis, Knoxville, 37996, TN, USA
| | - Russell Zaretzki
- National Institute for Mathematical and Biological Synthesis, Knoxville, 37996, TN, USA.,Department of Business Analytics and Statistics, University of Tennessee, Knoxville, 37996, TN, USA
| | - Michael A Gilchrist
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, 37996, TN, USA.,National Institute for Mathematical and Biological Synthesis, Knoxville, 37996, TN, USA
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14
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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15
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Wu B, Hao W. Mitochondrial‐encoded endonucleases drive recombination of protein‐coding genes in yeast. Environ Microbiol 2019; 21:4233-4240. [DOI: 10.1111/1462-2920.14783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/18/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Baojun Wu
- Department of Biological Sciences Wayne State University Detroit MI USA
| | - Weilong Hao
- Department of Biological Sciences Wayne State University Detroit MI USA
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16
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Fairhead C, Fischer G, Liti G, Neuvéglise C, Schacherer J. André Goffeau's imprinting on second generation yeast "genomologists". Yeast 2019; 36:167-175. [PMID: 30645763 DOI: 10.1002/yea.3377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/21/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022] Open
Abstract
All authors of the present paper have worked in labs that participated to the sequencing effort of the Saccharomyces cerevisiae reference genome, and we owe to this the fact that we have all chosen to work on genomics of yeasts. S. cerevisiae has been a popular model species for genetics since the 20th century as well as being a model for general eukaryotic cellular processes. Although it has also been used empirically in fermentation for millennia, there was until recently, a lack of knowledge about the natural and evolutionary history of this yeast. The achievement of the international effort to sequence its genome was the foundation for understanding many eukaryotic biological processes but also represented the first step towards the study of the genome and ecological diversity of yeast populations worldwide. We will describe recent advances in yeast comparative and population genomics that find their origins in the S. cerevisiae genome project initiated and pursued by André Goffeau.
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Affiliation(s)
- Cécile Fairhead
- UMR Génétique Quantitative et Evolution - Le Moulon, INRA - Université Paris-Sud - CNRS - AgroParisTech, Orsay, France
| | - Gilles Fischer
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Paris, France
| | - Gianni Liti
- INSERM, IRCAN, Université Côte d'Azur, CNRS, Nice, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Joseph Schacherer
- UMR 7156 Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, CNRS, Strasbourg, France
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17
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Peter J, De Chiara M, Friedrich A, Yue JX, Pflieger D, Bergström A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G, Schacherer J. Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature 2018; 556:339-344. [PMID: 29643504 PMCID: PMC6784862 DOI: 10.1038/s41586-018-0030-5] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
Abstract
Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole-genome sequencing and phenotyping of 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species-wide phenotypic landscape of this yeast. Genomic analyses support a single 'out-of-China' origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms. A common feature is the extensive loss of heterozygosity, which represents an essential source of inter-individual variation in this mainly asexual species. Most of the single nucleotide polymorphisms, including experimentally identified functional polymorphisms, are present at very low frequencies. The largest numbers of variants identified by genome-wide association are copy-number changes, which have a greater phenotypic effect than do single nucleotide polymorphisms. This resource will guide future population genomics and genotype-phenotype studies in this classic model system.
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Affiliation(s)
- Jackson Peter
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - David Pflieger
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | | | - Benjamin Barre
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Kelle Freel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Agnès Llored
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Corinne Cruaud
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Benjamin Istace
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, Sophia Antipolis, Valbonne, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Sophia Antipolis, Valbonne, France
| | - Stefan Engelen
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Arnaud Lemainque
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France.,CNRS UMR 8030, Université d'Evry Val d'Essonne, Evry, France
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
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18
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Ortiz-Merino RA, Varela JA, Coughlan AY, Hoshida H, da Silveira WB, Wilde C, Kuijpers NGA, Geertman JM, Wolfe KH, Morrissey JP. Ploidy Variation in Kluyveromyces marxianus Separates Dairy and Non-dairy Isolates. Front Genet 2018; 9:94. [PMID: 29619042 PMCID: PMC5871668 DOI: 10.3389/fgene.2018.00094] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/05/2018] [Indexed: 11/20/2022] Open
Abstract
Kluyveromyces marxianus is traditionally associated with fermented dairy products, but can also be isolated from diverse non-dairy environments. Because of thermotolerance, rapid growth and other traits, many different strains are being developed for food and industrial applications but there is, as yet, little understanding of the genetic diversity or population genetics of this species. K. marxianus shows a high level of phenotypic variation but the only phenotype that has been clearly linked to a genetic polymorphism is lactose utilisation, which is controlled by variation in the LAC12 gene. The genomes of several strains have been sequenced in recent years and, in this study, we sequenced a further nine strains from different origins. Analysis of the Single Nucleotide Polymorphisms (SNPs) in 14 strains was carried out to examine genome structure and genetic diversity. SNP diversity in K. marxianus is relatively high, with up to 3% DNA sequence divergence between alleles. It was found that the isolates include haploid, diploid, and triploid strains, as shown by both SNP analysis and flow cytometry. Diploids and triploids contain long genomic tracts showing loss of heterozygosity (LOH). All six isolates from dairy environments were diploid or triploid, whereas 6 out 7 isolates from non-dairy environment were haploid. This also correlated with the presence of functional LAC12 alleles only in dairy haplotypes. The diploids were hybrids between a non-dairy and a dairy haplotype, whereas triploids included three copies of a dairy haplotype.
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Affiliation(s)
- Raúl A Ortiz-Merino
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Aisling Y Coughlan
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Hisashi Hoshida
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | | | | | | | | | - Kenneth H Wolfe
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
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19
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Nieuwenhuis BPS, James TY. The frequency of sex in fungi. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0540. [PMID: 27619703 DOI: 10.1098/rstb.2015.0540] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 12/16/2022] Open
Abstract
Fungi are a diverse group of organisms with a huge variation in reproductive strategy. While almost all species can reproduce sexually, many reproduce asexually most of the time. When sexual reproduction does occur, large variation exists in the amount of in- and out-breeding. While budding yeast is expected to outcross only once every 10 000 generations, other fungi are obligate outcrossers with well-mixed panmictic populations. In this review, we give an overview of the costs and benefits of sexual and asexual reproduction in fungi, and the mechanisms that evolved in fungi to reduce the costs of either mode. The proximate molecular mechanisms potentiating outcrossing and meiosis appear to be present in nearly all fungi, making them of little use for predicting outcrossing rates, but also suggesting the absence of true ancient asexual lineages. We review how population genetic methods can be used to estimate the frequency of sex in fungi and provide empirical data that support a mixed mode of reproduction in many species with rare to frequent sex in between rounds of mitotic reproduction. Finally, we highlight how these estimates might be affected by the fungus-specific mechanisms that evolved to reduce the costs of sexual and asexual reproduction.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Bart P S Nieuwenhuis
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
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20
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Kolařík M, Vohník M. When the ribosomal DNA does not tell the truth: The case of the taxonomic position of Kurtia argillacea, an ericoid mycorrhizal fungus residing among Hymenochaetales. Fungal Biol 2017; 122:1-18. [PMID: 29248111 DOI: 10.1016/j.funbio.2017.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/13/2017] [Accepted: 09/27/2017] [Indexed: 11/19/2022]
Abstract
The nuclear ribosomal DNA (nuc-rDNA) is widely used for the identification and phylogenetic reconstruction of Agaricomycetes. However, nuc-rDNA-based phylogenies may sometimes be in conflict with phylogenetic relationships derived from protein coding genes. In this study, the taxonomic position of the basidiomycetous mycobiont that forms the recently discovered sheathed ericoid mycorrhiza was investigated, because its nuc-rDNA is highly dissimilar to any other available fungal sequences in terms of nucleotide composition and length, and its nuc-rDNA-based phylogeny is inconclusive and significantly disagrees with protein coding sequences and morphological data. In the present work, this mycobiont was identified as Kurtia argillacea (= Hyphoderma argillaceum) residing in the order Hymenochaetales (Basidiomycota). Bioinformatic screening of the Kurtia ribosomal DNA sequence indicates that it represents a gene with a non-standard substitution rate or nucleotide composition heterogeneity rather than a deep paralogue or a pseudogene. Such a phenomenon probably also occurs in other lineages of the Fungi and should be taken into consideration when nuc-rDNA (especially that with unusual nucleotide composition) is used as a sole marker for phylogenetic reconstructions. Kurtia argillacea so far represents the only confirmed non-sebacinoid ericoid mycorrhizal fungus in the Basidiomycota and its intriguing placement among mostly saprobic and parasitic Hymenochaetales begs further investigation of its eco-physiology.
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Affiliation(s)
- Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences (CAS), Vídeňská 1083, CZ-14220 Prague, Czech Republic.
| | - Martin Vohník
- Department of Mycorrhizal Symbioses, Institute of Botany CAS, CZ-252 43 Průhonice, Czech Republic; Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, CZ-128 44 Prague, Czech Republic
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21
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High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing. G3-GENES GENOMES GENETICS 2017; 7:3243-3250. [PMID: 28983066 PMCID: PMC5633375 DOI: 10.1534/g3.117.300128] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any nonmodel organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is to obtain the complete sequence and high-quality assembly of a reference genome. Here, we sequenced and assembled a reference genome of the nonconventional Dekkera bruxellensis yeast. While this species is a major cause of wine spoilage, it paradoxically contributes to the specific flavor profile of some Belgium beers. In addition, an extreme karyotype variability is observed across natural isolates, highlighting that D. bruxellensis genome is very dynamic. The whole genome of the D. bruxellensis UMY321 isolate was sequenced using a combination of Nanopore long-read and Illumina short-read sequencing data. We generated the most complete and contiguous de novo assembly of D. bruxellensis to date and obtained a first glimpse into the genomic variability within this species by comparing the sequences of several isolates. This genome sequence is therefore of high value for population genomic surveys and represents a reference to study genome dynamic in this yeast species.
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Brion C, Legrand S, Peter J, Caradec C, Pflieger D, Hou J, Friedrich A, Llorente B, Schacherer J. Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts. PLoS Genet 2017; 13:e1006917. [PMID: 28763437 PMCID: PMC5554000 DOI: 10.1371/journal.pgen.1006917] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 08/11/2017] [Accepted: 07/10/2017] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination is a major factor of genome evolution, deeply characterized in only a few model species, notably the yeast Saccharomyces cerevisiae. Consequently, little is known about variations of its properties across species. In this respect, we explored the recombination landscape of Lachancea kluyveri, a protoploid yeast species that diverged from the Saccharomyces genus more than 100 million years ago and we found striking differences with S. cerevisiae. These variations include a lower recombination rate, a higher frequency of chromosomes segregating without any crossover and the absence of recombination on the chromosome arm containing the sex locus. In addition, although well conserved within the Saccharomyces clade, the S. cerevisiae recombination hotspots are not conserved over a broader evolutionary distance. Finally and strikingly, we found evidence of frequent reversal of commitment to meiosis, resulting in return to mitotic growth after allele shuffling. Identification of this major but underestimated evolutionary phenomenon illustrates the relevance of exploring non-model species. Meiotic recombination promotes accurate chromosome segregation and genetic diversity. To date, the mechanisms and rules lying behind recombination were dissected using model organisms such as the budding yeast Saccharomyces cerevisiae. To assess the conservation and variation of this process over a broad evolutionary distance, we explored the meiotic recombination landscape in Lachancea kluyveri, a budding yeast species that diverged from S. cerevisiae more than 100 million years ago. The meiotic recombination map we generated revealed that the meiotic recombination landscape and properties significantly vary across distantly related yeast species, raising the yet to confirm possibility that recombination hotspots conservation across yeast species depends on synteny conservation. Finally, the frequent meiotic reversions we observed led us to re-evaluate their evolutionary importance.
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Affiliation(s)
- Christian Brion
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Sylvain Legrand
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Jackson Peter
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - David Pflieger
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Jing Hou
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail: (JS); (BL)
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- * E-mail: (JS); (BL)
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23
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Marsit S, Leducq JB, Durand É, Marchant A, Filteau M, Landry CR. Evolutionary biology through the lens of budding yeast comparative genomics. Nat Rev Genet 2017; 18:581-598. [DOI: 10.1038/nrg.2017.49] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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24
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Abstract
Cell differentiation in yeast species is controlled by a reversible, programmed DNA-rearrangement process called mating-type switching. Switching is achieved by two functionally similar but structurally distinct processes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In both species, haploid cells possess one active and two silent copies of the mating-type locus (a three-cassette structure), the active locus is cleaved, and synthesis-dependent strand annealing is used to replace it with a copy of a silent locus encoding the opposite mating-type information. Each species has its own set of components responsible for regulating these processes. In this review, we summarize knowledge about the function and evolution of mating-type switching components in these species, including mechanisms of heterochromatin formation, MAT locus cleavage, donor bias, lineage tracking, and environmental regulation of switching. We compare switching in these well-studied species to others such as Kluyveromyces lactis and the methylotrophic yeasts Ogataea polymorpha and Komagataella phaffii. We focus on some key questions: Which cells switch mating type? What molecular apparatus is required for switching? Where did it come from? And what is the evolutionary purpose of switching?
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25
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Blanc-Mathieu R, Krasovec M, Hebrard M, Yau S, Desgranges E, Martin J, Schackwitz W, Kuo A, Salin G, Donnadieu C, Desdevises Y, Sanchez-Ferandin S, Moreau H, Rivals E, Grigoriev IV, Grimsley N, Eyre-Walker A, Piganeau G. Population genomics of picophytoplankton unveils novel chromosome hypervariability. SCIENCE ADVANCES 2017; 3:e1700239. [PMID: 28695208 PMCID: PMC5498103 DOI: 10.1126/sciadv.1700239] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/25/2017] [Indexed: 05/18/2023]
Abstract
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 107) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes.
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Affiliation(s)
- Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marc Krasovec
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Maxime Hebrard
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, CNRS, and Université de Montpellier, 161 rue Ada, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, CNRS, and Université de Montpellier, 860 rue Saint Priest, 34095 Montpellier Cedex 5, France
| | - Sheree Yau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Elodie Desgranges
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Joel Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wendy Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerald Salin
- INRA, plateforme Génome et Transcriptome (GeT-PlaGe), GenoToul, Castanet-Tolosan, France
| | - Cecile Donnadieu
- INRA, plateforme Génome et Transcriptome (GeT-PlaGe), GenoToul, Castanet-Tolosan, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Sophie Sanchez-Ferandin
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Hervé Moreau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Eric Rivals
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, CNRS, and Université de Montpellier, 161 rue Ada, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, CNRS, and Université de Montpellier, 860 rue Saint Priest, 34095 Montpellier Cedex 5, France
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - Nigel Grimsley
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Gwenael Piganeau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
- Corresponding author.
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26
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Dujon BA, Louis EJ. Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina). Genetics 2017; 206:717-750. [PMID: 28592505 PMCID: PMC5499181 DOI: 10.1534/genetics.116.199216] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/03/2017] [Indexed: 12/15/2022] Open
Abstract
Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. horizontal genetic accidents in the making of populations. The facility with which novel yeast genomes can now be studied, combined with the already numerous available reference genomes, offer privileged perspectives to further examine these fundamental biological questions using yeasts both as eukaryotic models and as fungi of practical importance.
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Affiliation(s)
- Bernard A Dujon
- Department Genomes and Genetics, Institut Pasteur, Centre National de la Recherche Scientifique UMR3525, 75724-CEDEX15 Paris, France
- Université Pierre et Marie Curie UFR927, 75005 Paris, France
| | - Edward J Louis
- Centre for Genetic Architecture of Complex Traits, University of Leicester, LE1 7RH, United Kingdom
- Department of Genetics, University of Leicester, LE1 7RH, United Kingdom
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27
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The Hidden Complexity of Mendelian Traits across Natural Yeast Populations. Cell Rep 2016; 16:1106-1114. [PMID: 27396326 DOI: 10.1016/j.celrep.2016.06.048] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 03/15/2016] [Accepted: 06/10/2016] [Indexed: 11/21/2022] Open
Abstract
Mendelian traits are considered to be at the lower end of the complexity spectrum of heritable phenotypes. However, more than a century after the rediscovery of Mendel's law, the global landscape of monogenic variants, as well as their effects and inheritance patterns within natural populations, is still not well understood. Using the yeast Saccharomyces cerevisiae, we performed a species-wide survey of Mendelian traits across a large population of isolates. We generated offspring from 41 unique parental pairs and analyzed 1,105 cross/trait combinations. We found that 8.9% of the cases were Mendelian. Further tracing of causal variants revealed background-specific expressivity and modified inheritances, gradually transitioning from Mendelian to complex traits in 30% of the cases. In fact, when taking into account the natural population diversity, the hidden complexity of traits could be substantial, confounding phenotypic predictability even for simple Mendelian traits.
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28
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Sigwalt A, Caradec C, Brion C, Hou J, de Montigny J, Jung P, Fischer G, Llorente B, Friedrich A, Schacherer J. Dissection of quantitative traits by bulk segregant mapping in a protoploid yeast species. FEMS Yeast Res 2016; 16:fow056. [PMID: 27371856 DOI: 10.1093/femsyr/fow056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
Since more than a decade ago, Saccharomyces cerevisiae has been used as a model to dissect complex traits, revealing the genetic basis of a large number of traits in fine detail. However, to have a more global view of the genetic architecture of traits across species, the examination of the molecular basis of phenotypes within non-conventional species would undoubtedly be valuable. In this respect, the Saccharomycotina yeasts represent ideal and potential non-model organisms. Here we sought to assess the feasibility of genetic mapping by bulk segregant analysis in the protoploid Lachancea kluyveri (formerly S. kluyveri) yeast species, a distantly related species to S. cerevisiae For this purpose, we designed a fluorescent mating-type marker, compatible with any mating-competent strains representative of this species, to rapidly create a large population of haploid segregants (>10(5) cells). Quantitative trait loci can be mapped by selecting and sequencing an enriched pool of progeny with extreme phenotypic values. As a test bed, we applied this strategy and mapped the causal loci underlying halotolerance phenotypes in L. kluyveri Overall, this study demonstrates that bulk segregant mapping is a powerful way for investigating the genetic basis of natural variations in non-model yeast organisms and more precisely in L. kluyveri.
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Affiliation(s)
- Anastasie Sigwalt
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Claudia Caradec
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Christian Brion
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Jacky de Montigny
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Paul Jung
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Gilles Fischer
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France
| | - Bertrand Llorente
- CRCM, CNRS - UMR7258, Inserm - U1068, Institut Paoli-Calmettes, Aix-Marseille Université, UM105, F-13009 Marseille, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg - CNRS, UMR7156, 67000 Strasbourg, France
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29
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Hou J, Fournier T, Schacherer J. Species-wide survey reveals the various flavors of intraspecific reproductive isolation in yeast. FEMS Yeast Res 2016; 16:fow048. [PMID: 27288348 DOI: 10.1093/femsyr/fow048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 12/13/2022] Open
Abstract
Exploring the origin and extent of reproductive isolation within the same species is valuable to capture early events to the onset of speciation. In multiple genetic models, reproductive isolation was recently observed at the intraspecific scale, indicating that the raw potential for speciation segregates readily within populations, which could be a rule rather than an exception in a broad context. We briefly recapitulate the molecular evidence of intrinsic post-zygotic isolation in major model organisms including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and their close relatives. We then focus on recent advances in yeast and review the genetic basis of post-zygotic isolation within and between multiple members of the Saccharomyces genus, especially in Saccharomyces cerevisiae We discuss the role of various mechanisms involved in the onset of reproductive isolation including DNA sequence divergence, chromosomal rearrangement, cytonuclear as well as nuclear-nuclear genetic incompatibilities and provide a comparative view along a continuum of genetic differentiation, which encompasses intraspecific populations, recent delineating nascent species as well as closely related sister species in the same subphylum.
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Affiliation(s)
- Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
| | - Téo Fournier
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
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30
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Vakirlis N, Sarilar V, Drillon G, Fleiss A, Agier N, Meyniel JP, Blanpain L, Carbone A, Devillers H, Dubois K, Gillet-Markowska A, Graziani S, Huu-Vang N, Poirel M, Reisser C, Schott J, Schacherer J, Lafontaine I, Llorente B, Neuvéglise C, Fischer G. Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Res 2016; 26:918-32. [PMID: 27247244 PMCID: PMC4937564 DOI: 10.1101/gr.204420.116] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/28/2016] [Indexed: 12/22/2022]
Abstract
Reconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements, and protein divergence into a single evolutionary framework.
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Affiliation(s)
- Nikolaos Vakirlis
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Véronique Sarilar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Guénola Drillon
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Aubin Fleiss
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Nicolas Agier
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Jean-Philippe Meyniel
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Lou Blanpain
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Alessandra Carbone
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Kenny Dubois
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Alexandre Gillet-Markowska
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Stéphane Graziani
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Nguyen Huu-Vang
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marion Poirel
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Cyrielle Reisser
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR 7156, 67083 Strasbourg, France
| | - Jonathan Schott
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR 7156, 67083 Strasbourg, France
| | - Ingrid Lafontaine
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Bertrand Llorente
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gilles Fischer
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
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31
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Freel KC, Charron G, Leducq JB, Landry CR, Schacherer J. Lachancea quebecensis sp. nov., a yeast species consistently isolated from tree bark in the Canadian province of Québec. Int J Syst Evol Microbiol 2016; 65:3392-3399. [PMID: 26297665 DOI: 10.1099/ijsem.0.000426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A thorough sampling of maple, oak, birch, and apple tree bark in North America yielded a set of isolates that represent a yeast species not yet formally described. The strains obtained were all isolated from the Canadian province of Québec. These four isolates have identical electrophoretic karyotypes, distinct from other species of the genus Lachancea, and are most closely related to the formally recognized species Lachancea thermotolerans according to the D1/D2 domain of the LSU rDNA gene and 5.8S–ITS region. Previous studies revealed the existence of a population of strains closely related to L. thermotolerans, with unique D1/D2 sequences and the ability to grow on melibiose, which is also true for these isolates. The sequences obtained here (for the D1/D2, and 5.8S–ITS region) are identical among the four strains, and in a phylogenetic analysis of the D1/D2 region, the strains form a distinct clade with the previously described population closely related to L. thermotolerans, composed of isolates from Japan, as well as from the provinces of Ontario and Québec in Canada. On the basis of select physiological and phylogenetic characteristics, a novel ascosporogenous yeast species, Lachancea quebecensis sp. nov., is proposed. The type strain LL11_022T ( = CBS 14138T = CLIB 1763T = UCDFST 15-106T) was isolated from maple tree bark in the Station Duchesnay, QC region of Québec, Canada. The MycoBank number is MB811749.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Guillaume Charron
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Jean-Baptiste Leducq
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
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Bizzarri M, Giudici P, Cassanelli S, Solieri L. Chimeric Sex-Determining Chromosomal Regions and Dysregulation of Cell-Type Identity in a Sterile Zygosaccharomyces Allodiploid Yeast. PLoS One 2016; 11:e0152558. [PMID: 27065237 PMCID: PMC4827841 DOI: 10.1371/journal.pone.0152558] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/16/2016] [Indexed: 12/31/2022] Open
Abstract
Allodiploidization is a fundamental yet evolutionarily poorly characterized event, which impacts genome evolution and heredity, controlling organismal development and polyploid cell-types. In this study, we investigated the sex determination system in the allodiploid and sterile ATCC 42981 yeast, a member of the Zygosaccharomyces rouxii species complex, and used it to study how a chimeric mating-type gene repertoire contributes to hybrid reproductive isolation. We found that ATCC 42981 has 7 MAT-like (MTL) loci, 3 of which encode α-idiomorph and 4 encode a-idiomorph. Two phylogenetically divergent MAT expression loci were identified on different chromosomes, accounting for a hybrid a/α genotype. Furthermore, extra a-idimorph-encoding loci (termed MTLa copies 1 to 3) were recognized, which shared the same MATa1 ORFs but diverged for MATa2 genes. Each MAT expression locus was linked to a HML silent cassette, while the corresponding HMR loci were located on another chromosome. Two putative parental sex chromosome pairs contributed to this unusual genomic architecture: one came from an as-yet-undescribed taxon, which has the NCYC 3042 strain as a unique representative, while the other did not match any MAT-HML and HMR organizations previously described in Z. rouxii species. This chimeric rearrangement produces two copies of the HO gene, which encode for putatively functional endonucleases essential for mating-type switching. Although both a and α coding sequences, which are required to obtain a functional cell-type a1-α2 regulator, were present in the allodiploid ATCC 42981 genome, the transcriptional circuit, which regulates entry into meiosis in response to meiosis-inducing salt stress, appeared to be turned off. Furthermore, haploid and α-specific genes, such as MATα1 and HO, were observed to be actively transcribed and up-regulated under hypersaline stress. Overall, these evidences demonstrate that ATCC 42981 is unable to repress haploid α-specific genes and to activate meiosis in response to stress. We argue that sequence divergence within the chimeric a1-α2 heterodimer could be involved in the generation of negative epistasis, contributing to the allodiploid sterility and the dysregulation of cell identity.
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Affiliation(s)
- Melissa Bizzarri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
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Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species. G3-GENES GENOMES GENETICS 2016; 6:1063-71. [PMID: 26888866 PMCID: PMC4825641 DOI: 10.1534/g3.115.026682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
It is now clear that the exploration of the genetic and phenotypic diversity of nonmodel species greatly improves our knowledge in biology. In this context, we recently launched a population genomic analysis of the protoploid yeast Lachancea kluyveri (formerly Saccharomyces kluyveri), highlighting a broad genetic diversity (π = 17 × 10−3) compared to the yeast model organism, S. cerevisiae (π = 4 × 10−3). Here, we sought to generate a comprehensive view of the phenotypic diversity in this species. In total, 27 natural L. kluyveri isolates were subjected to trait profiling using the following independent approaches: (i) analyzing growth in 55 growth conditions and (ii) investigating 501 morphological changes at the cellular level. Despite higher genetic diversity, the fitness variance observed in L. kluyveri is lower than that in S. cerevisiae. However, morphological features show an opposite trend. In addition, there is no correlation between the origins (ecological or geographical) of the isolate and the phenotypic patterns, demonstrating that trait variation follows neither population history nor source environment in L. kluyveri. Finally, pairwise comparisons between growth rate correlation and genetic diversity show a clear decrease in phenotypic variability linked to genome variation increase, whereas no such a trend was identified for morphological changes. Overall, this study reveals for the first time the phenotypic diversity of a distantly related species to S. cerevisiae. Given its genetic properties, L. kluyveri might be useful in further linkage mapping analyses of complex traits, and could ultimately provide a better insight into the evolution of the genotype–phenotype relationship across yeast species.
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Brion C, Pflieger D, Souali-Crespo S, Friedrich A, Schacherer J. Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. Mol Biol Cell 2016; 27:1694-705. [PMID: 27009200 PMCID: PMC4865325 DOI: 10.1091/mbc.e15-12-0816] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/15/2016] [Indexed: 12/19/2022] Open
Abstract
Defining how organisms respond to environmental change has always been an important step toward understanding their adaptive capacity and physiology. Variation in transcription during stress has been widely described in model species, especially in the yeast Saccharomyces cerevisiae, which helped to shape general rules regarding how cells cope with environmental constraints, as well as to decipher the functions of many genes. Comparison of the environmental stress response (ESR) across species is essential to obtaining better insight into the common and species-specific features of stress defense. In this context, we explored the transcriptional landscape of the yeast Lachancea kluyveri (formerly Saccharomyces kluyveri) in response to diverse stresses, using RNA sequencing. We investigated variation in gene expression and observed a link between genetic plasticity and environmental sensitivity. We identified the ESR genes in this species and compared them to those already found in S. cerevisiae We observed common features between the two species, as well as divergence in the regulatory networks involved. Of interest, some changes were related to differences in species lifestyle. Thus we were able to decipher how adaptation to stress has evolved among different yeast species. Finally, by analyzing patterns of coexpression, we were able to propose potential biological functions for 42% of genes and also annotate 301 genes for which no function could be assigned by homology. This large data set allowed for the characterization of the evolution of gene regulation and provides an efficient tool for assessing gene function.
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Affiliation(s)
- Christian Brion
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| | - David Pflieger
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| | - Sirine Souali-Crespo
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
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Hou J, Schacherer J. Negative epistasis: a route to intraspecific reproductive isolation in yeast? Curr Genet 2016; 62:25-9. [PMID: 26164016 PMCID: PMC4710551 DOI: 10.1007/s00294-015-0505-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 01/14/2023]
Abstract
Exploring the molecular bases of intraspecific reproductive isolation captures the ongoing phenotypic consequences of genetic divergence and provides insights into the early onset of speciation. Recent species-wide surveys using natural populations of yeasts demonstrated that intrinsic post-zygotic reproductive isolation segregates readily within the same species, and revealed the multiplicity of the genetic mechanisms underlying such processes. These advances deepened our current understandings and opened further perspectives regarding the complete picture of molecular and evolutionary origins driving the onset of intraspecific reproductive isolation in yeasts.
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Affiliation(s)
- Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg / CNRS, UMR7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg / CNRS, UMR7156, Strasbourg, France.
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Peter J, Schacherer J. Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale. Yeast 2016; 33:73-81. [PMID: 26592376 DOI: 10.1002/yea.3142] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/08/2022] Open
Abstract
With the advent of high-throughput technologies for sequencing, the complete description of the genetic variation that occurs in populations, also known as population genomics, is foreseeable but far from being reached. Explaining the forces that govern patterns of genetic variation is essential to elucidate the evolutionary history of species. Genetic variation results from a wide assortment of evolutionary forces, among which mutation, selection, recombination and drift play major roles in shaping genomes. In addition, exploring the genetic variation within a population also corresponds to the first step towards dissecting the genotype-phenotype relationship. In this context, yeast species are of particular interest because they represent a unique resource for studying the evolution of intraspecific genetic diversity in a phylum spanning a broad evolutionary scale. Here, we briefly review recent progress in yeast population genomics and provide some perspective on this rapidly evolving field. In fact, we truly believe that it is of interest to supplement comparative and early population genomic studies with the deep sequencing of more extensive sets of individuals from the same species. In parallel, it would be more than valuable to uncover the intraspecific variation of a large number of unexplored species, including those that are closely and more distantly related. Altogether, these data would enable substantially more powerful genomic scans for functional dissection.
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Affiliation(s)
- Jackson Peter
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
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Freel KC, Friedrich A, Sarilar V, Devillers H, Neuvéglise C, Schacherer J. Whole-Genome Sequencing and Intraspecific Analysis of the Yeast Species Lachancea quebecensis. Genome Biol Evol 2016; 8:733-41. [PMID: 26733577 PMCID: PMC4823976 DOI: 10.1093/gbe/evv262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The gold standard in yeast population genomics has been the model organism Saccharomyces cerevisiae. However, the exploration of yeast species outside the Saccharomyces genus is essential to broaden the understanding of genome evolution. Here, we report the analyses of whole-genome sequences of nineisolates from the recently described yeast species Lachancea quebecensis. The genome of one isolate was assembled and annotated, and the intraspecific variability within L. quebecensis was surveyed by comparing the sequences from the eight other isolates to this reference sequence. Our study revealed that these strains harbor genomes with an average nucleotide diversity of π = 2 × 10−3 which is slightly lower, although on the same order of magnitude, as that previously determined for S. cerevisiae (π = 4 × 10−3). Our results show that even though these isolates were all obtained from a relatively isolated geographic location, the same ecological source, and represent a smaller sample size than is available for S. cerevisiae, the levels of divergence are similar to those observed in this model species. This divergence is essentially linked to the presence of two distinct clusters delineated according to geographic location. However, even with relatively similar ranges of genome divergence, L. quebecensis has an extremely low global phenotypic variance of 0.062 compared with 0.59 previously determined in S. cerevisiae.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Véronique Sarilar
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Hugo Devillers
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
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Genomics and the making of yeast biodiversity. Curr Opin Genet Dev 2015; 35:100-9. [PMID: 26649756 DOI: 10.1016/j.gde.2015.10.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 12/22/2022]
Abstract
Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies.
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Sheats J, Reifenberger JG, Cao H, Dorfman KD. Measurements of DNA barcode label separations in nanochannels from time-series data. BIOMICROFLUIDICS 2015; 9:064119. [PMID: 26759636 PMCID: PMC4698118 DOI: 10.1063/1.4938732] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/14/2015] [Indexed: 05/12/2023]
Abstract
We analyzed time-series data for fluctuations of intramolecular segments of barcoded E. coli genomic DNA molecules confined in nanochannels with sizes near the persistence length of DNA. These dynamic data allowed us to measure the probability distribution governing the distance between labels on the DNA backbone, which is a key input into the alignment methods used for genome mapping in nanochannels. Importantly, this dynamic method does not require alignment of the barcode to the reference genome, thereby removing a source of potential systematic error in a previous study of this type. The results thus obtained support previous evidence for a left-skewed probability density for the distance between labels, albeit at a lower magnitude of skewness. We further show that the majority of large fluctuations between labels are short-lived events, which sheds further light upon the success of the linearized DNA genome mapping technique. This time-resolved data analysis will improve existing genome map alignment algorithms, and the overall idea of using dynamic data could potentially improve the accuracy of genome mapping, especially for complex heterogeneous samples such as cancer cells.
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Affiliation(s)
- Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | | | - Han Cao
- BioNano Genomics , 9640 Towne Centre Drive Ste. 100, San Diego, California 92121, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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Skelly DA, Magwene PM. Population perspectives on functional genomic variation in yeast. Brief Funct Genomics 2015; 15:138-46. [PMID: 26467711 DOI: 10.1093/bfgp/elv044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Advances in high-throughput sequencing have facilitated large-scale surveys of genomic variation in the budding yeast,Saccharomyces cerevisiae These surveys have revealed extensive sequence variation between yeast strains. However, much less is known about how such variation influences the amount and nature of variation for functional genomic traits within and between yeast lineages. We review population-level studies of functional genomic variation, with a particular focus on how population functional genomic approaches can provide insights into both genome function and the evolutionary process. Although variation in functional genomics phenotypes is pervasive, our understanding of the consequences of this variation, either in physiological or evolutionary terms, is still rudimentary and thus motivates increased attention to appropriate null models. To date, much of the focus of population functional genomic studies has been on gene expression variation, but other functional genomic data types are just as likely to reveal important insights at the population level, suggesting a pressing need for more studies that go beyond transcription. Finally, we discuss how a population functional genomic perspective can be a powerful approach for developing a mechanistic understanding of the processes that link genomic variation to organismal phenotypes through gene networks.
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41
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Voordeckers K, Verstrepen KJ. Experimental evolution of the model eukaryote Saccharomyces cerevisiae yields insight into the molecular mechanisms underlying adaptation. Curr Opin Microbiol 2015. [PMID: 26202939 DOI: 10.1016/j.mib.2015.06.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding how changes in DNA drive the emergence of new phenotypes and fuel evolution remains a major challenge. One major hurdle is the lack of a fossil record of DNA that allows linking mutations to phenotypic changes. However, the emergence of high-throughput sequencing technologies now allows sequencing genomes of natural and experimentally evolved microbial populations to study how mutations arise and spread through a population, how new phenotypes arise and how this ultimately leads to adaptation. Here, we highlight key studies that have increased our mechanistic understanding of evolution. We specifically focus on the model eukaryote Saccharomyces cerevisiae because its relatively short replication time, much-studied biology and available molecular toolbox have made it a prime model for molecular evolution studies.
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Affiliation(s)
- Karin Voordeckers
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium; VIB Laboratory for Systems Biology, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Kevin J Verstrepen
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium; VIB Laboratory for Systems Biology, Gaston Geenslaan 1, B-3001 Leuven, Belgium.
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42
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Dujon B. Basic principles of yeast genomics, a personal recollection: Graphical Abstract Figure. FEMS Yeast Res 2015; 15:fov047. [DOI: 10.1093/femsyr/fov047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 12/12/2022] Open
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43
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Wolfe KH, Armisén D, Proux-Wera E, ÓhÉigeartaigh SS, Azam H, Gordon JL, Byrne KP. Clade- and species-specific features of genome evolution in the Saccharomycetaceae. FEMS Yeast Res 2015; 15:fov035. [PMID: 26066552 PMCID: PMC4629796 DOI: 10.1093/femsyr/fov035] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 12/12/2022] Open
Abstract
Many aspects of the genomes of yeast species in the family Saccharomycetaceae have been well conserved during evolution. They have similar genome sizes, genome contents, and extensive collinearity of gene order along chromosomes. Gene functions can often be inferred reliably by using information from Saccharomyces cerevisiae. Beyond this conservative picture however, there are many instances where a species or a clade diverges substantially from the S. cerevisiae paradigm—for example, by the amplification of a gene family, or by the absence of a biochemical pathway or a protein complex. Here, we review clade-specific features, focusing on genomes sequenced in our laboratory from the post-WGD genera Naumovozyma, Kazachstania and Tetrapisispora, and from the non-WGD species Torulaspora delbrueckii. Examples include the loss of the pathway for histidine synthesis in the cockroach-associated species Tetrapisispora blattae; the presence of a large telomeric GAL gene cluster in To. delbrueckii; losses of the dynein and dynactin complexes in several independent yeast lineages; fragmentation of the MAT locus and loss of the HO gene in Kazachstania africana; and the patchy phylogenetic distribution of RNAi pathway components. The authors review species-specific evolutionary attributes of yeast genomes.
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Affiliation(s)
- Kenneth H Wolfe
- UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - David Armisén
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon - CNRS UMR 5242 - INRA USC 1370, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Estelle Proux-Wera
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Science for Life Laboratory, Dept. of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Seán S ÓhÉigeartaigh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Centre for the Study of Existential Risk, University of Cambridge, CRASSH, Alison Richard Building, 7 West Road, Cambridge, CB3 9DT, UK
| | - Haleema Azam
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jonathan L Gordon
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland CIRAD, UMR CMAEE, Site de Duclos, Prise d'eau, F-97170, Petit-Bourg, Guadeloupe, France
| | - Kevin P Byrne
- UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
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Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast. Nat Commun 2015; 6:7214. [PMID: 26008139 PMCID: PMC4445460 DOI: 10.1038/ncomms8214] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/17/2015] [Indexed: 12/13/2022] Open
Abstract
Genetic variation within a species could cause negative epistasis leading to reduced hybrid fitness and post-zygotic reproductive isolation. Recent studies in yeasts revealed chromosomal rearrangements as a major mechanism dampening intraspecific hybrid fertility on rich media. Here, by analysing a large number of Saccharomyces cerevisiae crosses on different culture conditions, we show environment-specific genetic incompatibility segregates readily within yeast and contributes to reproductive isolation. Over 24% (117 out of 481) of cases tested show potential epistasis, among which 6.7% (32 out of 481) are severe, with at least 20% of progeny loss on tested conditions. Based on the segregation patterns, we further characterize a two-locus Dobzhansky–Müller incompatibility case leading to offspring respiratory deficiency caused by nonsense mutation in a nuclear-encoding mitochondrial gene and tRNA suppressor. We provide evidence that this precise configuration could be adaptive in fluctuating environments, highlighting the role of ecological selection in the onset of genetic incompatibility and reproductive isolation in yeast. Chromosomal rearrangements may hamper intraspecific hybrid fertility. Here the authors show that environment-specific genetic incompatibility segregates readily within intermating populations and leads to intrinsic reproductive isolation within a yeast species.
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45
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Brion C, Pflieger D, Friedrich A, Schacherer J. Evolution of intraspecific transcriptomic landscapes in yeasts. Nucleic Acids Res 2015; 43:4558-68. [PMID: 25897111 PMCID: PMC4482089 DOI: 10.1093/nar/gkv363] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/02/2015] [Indexed: 01/13/2023] Open
Abstract
Variations in gene expression have been widely explored in order to obtain an accurate overview of the changes in regulatory networks that underlie phenotypic diversity. Numerous studies have characterized differences in genomic expression between large numbers of individuals of model organisms such as Saccharomyces cerevisiae. To more broadly survey the evolution of the transcriptomic landscape across species, we measured whole-genome expression in a large collection of another yeast species: Lachancea kluyveri (formerly Saccharomyces kluyveri), using RNAseq. Interestingly, this species diverged from the S. cerevisiae lineage prior to its ancestral whole genome duplication. Moreover, L. kluyveri harbors a chromosome-scale compositional heterogeneity due to a 1-Mb ancestral introgressed region as well as a large set of unique unannotated genes. In this context, our comparative transcriptomic analysis clearly showed a link between gene evolutionary history and expression behavior. Indeed, genes that have been recently acquired or under function relaxation tend to be less transcribed show a higher intraspecific variation (plasticity) and are less involved in network (connectivity). Moreover, utilizing this approach in L. kluyveri also highlighted specific regulatory network signatures in aerobic respiration, amino-acid biosynthesis and glycosylation, presumably due to its different lifestyle. Our data set sheds an important light on the evolution of intraspecific transcriptomic variation across distant species.
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Affiliation(s)
- Christian Brion
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg, France
| | - David Pflieger
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg, France
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Jung PP, Christian N, Kay DP, Skupin A, Linster CL. Protocols and programs for high-throughput growth and aging phenotyping in yeast. PLoS One 2015; 10:e0119807. [PMID: 25822370 PMCID: PMC4379057 DOI: 10.1371/journal.pone.0119807] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/16/2015] [Indexed: 02/06/2023] Open
Abstract
In microorganisms, and more particularly in yeasts, a standard phenotyping approach consists in the analysis of fitness by growth rate determination in different conditions. One growth assay that combines high throughput with high resolution involves the generation of growth curves from 96-well plate microcultivations in thermostated and shaking plate readers. To push the throughput of this method to the next level, we have adapted it in this study to the use of 384-well plates. The values of the extracted growth parameters (lag time, doubling time and yield of biomass) correlated well between experiments carried out in 384-well plates as compared to 96-well plates or batch cultures, validating the higher-throughput approach for phenotypic screens. The method is not restricted to the use of the budding yeast Saccharomyces cerevisiae, as shown by consistent results for other species selected from the Hemiascomycete class. Furthermore, we used the 384-well plate microcultivations to develop and validate a higher-throughput assay for yeast Chronological Life Span (CLS), a parameter that is still commonly determined by a cumbersome method based on counting "Colony Forming Units". To accelerate analysis of the large datasets generated by the described growth and aging assays, we developed the freely available software tools GATHODE and CATHODE. These tools allow for semi-automatic determination of growth parameters and CLS behavior from typical plate reader output files. The described protocols and programs will increase the time- and cost-efficiency of a number of yeast-based systems genetics experiments as well as various types of screens.
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Affiliation(s)
- Paul P. Jung
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nils Christian
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel P. Kay
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California, United States of America
| | - Carole L. Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- * E-mail:
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