1
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Tellini N, De Chiara M, Mozzachiodi S, Tattini L, Vischioni C, Naumova ES, Warringer J, Bergström A, Liti G. Ancient and recent origins of shared polymorphisms in yeast. Nat Ecol Evol 2024; 8:761-776. [PMID: 38472432 DOI: 10.1038/s41559-024-02352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4-6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.
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Affiliation(s)
- Nicolò Tellini
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France
| | | | | | | | | | - Elena S Naumova
- Kurchatov Complex for Genetic Research (GosNIIgenetika), National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France.
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2
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Chou JY, Hsu PC, Leu JY. Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. Microbiol Mol Biol Rev 2022; 86:e0009822. [PMID: 36098649 PMCID: PMC9769731 DOI: 10.1128/mmbr.00098-22] [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] [Indexed: 01/01/2023] Open
Abstract
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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3
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Evolution of yeast hybrids by aborted meiosis. Curr Opin Genet Dev 2022; 77:101980. [PMID: 36084497 DOI: 10.1016/j.gde.2022.101980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/22/2022] [Accepted: 08/01/2022] [Indexed: 01/27/2023]
Abstract
Sterile hybrids are broadly considered evolutionary dead-ends because of their faulty sexual reproduction. While sterility in obligate sexual organisms is a clear constraint in perpetuating the species, some facultative sexual microbes such as yeasts can propagate asexually and maintain genome plasticity. Moreover, incomplete meiotic pathways in yeasts represent alternative routes to the standard meiosis that generates genetic combinations in the population and fuel adaptation. Here, we review how aborting meiosis promotes genome-wide allele shuffling in sterile Saccharomyces hybrids and describe approaches to identify evolved clones in a cell population. We further discuss possible implications of this process in generating phenotypic novelty and report cases of abortive meiosis across yeast species.
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4
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Bozdag GO, Ono J. Evolution and molecular bases of reproductive isolation. Curr Opin Genet Dev 2022; 76:101952. [PMID: 35849861 PMCID: PMC10210581 DOI: 10.1016/j.gde.2022.101952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/31/2022] [Accepted: 06/14/2022] [Indexed: 11/03/2022]
Abstract
The most challenging problem in speciation research is disentangling the relative strength and order in which different reproductive barriers evolve. Here, we review recent developments in the study of reproductive isolation in yeasts. With over a thousand genome-sequenced isolates readily available for testing the viability, sterility, and fitness of both intraspecies and interspecies hybrid crosses, Saccharomyces yeasts are an ideal model to study such fundamental questions. Our survey demonstrates that, while chromosomal-level mutations are widespread at the intraspecific level, anti-recombination-driven chromosome missegregation is the primary reproductive barrier between species. Finally, despite their strength, all of these postzygotic barriers can be resolved through the asexual life history of hybrids.
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Affiliation(s)
- G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA. https://twitter.com/ozan_g_b
| | - Jasmine Ono
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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5
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Abstract
Speciation is the process by which barriers to gene flow evolve between populations. Although we now know that speciation is largely driven by natural selection, knowledge of the agents of selection and the genetic and genomic mechanisms that facilitate divergence is required for a satisfactory theory of speciation. In this essay, we highlight three advances/problems in our understanding of speciation that have arisen from studies of the genes and genomic regions that underlie the evolution of reproductive isolation. First, we describe how the identification of “speciation” genes makes it possible to identify the agents of selection causing the evolution of reproductive isolation, while also noting that the link between the genetics of phenotypic divergence and intrinsic postzygotic reproductive barriers remains tenuous. Second, we discuss the important role of recombination suppressors in facilitating speciation with gene flow, but point out that the means and timing by which reproductive barriers become associated with recombination cold spots remains uncertain. Third, we establish the importance of ancient genetic variation in speciation, although we argue that the focus of speciation studies on evolutionarily young groups may bias conclusions in favor of ancient variation relative to new mutations.
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6
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The evolutionary and ecological potential of yeast hybrids. Curr Opin Genet Dev 2022; 76:101958. [PMID: 35834944 DOI: 10.1016/j.gde.2022.101958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 01/19/2023]
Abstract
Recent findings in yeast genetics and genomics have advanced our understanding of the evolutionary potential unlocked by hybridization, especially in the genus Saccharomyces. We now have a clearer picture of the prevalence of yeast hybrids in the environment, their ecological and evolutionary history, and the genetic mechanisms driving (and constraining) their adaptation. Here, we describe how the instability of hybrid genomes determines fitness across large evolutionary scales, highlight new hybrid strain engineering techniques, and review tools for comparative hybrid genome analysis. The recent push to take yeast research back 'into the wild' has resulted in new genomic and ecological resources. These provide an arena for quantitative genetics and allow us to investigate the architecture of complex traits and mechanisms of adaptation to rapidly changing environments. The vast genetic diversity of hybrid populations can yield insights beyond those possible with isogenic lines. Hybrids offer a limitless supply of genetic variation that can be tapped for industrial strain improvement but also, combined with experimental evolution, can be used to predict population responses to future climate change - a fundamental task for biologists.
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7
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Abstract
Breeding and domestication have generated widely exploited crops, animals and microbes. However, many Saccharomyces cerevisiae industrial strains have complex polyploid genomes and are sterile, preventing genetic improvement strategies based on breeding. Here, we present a strain improvement approach based on the budding yeasts' property to promote genetic recombination when meiosis is interrupted and cells return-to-mitotic-growth (RTG). We demonstrate that two unrelated sterile industrial strains with complex triploid and tetraploid genomes are RTG-competent and develop a visual screening for easy and high-throughput identification of recombined RTG clones based on colony phenotypes. Sequencing of the evolved clones reveal unprecedented levels of RTG-induced genome-wide recombination. We generate and extensively phenotype a RTG library and identify clones with superior biotechnological traits. Thus, we propose the RTG-framework as a fully non-GMO workflow to rapidly improve industrial yeasts that can be easily brought to the market.
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8
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Ruiz-de-Villa C, Poblet M, Bordons A, Reguant C, Rozès N. Differentiation of Saccharomyces species by lipid and metabolome profiles from a single colony. Food Microbiol 2022; 103:103964. [DOI: 10.1016/j.fm.2021.103964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 11/29/2022]
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9
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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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10
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He PY, Shao XQ, Duan SF, Han DY, Li K, Shi JY, Zhang RP, Han PJ, Wang QM, Bai FY. Highly diverged lineages of Saccharomyces paradoxus in temperate to subtropical climate zones in China. Yeast 2021; 39:69-82. [PMID: 34961959 DOI: 10.1002/yea.3688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/06/2022] Open
Abstract
The wild yeast Saccharomyces paradoxus has become a new model in ecology and evolutionary biology. Different lineages of S. paradoxus have been recognized across the world, but the distribution and genetic diversity of the species remain unknown in China, where the origin of its sibling species S. cerevisiae lies. In this study, we investigated the ecological and geographic distribution of S. paradoxus through an extensive field survey in China and performed population genomic analysis on a set of S. paradoxus strains, including 27 strains, representing different geographic and ecological origins within China, and 59 strains representing all the known lineages of the species recognized in the other regions of the world so far. We found two distinct lineages of S. paradoxus in China. The majority of the Chinese strains studied belong to the Far East lineage, and six strains belong to a novel highly diverged lineage. The distribution of these two lineages overlaps ecologically and geographically in temperate to subtropical climate zones in China. With the addition of the new China lineage, the Eurasian population of S. paradoxus exhibits higher genetic diversity than the American population. We observed more possible lineage-specific introgression events from the Eurasian lineages than from the American lineages. Our results expand the knowledge on ecology, genetic diversity, biogeography, and evolution of S. paradoxus.
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Affiliation(s)
- Peng-Yu He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Qian Shao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Genetic Engineering Division, China National Intellectual Property Administration (CNIPA), Beijing, China
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun-Yan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ri-Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Pei-Jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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11
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Solieri L, Cassanelli S, Huff F, Barroso L, Branduardi P, Louis EJ, Morrissey JP. Insights on life cycle and cell identity regulatory circuits for unlocking genetic improvement in Zygosaccharomyces and Kluyveromyces yeasts. FEMS Yeast Res 2021; 21:foab058. [PMID: 34791177 PMCID: PMC8673824 DOI: 10.1093/femsyr/foab058] [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: 09/09/2021] [Accepted: 11/14/2021] [Indexed: 11/14/2022] Open
Abstract
Evolution has provided a vast diversity of yeasts that play fundamental roles in nature and society. This diversity is not limited to genotypically homogeneous species with natural interspecies hybrids and allodiploids that blur species boundaries frequently isolated. Thus, life cycle and the nature of breeding systems have profound effects on genome variation, shaping heterozygosity, genotype diversity and ploidy level. The apparent enrichment of hybrids in industry-related environments suggests that hybridization provides an adaptive route against stressors and creates interest in developing new hybrids for biotechnological uses. For example, in the Saccharomyces genus where regulatory circuits controlling cell identity, mating competence and meiosis commitment have been extensively studied, this body of knowledge is being used to combine interesting traits into synthetic F1 hybrids, to bypass F1 hybrid sterility and to dissect complex phenotypes by bulk segregant analysis. Although these aspects are less known in other industrially promising yeasts, advances in whole-genome sequencing and analysis are changing this and new insights are being gained, especially in the food-associated genera Zygosaccharomyces and Kluyveromyces. We discuss this new knowledge and highlight how deciphering cell identity circuits in these lineages will contribute significantly to identify the genetic determinants underpinning complex phenotypes and open new avenues for breeding programmes.
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Affiliation(s)
- Lisa Solieri
- 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
| | - Franziska Huff
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Liliane Barroso
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Edward J Louis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John P Morrissey
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
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12
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Bendixsen DP, Frazão JG, Stelkens R. Saccharomyces yeast hybrids on the rise. Yeast 2021; 39:40-54. [PMID: 34907582 DOI: 10.1002/yea.3684] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/19/2021] [Accepted: 12/08/2021] [Indexed: 12/23/2022] Open
Abstract
Saccharomyces hybrid yeasts are receiving increasing attention as a powerful model system to understand adaptation to environmental stress and speciation mechanisms, using experimental evolution and omics techniques. We compiled all genomic resources available from public repositories of the eight recognized Saccharomyces species and their interspecific hybrids. We present the newest numbers on genomes sequenced, assemblies, annotations, and sequencing runs, and an updated species phylogeny using orthogroup inference. While genomic resources are highly skewed towards Saccharomyces cerevisiae, there is a noticeable movement to use wild, recently discovered yeast species in recent years. To illustrate the degree and potential causes of reproductive isolation, we reanalyzed published data on hybrid spore viabilities across the entire genus and tested for the role of genetic, geographic, and ecological divergence within and between species (28 cross types and 371 independent crosses). Hybrid viability generally decreased with parental genetic distance likely due to antirecombination and negative epistasis, but notable exceptions emphasize the importance of strain-specific structural variation and ploidy differences. Surprisingly, the viability of crosses within species varied widely, from near reproductive isolation to near-perfect viability. Geographic and ecological origins of the parents predicted cross viability to an extent, but with certain caveats. Finally, we highlight publication trends in the field and point out areas of special interest, where hybrid yeasts are particularly promising for innovation through research and development, and experimental evolution and fermentation.
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Affiliation(s)
- Devin P Bendixsen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - João G Frazão
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
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13
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Mozzachiodi S, Tattini L, Llored A, Irizar A, Škofljanc N, D'Angiolo M, De Chiara M, Barré BP, Yue JX, Lutazi A, Loeillet S, Laureau R, Marsit S, Stenberg S, Albaud B, Persson K, Legras JL, Dequin S, Warringer J, Nicolas A, Liti G. Aborting meiosis allows recombination in sterile diploid yeast hybrids. Nat Commun 2021; 12:6564. [PMID: 34772931 PMCID: PMC8589840 DOI: 10.1038/s41467-021-26883-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022] Open
Abstract
Hybrids between diverged lineages contain novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explore to what extent an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 Saccharomyces cerevisiae and S. paradoxus diploid hybrids with different genomic structures and levels of sterility. Genome analyses of 275 clones reveal that RTG promotes recombination and generates extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination is reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially arises in regions with low local heterozygosity and near meiotic recombination hotspots. The loss-of-heterozygosity has a profound impact on sexual and asexual fitness, and enables genetic mapping of phenotypic differences in sterile lineages where linkage analysis would fail. We propose that RTG gives sterile yeast hybrids access to a natural route for genome recombination and adaptation.
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Grants
- This work was supported by Agence Nationale de la Recherche (ANR-11-LABX-0028-01, ANR-13-BSV6-0006-01, ANR-15-IDEX-01, ANR-16-CE12-0019 and ANR-18-CE12-0004), Fondation pour la Recherche Médicale (FRM EQU202003010413), CEFIPRA, Cancéropôle PACA (AAP Equipment 2018), Meiogenix and the Swedish Research Council (2014-6547, 2014-4605 and 2018-03638). S.Mo. is funded by the convention CIFRE 2016/0582 between Meiogenix and ANRT. The Institut Curie NGS platform is supported by ANR-10-EQPX-03 (Equipex), ANR-10-INBS-09-08 (France Génomique Consortium), ITMO-CANCER and SiRIC INCA-DGOS (4654 program).
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Affiliation(s)
- Simone Mozzachiodi
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- Meiogenix, 38, rue Servan, Paris, 75011, France
| | | | - Agnes Llored
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Neža Škofljanc
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | | | | | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Angela Lutazi
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Sophie Loeillet
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
| | - Raphaelle Laureau
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Medical Center, New York, NY, USA
| | - Souhir Marsit
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
- Département de Biologie Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Benoit Albaud
- Institut Curie, ICGEX NGS Platform, Paris, 75005, France
| | - Karl Persson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jean-Luc Legras
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Sylvie Dequin
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Alain Nicolas
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- Meiogenix, 38, rue Servan, Paris, 75011, France
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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