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Chen J, Garfinkel DJ, Bergman CM. Horizontal Transfer and Recombination Fuel Ty4 Retrotransposon Evolution in Saccharomyces. Genome Biol Evol 2025; 17:evaf004. [PMID: 39786570 PMCID: PMC11739139 DOI: 10.1093/gbe/evaf004] [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: 01/10/2024] [Revised: 09/26/2024] [Accepted: 12/27/2024] [Indexed: 01/12/2025] Open
Abstract
Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes; however, the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two Saccharomyces mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of Saccharomyces paradoxus, Saccharomyces cerevisiae, Saccharomyces eubayanus, Saccharomyces kudriavzevii and the ancestor of the S. mikatae/Saccharomyces jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.
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Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, 120 E. Green St., Athens, GA, USA
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, USA
| | - Casey M Bergman
- Institute of Bioinformatics, University of Georgia, 120 E. Green St., Athens, GA, USA
- Department of Genetics, University of Georgia, 120 E. Green St., Athens, GA, USA
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2
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Hénault M, Marsit S, Charron G, Landry CR. The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate. eLife 2024; 12:RP89277. [PMID: 38411604 PMCID: PMC10911583 DOI: 10.7554/elife.89277] [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: 02/28/2024] Open
Abstract
Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, structural variants (SVs) can affect the genomic distribution of TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger TE mobilization and thus increase TE load in hybrids. We previously tested this hypothesis (Hénault et al., 2020) by performing a large-scale evolution experiment by mutation accumulation (MA) on multiple hybrid genotypes within and between wild populations of the yeasts Saccharomyces paradoxus and Saccharomyces cerevisiae. Using aggregate measures of TE load with short-read sequencing, we found no evidence for TE load increase in hybrid MA lines. Here, we resolve the genomes of the hybrid MA lines with long-read phasing and assembly to precisely characterize the role of SVs in shaping the TE landscape. Highly contiguous phased assemblies of 127 MA lines revealed that SV types like polyploidy, aneuploidy, and loss of heterozygosity have large impacts on the TE load. We characterized 18 de novo TE insertions, indicating that transposition only has a minor role in shaping the TE landscape in MA lines. Because the scarcity of TE mobilization in MA lines provided insufficient resolution to confidently dissect transposition rate variation in hybrids, we adapted an in vivo assay to measure transposition rates in various S. paradoxus hybrid backgrounds. We found that transposition rates are not increased by hybridization, but are modulated by many genotype-specific factors including initial TE load, TE sequence variants, and mitochondrial DNA inheritance. Our results show the multiple scales at which TE load is shaped in hybrid genomes, being highly impacted by SV dynamics and finely modulated by genotype-specific variation in transposition rates.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
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3
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Chen J, Garfinkel DJ, Bergman CM. Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572574. [PMID: 38187645 PMCID: PMC10769310 DOI: 10.1101/2023.12.20.572574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely-related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two S. mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of S. paradoxus, S. cerevisiae, S. eubayanus, S. kudriavzevii and the ancestor of the S. mikatae/S. jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally-transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.
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Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Casey M. Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
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4
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Peris D, Ubbelohde EJ, Kuang MC, Kominek J, Langdon QK, Adams M, Koshalek JA, Hulfachor AB, Opulente DA, Hall DJ, Hyma K, Fay JC, Leducq JB, Charron G, Landry CR, Libkind D, Gonçalves C, Gonçalves P, Sampaio JP, Wang QM, Bai FY, Wrobel RL, Hittinger CT. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nat Commun 2023; 14:690. [PMID: 36755033 PMCID: PMC9908912 DOI: 10.1038/s41467-023-36139-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.
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Grants
- R01 GM080669 NIGMS NIH HHS
- T32 GM007133 NIGMS NIH HHS
- We thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing Illumina and Sanger sequencing facilities and services; Maria Sardi, Audrey Gasch, and Ursula Bond for providing strains; Sean McIlwain for providing guidance for genome ultra-scaffolding; Yury V. Bukhman for discussing applications of the Growth Curve Analysis Tool (GCAT); Mick McGee for HPLC analysis; Raúl Ortíz-Merino for assistance during YGAP annotations; Jessica Leigh for assistance with PopART; Cecile Ané for suggestions about BUCKy utilization and phylogenetic network analyses; Samina Naseeb and Daniela Delneri for sharing preliminary multi-locus Saccharomyces jurei data; and Branden Timm, Brian Kyle, and Dan Metzger for computational assistance. Some computations were performed on Tirant III of the Spanish Supercomputing Network (‘‘Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin-Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. DP is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. QKL was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB-1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. CRL holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by a NSERC Discovery Grant.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain.
| | - Emily J Ubbelohde
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Meihua Christina Kuang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacek Kominek
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin A Koshalek
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Katie Hyma
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Guillaume Charron
- Canada Natural Resources, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Carla Gonçalves
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Vanderbilt University, Department of Biological Sciences, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Paula Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Qi-Ming Wang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Russel L Wrobel
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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5
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The teenage years of yeast population genomics trace history, admixing and getting wilder. Curr Opin Genet Dev 2022; 75:101942. [PMID: 35753210 DOI: 10.1016/j.gde.2022.101942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/22/2022]
Abstract
Population genomics studies the evolutionary processes that shape intraspecies genetic variations. In this review, I explore the insights into yeast-population genomics that have emerged from recent advances in sequencing. Genomes of the model Saccharomyces cerevisiae and many new yeast species from around the world are being used to address various aspects of population biology, including geographical origin, the level of introgression, domestication signatures, and outcrossing frequency. New long-read sequencing has enabled a greater capacity to quantify these variations at a finer resolution from complete de novo genomes at the population scale to phasing subgenomes of different origins. These resources provide a platform to dissect the relationship between phenotypes across environmental niches.
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6
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Belessi CE, Chalvantzi I, Marmaras I, Nisiotou A. The effect of vine variety and vintage on wine yeast community structure of grapes and ferments. J Appl Microbiol 2022; 132:3672-3684. [PMID: 35113470 DOI: 10.1111/jam.15471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 11/26/2022]
Abstract
AIMS The yeast community structure associated with grapes is an essential part of the wine-growing chain with a significant effect on wine quality. The aim of the present study was to evaluate the effect of the varietal factor on the yeast community assembly on grapes and during must fermentation. METHODS AND RESULTS We analysed the wine yeast populations associated with four different grape varieties from the Greek national collection vineyard of Lykovryssi. The vintage effect was also considered by sampling the grapes for two consecutive years. Fourteen yeast species were recovered and genotyped to distinct subpopulations. A relatively stable yeast community structure was detected across vintages, with Hanseniaspora guilliermondii being the core species of the vineyard under study. The detected species subpopulations shared a relatively high genetic similarity with several genotypes persisting across vintages. CONCLUSIONS It was shown that different grape cultivars were associated with distinct yeast communities, pointing to their possible implication on wine chemical diversity. SIGNIFICANCE AND IMPACT OF THE STUDY Present findings show that the varietal factor is an important sharpener of the vineyard-associated wine yeast community, which may interfere with the organoleptic profile of the resulting wines.
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Affiliation(s)
- C-E Belessi
- Hellenic Agricultural Organisation-DEMETER, Institute of Technology of Agricultural Products, S. Venizelou 1, 14123, Athens, Greece
| | - I Chalvantzi
- Hellenic Agricultural Organisation-DEMETER, Institute of Technology of Agricultural Products, S. Venizelou 1, 14123, Athens, Greece
| | - I Marmaras
- Hellenic Agricultural Organisation-DEMETER, Institute of Technology of Agricultural Products, S. Venizelou 1, 14123, Athens, Greece
| | - A Nisiotou
- Hellenic Agricultural Organisation-DEMETER, Institute of Technology of Agricultural Products, S. Venizelou 1, 14123, Athens, Greece
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7
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Bai FY, Han DY, Duan SF, Wang QM. The Ecology and Evolution of the Baker's Yeast Saccharomyces cerevisiae. Genes (Basel) 2022; 13:230. [PMID: 35205274 PMCID: PMC8871604 DOI: 10.3390/genes13020230] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/01/2023] Open
Abstract
The baker's yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an 'out-of-China' origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.
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Affiliation(s)
- Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China;
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8
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Hénault M, Marsit S, Charron G, Landry CR. Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance. Genome Res 2022; 32:2043-2056. [PMID: 36351770 PMCID: PMC9808621 DOI: 10.1101/gr.276885.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Mitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. Although uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we use Saccharomyces yeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but the recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which led to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism, and the emergence of reproductive isolation.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
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9
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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: 5] [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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10
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Interspecific hybridization as a driver of fungal evolution and adaptation. Nat Rev Microbiol 2021; 19:485-500. [PMID: 33767366 DOI: 10.1038/s41579-021-00537-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 02/01/2023]
Abstract
Cross-species gene transfer is often associated with bacteria, which have evolved several mechanisms that facilitate horizontal DNA exchange. However, the increased availability of whole-genome sequences has revealed that fungal species also exchange DNA, leading to intertwined lineages, blurred species boundaries or even novel species. In contrast to prokaryotes, fungal DNA exchange originates from interspecific hybridization, where two genomes are merged into a single, often highly unstable, polyploid genome that evolves rapidly into stabler derivatives. The resulting hybrids can display novel combinations of genetic and phenotypic variation that enhance fitness and allow colonization of new niches. Interspecific hybridization led to the emergence of important pathogens of humans and plants (for example, various Candida and 'powdery mildew' species, respectively) and industrially important yeasts, such as Saccharomyces hybrids that are important in the production of cold-fermented lagers or cold-cellared Belgian ales. In this Review, we discuss the genetic processes and evolutionary implications of fungal interspecific hybridization and highlight some of the best-studied examples. In addition, we explain how hybrids can be used to study molecular mechanisms underlying evolution, adaptation and speciation, and serve as a route towards development of new variants for industrial applications.
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11
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Alsammar H, Delneri D. An update on the diversity, ecology and biogeography of the Saccharomyces genus. FEMS Yeast Res 2021; 20:5810663. [PMID: 32196094 PMCID: PMC7150579 DOI: 10.1093/femsyr/foaa013] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Saccharomyces cerevisiae is the most extensively studied yeast and, over the last century, provided insights on the physiology, genetics, cellular biology and molecular mechanisms of eukaryotes. More recently, the increase in the discovery of wild strains, species and hybrids of the genus Saccharomyces has shifted the attention towards studies on genome evolution, ecology and biogeography, with the yeast becoming a model system for population genomic studies. The genus currently comprises eight species, some of clear industrial importance, while others are confined to natural environments, such as wild forests devoid from human domestication activities. To date, numerous studies showed that some Saccharomyces species form genetically diverged populations that are structured by geography, ecology or domestication activity and that the yeast species can also hybridize readily both in natural and domesticated environments. Much emphasis is now placed on the evolutionary process that drives phenotypic diversity between species, hybrids and populations to allow adaptation to different niches. Here, we provide an update of the biodiversity, ecology and population structure of the Saccharomyces species, and recapitulate the current knowledge on the natural history of Saccharomyces genus.
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Affiliation(s)
- Haya Alsammar
- Department of Biological Sciences, Faculty of Science, Kuwait University, P. O. Box 5969, Safat 13060, Kuwait
| | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, M1 7DN, UK
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12
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Orihara T, Healy R, Corrales A, Smith ME. Multilocus phylogenies reveal three new truffle-like taxa and the traces of interspecific hybridization in Octaviania (Boletaceae, Boletales). IMA Fungus 2021; 12:14. [PMID: 34116729 PMCID: PMC8194053 DOI: 10.1186/s43008-021-00066-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 05/09/2021] [Indexed: 01/11/2023] Open
Abstract
Among many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subg. Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multilocus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri stat. nov. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multilocus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity found within the genus.
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Affiliation(s)
- Takamichi Orihara
- Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Odawara, Kanagawa, 250-0031, Japan.
| | - Rosanne Healy
- Department of Plant Pathology, University of Florida, Gainesville, Florida, 32611-0680, USA
| | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111221, Colombia
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, Florida, 32611-0680, USA
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13
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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14
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Wang B, Li K, He Z. The genetic differentiation of a cricket ( Velarifictorus micado) with two modes of life cycle in East Asia after the middle Pleistocene and the invasion origin of the United States of America. Ecol Evol 2020; 10:13767-13786. [PMID: 33391679 PMCID: PMC7771141 DOI: 10.1002/ece3.6967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/29/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
The cricket Velarifictorus micado is widely distributed in East Asia and colonized the United States of America (the USA) in 1959. It has two life cycles: egg and nymph diapause. We aimed to investigate the biogeographic boundary between them and determine when and why V. micado diverged. Mitochondrial fragments including COI and CytB were used for haplotype network, demographic analysis, and divergence time estimation in individuals of East Asia. We selected several samples from the USA to find out the colonization origin. The haplotype network indicated there were three lineages based on COI, NE lineage (the egg diapause and mainly distributed in the northern regions), SE lineage (the egg diapause and mainly distributed in the southern regions), and SN lineage (the nymph diapause and mainly distributed in the southern regions). The molecular chronograms indicated that the first divergence of V. micado into two main lineages, NE and southern lineages (SE and SN), was essentially bounded by the Yangtze River. It occurred around ~0.79 Ma (95% HPD: 1.13-0.46 Ma) in the Middle Pleistocene Transition. This was followed by the divergence of the southern lineage into two sublineages, SE and SN lineage, occurred around ~0.50 Ma (95% HPD: 0.71-0.25 Ma), corresponding to the time of development of glaciers in various parts of the Qinghai-Tibet Plateau (QTP) (0.73-0.46 Ma). SE lineage might originate from southwestern China based on the comparison between the haplotype network based on COI and CytB. Our study suggested that divergences of lineages have twice co-occurred with tendency of cooling climatic in Asia after the Mid-Pleistocene, and the life-history strategy may play an important role in lineage diversification. Additionally, our results indicated that the USA populations were revealed at least twice separate Asian invasions. These both belonged to the egg diapause, which might provide a new perspective for invasion control.
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Affiliation(s)
- Baiqiu Wang
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Kai Li
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Zhu‐Qing He
- School of Life SciencesEast China Normal UniversityShanghaiChina
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15
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Abstract
The genus Saccharomyces is an evolutionary paradox. On the one hand, it is composed of at least eight clearly phylogenetically delineated species; these species are reproductively isolated from each other, and hybrids usually cannot complete their sexual life cycles. On the other hand, Saccharomyces species have a long evolutionary history of hybridization, which has phenotypic consequences for adaptation and domestication. A variety of cellular, ecological, and evolutionary mechanisms are responsible for this partial reproductive isolation among Saccharomyces species. These mechanisms have caused the evolution of diverse Saccharomyces species and hybrids, which occupy a variety of wild and domesticated habitats. In this article, we introduce readers to the mechanisms isolating Saccharomyces species, the circumstances in which reproductive isolation mechanisms are effective and ineffective, and the evolutionary consequences of partial reproductive isolation. We discuss both the evolutionary history of the genus Saccharomyces and the human history of taxonomists and biologists struggling with species concepts in this fascinating genus.
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Affiliation(s)
- Jasmine Ono
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
| | - Duncan Greig
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
| | - Primrose J Boynton
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
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16
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Langdon QK, Peris D, Eizaguirre JI, Opulente DA, Buh KV, Sylvester K, Jarzyna M, Rodríguez ME, Lopes CA, Libkind D, Hittinger CT. Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids. PLoS Genet 2020; 16:e1008680. [PMID: 32251477 PMCID: PMC7162524 DOI: 10.1371/journal.pgen.1008680] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 04/16/2020] [Accepted: 02/18/2020] [Indexed: 01/19/2023] Open
Abstract
The wild, cold-adapted parent of hybrid lager-brewing yeasts, Saccharomyces eubayanus, has a complex and understudied natural history. The exploration of this diversity can be used both to develop new brewing applications and to enlighten our understanding of the dynamics of yeast evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. eubayanus strains, the largest collection known to date. S. eubayanus has a multilayered population structure, consisting of two major populations that are further structured into six subpopulations. Four of these subpopulations are found exclusively in the Patagonian region of South America; one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is specific to the Holarctic ecozone. Plant host associations differed between subpopulations and between S. eubayanus and its sister species, Saccharomyces uvarum. S. eubayanus is most abundant and genetically diverse in northern Patagonia, where some locations harbor more genetic diversity than is found outside of South America, suggesting that northern Patagonia east of the Andes was a glacial refugium for this species. All but one subpopulation shows isolation-by-distance, and gene flow between subpopulations is low. However, there are strong signals of ancient and recent outcrossing, including two admixed lineages, one that is sympatric with and one that is mostly isolated from its parental populations. Using our extensive biogeographical data, we build a robust model that predicts all known and a handful of additional regions of the globe that are climatically suitable for S. eubayanus, including Europe where host accessibility and competitive exclusion by other Saccharomyces species may explain its continued elusiveness. We conclude that this industrially relevant species has rich natural diversity with many factors contributing to its complex distribution and natural history. The mysterious wild parent of hybrid-lager brewing yeasts, Saccharomyces eubayanus, has been known for less than 10 years. In this time, it has become clear that lager hybrids arose from a subpopulation that has only been isolated in Tibet and North Carolina, USA; but the global diversity of this species has been less explored. Here, we use whole genome sequencing data for 200 strains (174 newly sequenced) to investigate the genetic diversity and geographical distribution of S. eubayanus. We find that its extensive wild diversity is largely centered in northern Patagonia, which likely was a glacial refugium for this species as three of six subpopulations are endemic to this region. In contrast, S. eubayanus is rarely isolated outside of Patagonia. In North America, isolates are dominated by an invasive, near-clonal admixed lineage; the result of an outcrossing and migration event. All subpopulations are well-differentiated, with low gene flow between them. This genetic isolation of subpopulations could be due to ecological factors, such as plant host associations. With modeling, we find that many areas of the world are climatically suitable to S. eubayanus, including Europe, where it has never been isolated. We propose complex ancestries and rich ecologies underlie the global distribution and diversity of this elusive and industrially important species.
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Affiliation(s)
- Quinn K. Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Juan I. Eizaguirre
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
| | - Dana A. Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - Kelly V. Buh
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
| | - Kayla Sylvester
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - Martin Jarzyna
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - María E. Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Christian A. Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
- * E-mail: (CTH); (DL)
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
- * E-mail: (CTH); (DL)
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17
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Competition experiments in a soil microcosm reveal the impact of genetic and biotic factors on natural yeast populations. ISME JOURNAL 2020; 14:1410-1421. [PMID: 32080356 DOI: 10.1038/s41396-020-0612-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023]
Abstract
The ability to measure microbial fitness directly in natural conditions and in interaction with other microbes is a challenge that needs to be overcome if we want to gain a better understanding of microbial fitness determinants in nature. Here we investigate the influence of the natural microbial community on the relative fitness of the North American populations SpB, SpC and SpC* of the wild yeast Saccharomyces paradoxus using DNA barcodes and a soil microcosm derived from soil associated with oak trees. We find that variation in fitness among these genetically distinct groups is influenced by the microbial community. Altering the microbial community load and diversity with an irradiation treatment significantly diminishes the magnitude of fitness differences among populations. Our findings suggest that microbial interactions could affect the evolution of yeast lineages in nature by modulating variation in fitness.
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18
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Barnes EM, Carter EL, Lewis JD. Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa. Front Microbiol 2020; 11:101. [PMID: 32117131 PMCID: PMC7018939 DOI: 10.3389/fmicb.2020.00101] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/17/2020] [Indexed: 12/30/2022] Open
Abstract
Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.
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Affiliation(s)
- Elle M Barnes
- Department of Biological Sciences, Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, United States.,Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
| | - Erin L Carter
- Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
| | - J D Lewis
- Department of Biological Sciences, Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, United States.,Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
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19
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Liu D, Zhang P, Chen D, Howell K. From the Vineyard to the Winery: How Microbial Ecology Drives Regional Distinctiveness of Wine. Front Microbiol 2019; 10:2679. [PMID: 31824462 PMCID: PMC6880775 DOI: 10.3389/fmicb.2019.02679] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/05/2019] [Indexed: 11/13/2022] Open
Abstract
Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.
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Affiliation(s)
| | | | | | - Kate Howell
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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20
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Craig RJ, Böndel KB, Arakawa K, Nakada T, Ito T, Bell G, Colegrave N, Keightley PD, Ness RW. Patterns of population structure and complex haplotype sharing among field isolates of the green algaChlamydomonas reinhardtii. Mol Ecol 2019; 28:3977-3993. [DOI: 10.1111/mec.15193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/05/2019] [Accepted: 07/17/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Rory J. Craig
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
| | - Katharina B. Böndel
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
- Institute of Plant Breeding, Seed Science and Population Genetics University of Hohenheim Stuttgart Germany
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
| | - Takashi Nakada
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
- Faculty of Environment and Information Sciences Yokohama National University Yokohama Japan
| | - Takuro Ito
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
| | - Graham Bell
- Department of Biology McGill University Montreal QC Canada
| | - Nick Colegrave
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Peter D. Keightley
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Rob W. Ness
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
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21
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Charron G, Marsit S, Hénault M, Martin H, Landry CR. Spontaneous whole-genome duplication restores fertility in interspecific hybrids. Nat Commun 2019; 10:4126. [PMID: 31511504 PMCID: PMC6739354 DOI: 10.1038/s41467-019-12041-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/19/2019] [Indexed: 11/21/2022] Open
Abstract
Interspecies hybrids often show some advantages over parents but also frequently suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out genetic incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in species such as fungi that can also propagate asexually. Here, to test this, we evolve in parallel and under relaxed selection more than 600 diploid yeast inter-specific hybrids that span from 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occur in both hybrids between young and well-established species. Our results show that the instability of ploidy in hybrid is an accessible path to spontaneous fertility recovery. Hybridization across species can lead to offspring with reduced fertility. Here, the authors experimentally evolve yeast and show that whole-genome duplication during asexual reproduction can restore fertility in hybrids over a relatively short evolutionary timespan.
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Affiliation(s)
- Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biologie, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biologie, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biochimie, microbiologie et bio-informatique, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada
| | - Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biochimie, microbiologie et bio-informatique, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada
| | - Hélène Martin
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biologie, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.,Département de biochimie, microbiologie et bio-informatique, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, 1030 avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada. .,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada. .,Département de biologie, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada. .,Département de biochimie, microbiologie et bio-informatique, 1045 Avenue de la Médecine, Université Laval, Québec (Qc), G1V 0A6, Canada.
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22
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Dean LL, Magalhaes IS, Foote A, D'Agostino D, McGowan S, MacColl ADC. Admixture between ancient lineages, selection, and the formation of sympatric stickleback species-pairs. Mol Biol Evol 2019; 36:2481-2497. [PMID: 31297536 PMCID: PMC6805233 DOI: 10.1093/molbev/msz161] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 12/14/2022] Open
Abstract
Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data has revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic re-analysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping and genome-wide single nucleotide polymorphism (SNP) data we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead we reveal a complex colonisation history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel S Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK.,Department of Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Andrew Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd, UK
| | - Daniele D'Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Suzanne McGowan
- School of Geography, The University of Nottingham, University Park, Nottingham, UK
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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23
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Jacques N, Casaregola S. Large biodiversity of yeasts in French Guiana and the description of Suhomyces coccinellae f.a. sp. nov. and Suhomyces faveliae f.a. sp. nov. Int J Syst Evol Microbiol 2019; 69:1634-1649. [PMID: 31033433 DOI: 10.1099/ijsem.0.003369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extent of the diversity of yeasts in tropical rain forest and different environments from French Guiana was investigated. A total of 365 samples were collected from various substrates, such as plants, fruits and insects, at 13 locations, yielding 276 pure yeast isolates. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene indicated that 210 isolates out of 276 belonged to 82 described species (67 Saccharomycotina, 14 Basidiomycota and 1 Pezizomycotina). In addition to these, a total of 54 Saccharomycotina isolates could not be assigned to a known species. These belonged to 14 genera and should be studied further from a taxonomic point of view. In addition, among the 43 Basidiomycotina isolates found, 12 could not be assigned to a known species. This report shows an unexpected biodiversity and indicates that oversea territories, such as French Guiana, constitute a largely unexplored reservoir for yeast diversity. Two Saccharomycotina strains, CLIB 1706 and CLIB 1725, isolated from an insect and from a fern respectively, were characterized further and were shown to belong to the Suhomyces clade on the basis of the rDNA sequence comparison. CLIB 1706TrDNA sequences showed nine substitutions and three indels out of 556 bp (D1/D2 domains) and 32 substitutions and 12 indels out of 380 bp [internal transcribed spacer (ITS)] with that of the most closely related species Suhomyces guaymorum CBS 9823T. CLIB 1725T rDNA sequences presented 18 substitutions and one indel out of 549 bp (D1/D2 domains) and 48 substitutions and 11 indels out of 398 bp (ITS) with that of its closest relative Suhomyces vadensis CBS 9454T. Two novel species of the genus Suhomyces were described to accommodate these two strains: Suhomyces coccinellae f.a. sp. nov. (CLIB 1706T=CBS 14298T) and Suhomyces faveliae f.a. sp. nov. (CLIB 1725T=CBS 14299T).
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Affiliation(s)
- Noémie Jacques
- CIRM-Levures, INRA, Micalis Institute, Jouy-en-Josas, France.,†Present address: Bioger, INRA, Thiverval-Grignon, France
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24
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Eberlein C, Hénault M, Fijarczyk A, Charron G, Bouvier M, Kohn LM, Anderson JB, Landry CR. Hybridization is a recurrent evolutionary stimulus in wild yeast speciation. Nat Commun 2019; 10:923. [PMID: 30804385 PMCID: PMC6389940 DOI: 10.1038/s41467-019-08809-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/31/2019] [Indexed: 01/30/2023] Open
Abstract
Hybridization can result in reproductively isolated and phenotypically distinct lineages that evolve as independent hybrid species. How frequently hybridization leads to speciation remains largely unknown. Here we examine the potential recurrence of hybrid speciation in the wild yeast Saccharomyces paradoxus in North America, which comprises two endemic lineages SpB and SpC, and an incipient hybrid species, SpC*. Using whole-genome sequences from more than 300 strains, we uncover the hybrid origin of another group, SpD, that emerged from hybridization between SpC* and one of its parental species, the widespread SpB. We show that SpD has the potential to evolve as a novel hybrid species, because it displays phenotypic novelties that include an intermediate transcriptome profile, and partial reproductive isolation with its most abundant sympatric parental species, SpB. Our findings show that repetitive cycles of divergence and hybridization quickly generate diversity and reproductive isolation, providing the raw material for speciation by hybridization. Hybridization can contribute to diversity from the genomic to the species level. Here, Eberlein, Hénault et al. investigate genomic, transcriptomic and phenotypic variation among wild lineages of the yeast Saccharomyces paradoxus and suggest that an incipient species has formed by recurrent hybridization.
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Affiliation(s)
- Chris Eberlein
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
| | - Mathieu Hénault
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Anna Fijarczyk
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Guillaume Charron
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Matteo Bouvier
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Linda M Kohn
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - James B Anderson
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Christian R Landry
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada. .,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada.
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25
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Bleuven C, Dubé AK, Nguyen GQ, Gagnon‐Arsenault I, Martin H, Landry CR. A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology. Microbiologyopen 2018; 8:e00773. [PMID: 30569485 PMCID: PMC6612553 DOI: 10.1002/mbo3.773] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 01/24/2023] Open
Abstract
While the use of barcoded collections of laboratory microorganisms and the development of barcode-based cell tracking are rapidly developing in genetics and genomics research, tools to track natural populations are still lacking. The yeast Saccharomyces paradoxus is an emergent microbial model in ecology and evolution. More than five allopatric and sympatric lineages have been identified and hundreds of strains have been isolated for this species, allowing to assess the impact of natural diversity on complex traits. We constructed a collection of 550 barcoded and traceable strains of S. paradoxus, including all three North American lineages SpB, SpC, and SpC*. These strains are diploid, many have their genome fully sequenced and are barcoded with a unique 20 bp sequence that allows their identification and quantification. This yeast collection is functional for competitive experiments in pools as the barcodes allow to measure each lineage's and individual strains' fitness in common conditions. We used this tool to demonstrate that in the tested conditions, there are extensive genotype-by-environment interactions for fitness among S. paradoxus strains, which reveals complex evolutionary potential in variable environments. This barcoded collection provides a valuable resource for ecological genomics studies that will allow gaining a better understanding of S. paradoxus evolution and fitness-related traits.
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Affiliation(s)
- Clara Bleuven
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada
| | - Alexandre K. Dubé
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Guillaume Q. Nguyen
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département des Sciences des aliments, Institut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQuébecCanada
| | - Isabelle Gagnon‐Arsenault
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Hélène Martin
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Christian R. Landry
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
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26
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Zhang W, Manawasinghe IS, Zhao W, Xu J, Brooks S, Zhao X, Hyde KD, Chethana KWT, Liu J, Li X, Yan J. Multiple gene genealogy reveals high genetic diversity and evidence for multiple origins of Chinese Plasmopara viticola population. Sci Rep 2017; 7:17304. [PMID: 29230063 PMCID: PMC5725484 DOI: 10.1038/s41598-017-17569-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/28/2017] [Indexed: 11/14/2022] Open
Abstract
Downy mildew caused by Plasmopara viticola is one of the most devastating diseases of grapevines worldwide. So far, the genetic diversity and origin of the Chinese P. viticola population are unclear. In the present study, 103 P. viticola isolates were sequenced at four gene regions: internal transcribed spacer one (ITS), large subunit of ribosomal RNA (LSU), actin gene (ACT) and beta-tubulin (TUB). The sequences were analyzed to obtain polymorphism and diversity information of the Chinese population as well as to infer the relationships between Chinese and American isolates. High genetic diversity was observed for the Chinese population, with evidence of sub-structuring based on climate. Phylogenetic analysis and haplotype networks showed evidence of close relationships between some American and Chinese isolates, consistent with recent introduction from America to China via planting materials. However, there is also evidence for endemic Chinese P. viticola isolates. Our results suggest that the current Chinese Plasmopara viticola population is an admixture of endemic and introduced isolates.
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Affiliation(s)
- Wei Zhang
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.,College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ishara S Manawasinghe
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Wensheng Zhao
- College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Siraprapa Brooks
- School of Science, Mae Fah Luang University, Chiang, Rai, 57100, Thailand
| | - Xueyan Zhao
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - K W Thilini Chethana
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Jianhua Liu
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Xinghong Li
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Jiye Yan
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
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27
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Charron G, Landry CR. No evidence for extrinsic post-zygotic isolation in a wild Saccharomyces yeast system. Biol Lett 2017; 13:rsbl.2017.0197. [PMID: 28592521 DOI: 10.1098/rsbl.2017.0197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/12/2017] [Indexed: 12/12/2022] Open
Abstract
Although microorganisms account for the largest fraction of Earth's biodiversity, we know little about how their reproductive barriers evolve. Sexual microorganisms such as Saccharomyces yeasts rapidly develop strong intrinsic post-zygotic isolation, but the role of extrinsic isolation in the early speciation process remains to be investigated. We measured the growth of F1 hybrids between two incipient species of Saccharomyces paradoxus to assess the presence of extrinsic post-zygotic isolation across 32 environments. More than 80% of hybrids showed either partial dominance of the best parent or over-dominance for growth, revealing no fitness defects in F1 hybrids. Extrinsic reproductive isolation therefore likely plays little role in limiting gene flow between incipient yeast species and is not a requirement for speciation.
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Affiliation(s)
- Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, 1030 avenue de la Médecine - Université Laval, Québec, Canada G1 V 0A6
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, 1030 avenue de la Médecine - Université Laval, Québec, Canada G1 V 0A6
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28
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Eberlein C, Nielly-Thibault L, Maaroufi H, Dubé AK, Leducq JB, Charron G, Landry CR. The Rapid Evolution of an Ohnolog Contributes to the Ecological Specialization of Incipient Yeast Species. Mol Biol Evol 2017; 34:2173-2186. [PMID: 28482005 DOI: 10.1093/molbev/msx153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Identifying the molecular changes that lead to ecological specialization during speciation is one of the major goals of molecular evolution. One question that remains to be thoroughly investigated is whether ecological specialization derives strictly from adaptive changes and their associated trade-offs, or from conditionally neutral mutations that accumulate under relaxed selection. We used whole-genome sequencing, genome annotation and computational analyses to identify genes that have rapidly diverged between two incipient species of Saccharomyces paradoxus that occupy different climatic regions along a south-west to north-east gradient. As candidate loci for ecological specialization, we identified genes that show signatures of adaptation and accelerated rates of amino acid substitutions, causing asymmetric evolution between lineages. This set of genes includes a glycyl-tRNA-synthetase, GRS2, which is known to be transcriptionally induced under heat stress in the model and sister species S. cerevisiae. Molecular modelling, expression analysis and fitness assays suggest that the accelerated evolution of this gene in the Northern lineage may be caused by relaxed selection. GRS2 arose during the whole-genome duplication (WGD) that occurred 100 million years ago in the yeast lineage. While its ohnolog GRS1 has been preserved in all post-WGD species, GRS2 has frequently been lost and is evolving rapidly, suggesting that the fate of this ohnolog is still to be resolved. Our results suggest that the asymmetric evolution of GRS2 between the two incipient S. paradoxus species contributes to their restricted climatic distributions and thus that ecological specialization derives at least partly from relaxed selection rather than a molecular trade-off resulting from adaptive evolution.
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Affiliation(s)
- Chris Eberlein
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Lou Nielly-Thibault
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada.,Big Data Research Center (CRDM), Université Laval, Québec, QC, Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Jean-Baptiste Leducq
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Guillaume Charron
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Christian R Landry
- Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada.,Big Data Research Center (CRDM), Université Laval, Québec, QC, Canada
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29
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Guillamón JM, Barrio E. Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection. Front Microbiol 2017; 8:806. [PMID: 28522998 PMCID: PMC5415627 DOI: 10.3389/fmicb.2017.00806] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/19/2017] [Indexed: 01/09/2023] Open
Abstract
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.
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Affiliation(s)
- José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain.,Departamento de Genética, Universidad de ValenciaValencia, Spain
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30
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Schield DR, Adams RH, Card DC, Perry BW, Pasquesi GM, Jezkova T, Portik DM, Andrew AL, Spencer CL, Sanchez EE, Fujita MK, Mackessy SP, Castoe TA. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecol Evol 2017; 7:3951-3966. [PMID: 28616190 PMCID: PMC5468163 DOI: 10.1002/ece3.2996] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater‐than‐expected overlap between genes linked to lineage‐specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome‐scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.
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Affiliation(s)
- Drew R Schield
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Richard H Adams
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Daren C Card
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Blair W Perry
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Giulia M Pasquesi
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
| | - Daniel M Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Audra L Andrew
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Carol L Spencer
- Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Elda E Sanchez
- National Natural Toxins Research Center and Department of Chemistry Texas A&M University Kingsville Kingsville TX USA
| | - Matthew K Fujita
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Stephen P Mackessy
- School of Biological Sciences University of Northern Colorado Greeley CO USA
| | - Todd A Castoe
- Department of Biology The University of Texas at Arlington Arlington TX USA
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31
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Filteau M, Charron G, Landry CR. Identification of the fitness determinants of budding yeast on a natural substrate. THE ISME JOURNAL 2017; 11:959-971. [PMID: 27935595 PMCID: PMC5364353 DOI: 10.1038/ismej.2016.170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/15/2016] [Accepted: 10/20/2016] [Indexed: 12/21/2022]
Abstract
The budding yeasts are prime models in genomics and cell biology, but the ecological factors that determine their success in non-human-associated habitats is poorly understood. In North America Saccharomyces yeasts are present on the bark of deciduous trees, where they feed on bark and sap exudates. In the North East, Saccharomyces paradoxus is found on maples, which makes maple sap a natural substrate for this species. We measured growth rates of S. paradoxus natural isolates on maple sap and found variation along a geographical gradient not explained by the inherent variation observed under optimal laboratory conditions. We used a functional genomic screen to reveal the ecologically relevant genes and conditions required for optimal growth in this substrate. We found that the allantoin degradation pathway is required for optimal growth in maple sap, in particular genes necessary for allantoate utilization, which we demonstrate is the major nitrogen source available to yeast in this environment. Growth with allantoin or allantoate as the sole nitrogen source recapitulated the variation in growth rates in maple sap among strains. We also show that two lineages of S. paradoxus display different life-history traits on allantoin and allantoate media, highlighting the ecological relevance of this pathway.
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Affiliation(s)
- Marie Filteau
- Département de Biologie, PROTEO, Big Data Research Center and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département des Sciences des aliments, Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Québec, Québec, Canada
| | - Guillaume Charron
- Département de Biologie, PROTEO, Big Data Research Center and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO, Big Data Research Center and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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32
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Peris D, Moriarty RV, Alexander WG, Baker E, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK, Hittinger CT. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:78. [PMID: 28360936 PMCID: PMC5369230 DOI: 10.1186/s13068-017-0763-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/18/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research. RESULTS To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of S. cerevisiae with wild strains from various Saccharomyces species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to cellulosic biofuel production. Notably, Saccharomyces mikatae strains have high innate tolerance to hydrolysate toxins, while some Saccharomyces species have a robust native capacity to consume xylose. CONCLUSIONS This research demonstrates that hybridization is a viable method to combine industrially relevant traits from diverse yeast species and that members of the genus Saccharomyces beyond S. cerevisiae may offer advantageous genes and traits of interest to the lignocellulosic biofuel industry.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Ryan V. Moriarty
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - William G. Alexander
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - EmilyClare Baker
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Kayla Sylvester
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Maria Sardi
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, IPATEC (CONICET-UNComahue), Centro Regional Universitario Bariloche, Bariloche, Río Negro Argentina
| | - Qi-Ming Wang
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC Canada
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - Guillaume Charron
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - Christian R. Landry
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Katie E. Hyma
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Justin C. Fay
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
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33
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Xia W, Nielly-Thibault L, Charron G, Landry CR, Kasimer D, Anderson JB, Kohn LM. Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland. Mol Ecol 2017; 26:995-1007. [PMID: 27988980 DOI: 10.1111/mec.13954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/28/2016] [Indexed: 12/23/2022]
Abstract
Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and Saccharomyces paradoxus, has been well described at the global scale. We investigated the population genomics of a local population on a small spatial scale to address two main questions. First, is there genomic variation in a S. paradoxus population at a spatial scale spanning centimetres (microsites) to tens of metres? Second, does the distribution of genomic variants persist over time? Our sample consisted of 42 S. paradoxus strains from 2014 and 43 strains from 2015 collected from the same 72 microsites around four host trees (Quercus rubra and Quercus alba) within 1 km2 in a mixed hardwood forest in southern Ontario. Six additional S. paradoxus strains recovered from adjacent maple and beech trees in 2015 are also included in the sample. Whole-genome sequencing and genomic SNP analysis revealed five differentiated groups (clades) within the sampled area. The signal of persistence of genotypes in their microsites from 2014 to 2015 was highly significant. Isolates from the same tree tended to be more related than strains from different trees, with limited evidence of dispersal between trees. In growth assays, one genotype had a significantly longer lag phase than the other strains. Our results indicate that different clades coexist at fine spatial scale and that population structure persists over at least a one-year interval in these wild yeasts, suggesting the efficacy of yearly sampling to follow longer term genetic dynamics in future studies.
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Affiliation(s)
- Wenjing Xia
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Lou Nielly-Thibault
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Guillaume Charron
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Dahlia Kasimer
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - James B Anderson
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Linda M Kohn
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
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34
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Yeast Population Genomics Goes Wild: The Case of Saccharomyces paradoxus. POPULATION GENOMICS: MICROORGANISMS 2017. [DOI: 10.1007/13836_2017_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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35
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Peris D, Langdon QK, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D, Hittinger CT. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus. PLoS Genet 2016; 12:e1006155. [PMID: 27385107 PMCID: PMC4934787 DOI: 10.1371/journal.pgen.1006155] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/08/2016] [Indexed: 12/05/2022] Open
Abstract
Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Quinn K. Langdon
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kayla Sylvester
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Martin Bontrager
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Jean-Baptiste Leducq
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagonico de Tecnologías Biológicas y Geoambientales, IPATEC (CONICET-UNComahue), Centro Regional Universitario Bariloche, Bariloche, Río Negro, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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36
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Stukenbrock EH. The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens. PHYTOPATHOLOGY 2016; 106:104-12. [PMID: 26824768 DOI: 10.1094/phyto-08-15-0184-rvw] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hybridization in fungi has recently been recognized as a major force in the generation of new fungal plant pathogens. These include the grass pathogen Zymoseptoria pseudotritici and the powdery mildew pathogen Blumeria graminis triticale of triticale. Hybridization also plays an important role in the transfer of genetic material between species. This process is termed introgressive hybridization and involves extensive backcrossing between hybrid and the parental species. Introgressive hybridization has contributed substantially to the successful spread of plant pathogens such as Ophiostoma ulmi and O. novo-ulmi, the causal agents of Dutch elm disease, and other tree pathogens such as the rust pathogen Melampsora. Hybridization occurs more readily between species that have previously not coexisted, so-called allopatric species. Reproductive barriers between allopatric species are likely to be more permissive allowing interspecific mating to occur. The bringing together of allopatric species of plant pathogens by global agricultural trade consequently increases the potential for hybridization between pathogen species. In light of global environmental changes, agricultural development, and the facilitated long-distance spread of fungal plant pathogens, hybridization should be considered an important mechanism whereby new pathogens may emerge. Recent studies have gained insight into the genetics and biology of fungal hybrids. Here I summarize current knowledge about hybrid speciation and introgressive hybridization. I propose that future studies will benefit greatly from the availability of large genome data sets and that genome data provide a powerful resource in combination with experimental approaches for analyses of hybrid species.
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Affiliation(s)
- Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118 Kiel, Germany and Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
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37
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Robinson HA, Pinharanda A, Bensasson D. Summer temperature can predict the distribution of wild yeast populations. Ecol Evol 2016; 6:1236-50. [PMID: 26941949 PMCID: PMC4761769 DOI: 10.1002/ece3.1919] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/23/2022] Open
Abstract
The wine yeast, Saccharomyces cerevisiae, is the best understood microbial eukaryote at the molecular and cellular level, yet its natural geographic distribution is unknown. Here we report the results of a field survey for S. cerevisiae,S. paradoxus and other budding yeast on oak trees in Europe. We show that yeast species differ in their geographic distributions, and investigated which ecological variables can predict the isolation rate of S. paradoxus, the most abundant species. We find a positive association between trunk girth and S. paradoxus abundance suggesting that older trees harbor more yeast. S. paradoxus isolation frequency is also associated with summer temperature, showing highest isolation rates at intermediate temperatures. Using our statistical model, we estimated a range of summer temperatures at which we expect high S. paradoxus isolation rates, and show that the geographic distribution predicted by this optimum temperature range is consistent with the worldwide distribution of sites where S. paradoxus has been isolated. Using laboratory estimates of optimal growth temperatures for S. cerevisiae relative to S. paradoxus, we also estimated an optimum range of summer temperatures for S. cerevisiae. The geographic distribution of these optimum temperatures is consistent with the locations where wild S. cerevisiae have been reported, and can explain why only human-associated S. cerevisiae strains are isolated at northernmost latitudes. Our results provide a starting point for targeted isolation of S. cerevisiae from natural habitats, which could lead to a better understanding of climate associations and natural history in this important model microbe.
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Affiliation(s)
| | - Ana Pinharanda
- Faculty of Life Sciences University of Manchester Manchester M13 9PT UK
| | - Douda Bensasson
- Faculty of Life Sciences University of Manchester Manchester M13 9PT UK
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38
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Barbosa R, Almeida P, Safar SVB, Santos RO, Morais PB, Nielly-Thibault L, Leducq JB, Landry CR, Gonçalves P, Rosa CA, Sampaio JP. Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae. Genome Biol Evol 2016; 8:317-29. [PMID: 26782936 PMCID: PMC4779607 DOI: 10.1093/gbe/evv263] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The natural biology of Saccharomyces cerevisiae, the best known unicellular model eukaryote, remains poorly documented and understood although recent progress has started to change this situation. Studies carried out recently in the Northern Hemisphere revealed the existence of wild populations associated with oak trees in North America, Asia, and in the Mediterranean region. However, in spite of these advances, the global distribution of natural populations of S. cerevisiae, especially in regions were oaks and other members of the Fagaceae are absent, is not well understood. Here we investigate the occurrence of S. cerevisiae in Brazil, a tropical region where oaks and other Fagaceae are absent. We report a candidate natural habitat of S. cerevisiae in South America and, using whole-genome data, we uncover new lineages that appear to have as closest relatives the wild populations found in North America and Japan. A population structure analysis revealed the penetration of the wine genotype into the wild Brazilian population, a first observation of the impact of domesticated microbe lineages on the genetic structure of wild populations. Unexpectedly, the Brazilian population shows conspicuous evidence of hybridization with an American population of Saccharomyces paradoxus. Introgressions from S. paradoxus were significantly enriched in genes encoding secondary active transmembrane transporters. We hypothesize that hybridization in tropical wild lineages may have facilitated the habitat transition accompanying the colonization of the tropical ecosystem.
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Affiliation(s)
- Raquel Barbosa
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Pedro Almeida
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Silvana V B Safar
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Renata Oliveira Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Paula B Morais
- Laboratório de Microbiologia Ambiental e Biotecnologia, Universidade Federal de Tocantins, Palmas, TO, Brazil
| | - Lou Nielly-Thibault
- Département de Biologie, Institut de Biologie Intégrative et Des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugènes-Marchand, QC, Canada
| | - Jean-Baptiste Leducq
- Département des Sciences Biologiques, Pavillon Marie-Victorin, 90 Rue Vincent D'indy-Université de Montréal, Montréal, QC, Canada
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et Des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugènes-Marchand, QC, Canada
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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39
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Speciation driven by hybridization and chromosomal plasticity in a wild yeast. Nat Microbiol 2016; 1:15003. [PMID: 27571751 DOI: 10.1038/nmicrobiol.2015.3] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/18/2015] [Indexed: 02/07/2023]
Abstract
Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfil all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the interpretation that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here, we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.
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Zheng YL, Wang SA. Stress Tolerance Variations in Saccharomyces cerevisiae Strains from Diverse Ecological Sources and Geographical Locations. PLoS One 2015; 10:e0133889. [PMID: 26244846 PMCID: PMC4526645 DOI: 10.1371/journal.pone.0133889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/03/2015] [Indexed: 11/17/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a platform organism for bioethanol production from various feedstocks and robust strains are desirable for efficient fermentation because yeast cells inevitably encounter stressors during the process. Recently, diverse S. cerevisiae lineages were identified, which provided novel resources for understanding stress tolerance variations and related shaping factors in the yeast. This study characterized the tolerance of diverse S. cerevisiae strains to the stressors of high ethanol concentrations, temperature shocks, and osmotic stress. The results showed that the isolates from human-associated environments overall presented a higher level of stress tolerance compared with those from forests spared anthropogenic influences. Statistical analyses indicated that the variations of stress tolerance were significantly correlated with both ecological sources and geographical locations of the strains. This study provides guidelines for selection of robust S. cerevisiae strains for bioethanol production from nature.
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Affiliation(s)
- Yan-Lin Zheng
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Shi-An Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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Abstract
Diverse forms of kin discrimination, broadly defined as alteration of social behavior as a function of genetic relatedness among interactants, are common among social organisms from microbes to humans. However, the evolutionary origins and causes of kin-discriminatory behavior remain largely obscure. One form of kin discrimination observed in microbes is the failure of genetically distinct colonies to merge freely upon encounter. Here, we first use natural isolates of the highly social bacterium Myxococcus xanthus to show that colony-merger incompatibilities can be strong barriers to social interaction, particularly by reducing chimerism in multicellular fruiting bodies that develop near colony-territory borders. We then use experimental laboratory populations to test hypotheses regarding the evolutionary origins of kin discrimination. We show that the generic process of adaptation, irrespective of selective environment, is sufficient to repeatedly generate kin-discriminatory behaviors between evolved populations and their common ancestor. Further, we find that kin discrimination pervasively evolves indirectly between allopatric replicate populations that adapt to the same ecological habitat and that this occurs generically in many distinct habitats. Patterns of interpopulation discrimination imply that kin discrimination phenotypes evolved via many diverse genetic mechanisms and mutation-accumulation patterns support this inference. Strong incompatibility phenotypes emerged abruptly in some populations but strengthened gradually in others. The indirect evolution of kin discrimination in an asexual microbe is analogous to the indirect evolution of reproductive incompatibility in sexual eukaryotes and linguistic incompatibility among human cultures, the commonality being indirect, noncoordinated divergence of complex systems evolving in isolation.
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Murphy HA, Zeyl CW. A Potential Case of Reinforcement in a Facultatively Sexual Unicellular Eukaryote. Am Nat 2015; 186:312-9. [PMID: 26655159 DOI: 10.1086/682071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The origin of a new species requires a mechanism to prevent divergent populations from interbreeding. In the classic allopatric model, divided populations evolve independently and accumulate genetic differences. If contact is restored, hybrids suffer reduced fitness and selection may favor traits that prevent mistakes in mating, a process known as reinforcement. This decisive but transient phase is challenging to document and has been reported mostly in macroorganisms. Very little is known about the processes through which new microbial species originate. In particular, it is unclear whether microbial eukaryotes, many of which can reproduce sexually during complex life cycles, speciate in much the same way as do well-studied plants and animals. Using individual cellular mate choice trials, we investigated the mating behavior of sympatric and allopatric woodland populations of the yeast Saccharomyces paradoxus. We find evidence consistent with reinforcement, potentially representing an example of microbial speciation in progress.
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Affiliation(s)
- Helen A Murphy
- Department of Biology, Wake Forest University, Box 7325 Reynolda Station, Winston-Salem, North Carolina 27109
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Tartakoff AM. Cell biology of yeast zygotes, from genesis to budding. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1702-14. [PMID: 25862405 DOI: 10.1016/j.bbamcr.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/28/2015] [Accepted: 03/31/2015] [Indexed: 12/23/2022]
Abstract
The zygote is the essential intermediate that allows interchange of nuclear, mitochondrial and cytosolic determinants between cells. Zygote formation in Saccharomyces cerevisiae is accomplished by mechanisms that are not characteristic of mitotic cells. These include shifting the axis of growth away from classical cortical landmarks, dramatically reorganizing the cell cortex, remodeling the cell wall in preparation for cell fusion, fusing with an adjacent partner, accomplishing nuclear fusion, orchestrating two steps of septin morphogenesis that account for a delay in fusion of mitochondria, and implementing new norms for bud site selection. This essay emphasizes the sequence of dependent relationships that account for this progression from cell encounters through zygote budding. It briefly summarizes classical studies of signal transduction and polarity specification and then focuses on downstream events.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology and Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA.
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Sylvester K, Wang QM, James B, Mendez R, Hulfachor AB, Hittinger CT. Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species. FEMS Yeast Res 2015; 15:fov002. [PMID: 25743785 DOI: 10.1093/femsyr/fov002] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2015] [Indexed: 01/08/2023] Open
Abstract
Compared to its status as an experimental model system and importance to industry, the ecology and genetic diversity of the genus Saccharomyces has received less attention. To investigate systematically the biogeography, community members and habitat of these important yeasts, we isolated and identified nearly 600 yeast strains using sugar-rich enrichment protocols. Isolates were highly diverse and contained representatives of more than 80 species from over 30 genera, including eight novel species that we describe here: Kwoniella betulae f.a. (yHKS285(T) = NRRL Y-63732(T) = CBS 13896(T)), Kwoniella newhampshirensis f.a. (yHKS256(T) = NRRL Y-63731(T) = CBS 13917(T)), Cryptococcus wisconsinensis (yHKS301(T) = NRRL Y-63733(T) = CBS 13895(T)), Cryptococcus tahquamenonensis (yHAB242(T) = NRRL Y-63730(T) = CBS 13897(T)), Kodamaea meredithiae f.a. (yHAB239(T) = NRRL Y-63729(T) = CBS 13899(T)), Blastobotrys buckinghamii (yHAB196(T) = NRRL Y-63727(T) = CBS 13900(T)), Candida sungouii (yHBJ21(T) = NRRL Y-63726(T) = CBS 13907(T)) and Cyberlindnera culbertsonii f.a. (yHAB218(T) = NRRL Y-63728(T) = CBS 13898(T)), spp. nov. Saccharomyces paradoxus was one of the most frequently isolated species and was represented by three genetically distinct lineages in Wisconsin alone. We found a statistically significant association between Quercus (oak) samples and the isolation of S. paradoxus, as well as several novel associations. Variation in temperature preference was widespread across taxonomic ranks and evolutionary timescales. This survey highlights the genetic and taxonomic diversity of yeasts and suggests that host and temperature preferences are major ecological factors.
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Affiliation(s)
- Kayla Sylvester
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qi-Ming Wang
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Brielle James
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Russell Mendez
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
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45
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Miller EL, Greig D. Spore germination determines yeast inbreeding according to fitness in the local environment. Am Nat 2014; 185:291-301. [PMID: 25616146 DOI: 10.1086/679347] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Gene combinations conferring local fitness may be destroyed by mating with individuals that are adapted to a different environment. This form of outbreeding depression provides an evolutionary incentive for self-fertilization. We show that the yeast Saccharomyces paradoxus tends to self-fertilize when it is well adapted to its local environment but tends to outcross when it is poorly adapted. This behavior could preserve combinations of genes when they are beneficial and break them up when they are not, thereby helping adaptation. Haploid spores must germinate before mating, and we found that fitter spores had higher rates of germination across a 24-hour period, increasing the probability that they mate with germinated spores from the same meiotic tetrad. The ability of yeast spores to detect local conditions before germinating and mating suggests the novel possibility that these gametes directly sense their own adaptation and plastically adjust their breeding strategy accordingly.
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Affiliation(s)
- Eric L Miller
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
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46
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Boynton PJ, Greig D. The ecology and evolution of non-domesticated Saccharomyces species. Yeast 2014; 31:449-62. [PMID: 25242436 PMCID: PMC4282469 DOI: 10.1002/yea.3040] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/11/2014] [Accepted: 09/15/2014] [Indexed: 12/13/2022] Open
Abstract
Yeast researchers need model systems for ecology and evolution, but the model yeast Saccharomyces cerevisiae is not ideal because its evolution has been affected by domestication. Instead, ecologists and evolutionary biologists are focusing on close relatives of S. cerevisiae, the seven species in the genus Saccharomyces. The best-studied Saccharomyces yeast, after S. cerevisiae, is S. paradoxus, an oak tree resident throughout the northern hemisphere. In addition, several more members of the genus Saccharomyces have recently been discovered. Some Saccharomyces species are only found in nature, while others include both wild and domesticated strains. Comparisons between domesticated and wild yeasts have pinpointed hybridization, introgression and high phenotypic diversity as signatures of domestication. But studies of wild Saccharomyces natural history, biogeography and ecology are only beginning. Much remains to be understood about wild yeasts' ecological interactions and life cycles in nature. We encourage researchers to continue to investigate Saccharomyces yeasts in nature, both to place S. cerevisiae biology into its ecological context and to develop the genus Saccharomyces as a model clade for ecology and evolution.
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Affiliation(s)
| | - Duncan Greig
- Max Planck Institute for Evolutionary BiologyPlön, Germany
- Galton Laboratory, Department of Genetics, Evolution and Environment, University College LondonUK
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47
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Bozdag GO, Greig D. The genetics of a putative social trait in natural populations of yeast. Mol Ecol 2014; 23:5061-71. [PMID: 25169714 PMCID: PMC4285311 DOI: 10.1111/mec.12904] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 08/21/2014] [Accepted: 08/25/2014] [Indexed: 11/29/2022]
Abstract
The sharing of secreted invertase by yeast cells is a well-established laboratory model for cooperation, but the only evidence that such cooperation occurs in nature is that the SUC loci, which encode invertase, vary in number and functionality. Genotypes that do not produce invertase can act as ‘cheats’ in laboratory experiments, growing on the glucose that is released when invertase producers, or ‘cooperators’, digest sucrose. However, genetic variation for invertase production might instead be explained by adaptation of different populations to different local availabilities of sucrose, the substrate for invertase. Here we find that 110 wild yeast strains isolated from natural habitats, and all contained a single SUC locus and produced invertase; none were ‘cheats’. The only genetic variants we found were three strains isolated instead from sucrose-rich nectar, which produced higher levels of invertase from three additional SUC loci at their subtelomeres. We argue that the pattern of SUC gene variation is better explained by local adaptation than by social conflict.
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Affiliation(s)
- G O Bozdag
- Max Planck Institute for Evolutionary Biology, August Thienemann Strasse 2, Plön, 24306, Germany
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48
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Charron G, Leducq JB, Landry CR. Chromosomal variation segregates within incipient species and correlates with reproductive isolation. Mol Ecol 2014; 23:4362-72. [PMID: 25039979 DOI: 10.1111/mec.12864] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/11/2014] [Accepted: 07/14/2014] [Indexed: 12/19/2022]
Abstract
Reproductive isolation is a critical step in the process of speciation. Among the most important factors driving reproductive isolation are genetic incompatibilities. Whether these incompatibilities are already present before extrinsic factors prevent gene flow between incipient species remains largely unresolved in natural systems. This question is particularly challenging because it requires that we catch speciating populations in the act before they reach the full-fledged species status. We measured the extent of intrinsic postzygotic isolation within and between phenotypically and genetically divergent lineages of the wild yeast Saccharomyces paradoxus that have partially overlapping geographical distributions. We find that hybrid viability between lineages progressively decreases with genetic divergence. A large proportion of postzygotic inviability within lineages is associated with chromosomal rearrangements, suggesting that chromosomal differences substantially contribute to the early steps of reproductive isolation within lineages before reaching fixation. Our observations show that polymorphic intrinsic factors may segregate within incipient species before they contribute to their full reproductive isolation and highlight the role of chromosomal rearrangements in speciation. We propose different hypotheses based on adaptation, biogeographical events and life history evolution that could explain these observations.
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Affiliation(s)
- Guillaume Charron
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Québec, QC, G1V 0A6, Canada
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49
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Bing J, Han PJ, Liu WQ, Wang QM, Bai FY. Evidence for a Far East Asian origin of lager beer yeast. Curr Biol 2014; 24:R380-1. [DOI: 10.1016/j.cub.2014.04.031] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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50
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Albertin W, Chasseriaud L, Comte G, Panfili A, Delcamp A, Salin F, Marullo P, Bely M. Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii. PLoS One 2014; 9:e94246. [PMID: 24718638 PMCID: PMC3981792 DOI: 10.1371/journal.pone.0094246] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/14/2014] [Indexed: 11/19/2022] Open
Abstract
The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼ 1900 years ago), and to the Neolithic era for bioprocesses (∼ 4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses.
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Affiliation(s)
- Warren Albertin
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Biolaffort, Bordeaux, France
| | - Laura Chasseriaud
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Biolaffort, Bordeaux, France
| | - Guillaume Comte
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
| | - Aurélie Panfili
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
| | - Adline Delcamp
- INRA, UMR Biodiversité Gènes et Ecosystèmes, PlateForme Génomique, Cestas, France
| | - Franck Salin
- INRA, UMR Biodiversité Gènes et Ecosystèmes, PlateForme Génomique, Cestas, France
| | - Philippe Marullo
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Biolaffort, Bordeaux, France
| | - Marina Bely
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
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