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Villarreal P, O'Donnell S, Agier N, Muñoz-Guzman F, Benavides-Parra J, Urbina K, Peña TA, Solomon M, Nespolo RF, Fischer G, Varela C, Cubillos FA. Domestication signatures in the non-conventional yeast Lachancea cidri. mSystems 2024; 9:e0105823. [PMID: 38085042 PMCID: PMC10805023 DOI: 10.1128/msystems.01058-23] [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: 10/03/2023] [Accepted: 11/06/2023] [Indexed: 01/24/2024] Open
Abstract
Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a Lachancea cidri yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain's phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the L. cidri CBS2950. In addition, the large reciprocal translocation affects a proline permease (PUT4) regulatory region, resulting in higher PUT4 transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.IMPORTANCEThe exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as Saccharomyces cerevisiae, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in Lachancea cidri, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.
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Affiliation(s)
- Pablo Villarreal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Samuel O'Donnell
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Felipe Muñoz-Guzman
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jose Benavides-Parra
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Kami Urbina
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Tomas A. Peña
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Mark Solomon
- The Australian Wine Research Institute, Glen Osmond, Adelaide, SA, Australia
| | - Roberto F. Nespolo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago, Chile
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Cristian Varela
- The Australian Wine Research Institute, Glen Osmond, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, Adelaide, SA, Australia
| | - Francisco A. Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
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2
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Tullio V. Yeast Genomics and Its Applications in Biotechnological Processes: What Is Our Present and Near Future? J Fungi (Basel) 2022; 8:jof8070752. [PMID: 35887507 PMCID: PMC9315801 DOI: 10.3390/jof8070752] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Since molecular biology and advanced genetic techniques have become important tools in a variety of fields of interest, including taxonomy, identification, classification, possible production of substances and proteins, applications in pharmacology, medicine, and the food industry, there has been significant progress in studying the yeast genome and its potential applications. Because of this potential, as well as their manageability, safety, ease of cultivation, and reproduction, yeasts are now being extensively researched in order to evaluate a growing number of natural and sustainable applications to provide many benefits to humans. This review will describe what yeasts are, how they are classified, and attempt to provide a rapid overview of the many current and future applications of yeasts. The review will then discuss how yeasts—including those molecularly modified—are used to produce biofuels, proteins such as insulin, vaccines, probiotics, beverage preparations, and food additives and how yeasts could be used in environmental bioremediation and biocontrol for plant infections. This review does not delve into the issues raised during studies and research, but rather presents the positive outcomes that have enabled several industrial, clinical, and agricultural applications in the past and future, including the most recent on cow-free milk.
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Affiliation(s)
- Vivian Tullio
- Department Public Health and Pediatrics, Microbiology Division, University of Turin, Via Santena 9, 10126 Torino, Italy
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3
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Cavalieri D, Valentini B, Stefanini I. Going wild: ecology and genomics are crucial to understand yeast evolution. Curr Opin Genet Dev 2022; 75:101922. [PMID: 35691146 DOI: 10.1016/j.gde.2022.101922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/03/2022]
Abstract
Improved and more accessible genome-sequencing approaches have allowed the analysis of large sets of natural yeast isolates. As a consequence, this unprecedented level of description of yeast-genome characteristics and variations in natural environments has provided crucial insights on yeast ecology and evolution. Here, we review some of the most relevant and intriguing aspects of yeast evolution pointed out, thanks to the combination of yeast ecology and genomics, and critically examine the resulting improvement of our knowledge on this field. Only integrated approaches, taking into consideration not only the characteristics of the microbe but also those of the hosting environment, will significantly move forward the exploration of yeast diversity, ecology, and evolution.
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Affiliation(s)
| | - Beatrice Valentini
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Irene Stefanini
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
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4
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Microfluidic-Enabled Multi-Cell-Densities-Patterning and Culture Device for Characterization of Yeast Strains’ Growth Rates under Mating Pheromone. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10040141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Yeast studies usually focus on exploring diversity in terms of a specific trait (such as growth rate, antibiotic resistance, or fertility) among extensive strains. Microfluidic chips improve these biological studies in a manner of high throughput and high efficiency. For a population study of yeast, it is of great significance to set a proper initial cell density for every strain under specific circumstances. Herein, we introduced a novel design of chip, which enables users to load cells in a gradient order (six alternatives) of initial cell density within one channel. We discussed several guidelines to choose the appropriate chamber to ensure successful data recording. With this chip, we successfully studied the growth rate of yeast strains under a mating response, which is crucial for yeasts to control growth behaviors for prosperous mating. We investigated the growth rate of eight different yeast strains under three different mating pheromone levels (0.3 μM, 1 μM, and 10 μM). Strains with, even, a six-fold in growth rate can be recorded, with the available data produced simultaneously. This work has provided an efficient and time-saving microfluidic platform, which enables loading cells in a pattern of multi-cell densities for a yeast population experiment, especially for a high-throughput study. Besides, a quantitatively analyzed growth rate of different yeast strains shall reveal inspiring perspectives for studies concerning yeast population behavior with a stimulated mating pheromone.
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5
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Mechanisms of Yeast Adaptation to Wine Fermentations. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:37-59. [PMID: 30911888 DOI: 10.1007/978-3-030-13035-0_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cells face genetic and/or environmental changes in order to outlast and proliferate. Characterization of changes after stress at different "omics" levels is crucial to understand the adaptation of yeast to changing conditions. Wine fermentation is a stressful situation which yeast cells have to cope with. Genome-wide analyses extend our cellular physiology knowledge by pointing out the mechanisms that contribute to sense the stress caused by these perturbations (temperature, ethanol, sulfites, nitrogen, etc.) and related signaling pathways. The model organism, Saccharomyces cerevisiae, was studied in response to industrial stresses and changes at different cellular levels (transcriptomic, proteomic, and metabolomics), which were followed statically and/or dynamically in the short and long terms. This chapter focuses on the response of yeast cells to the diverse stress situations that occur during wine fermentations, which induce perturbations, including nutritional changes, ethanol stress, temperature stress, oxidative stress, etc.
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6
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Drumonde-Neves J, Franco-Duarte R, Vieira E, Mendes I, Lima T, Schuller D, Pais C. Differentiation of Saccharomyces cerevisiae populations from vineyards of the Azores Archipelago: Geography vs Ecology. Food Microbiol 2018; 74:151-162. [DOI: 10.1016/j.fm.2018.03.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 03/30/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
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7
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Hittinger CT, Steele JL, Ryder DS. Diverse yeasts for diverse fermented beverages and foods. Curr Opin Biotechnol 2018; 49:199-206. [DOI: 10.1016/j.copbio.2017.10.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/25/2022]
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8
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Wloch-Salamon DM, Fisher RM, Regenberg B. Division of labour in the yeast:Saccharomyces cerevisiae. Yeast 2017; 34:399-406. [DOI: 10.1002/yea.3241] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/24/2017] [Accepted: 06/27/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Roberta M. Fisher
- Department of Biology; University of Copenhagen; Universitetsparken 13 DK-2100 Copenhagen Denmark
- Centre for Social Evolution, Department of Biology; University of Copenhagen; Universitetsparken 15 Copenhagen Denmark
| | - Birgitte Regenberg
- Department of Biology; University of Copenhagen; Universitetsparken 13 DK-2100 Copenhagen Denmark
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9
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Abstract
ABSTRACT
In this article, we review some of the best-studied fungi used as food sources, in particular, the cheese fungi, the truffles, and the fungi used for drink fermentation such as beer, wine, and sake. We discuss their history of consumption by humans and the genomic mechanisms of adaptation during artificial selection.
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10
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Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J, Liti G. Powerful decomposition of complex traits in a diploid model. Nat Commun 2016; 7:13311. [PMID: 27804950 PMCID: PMC5097135 DOI: 10.1038/ncomms13311] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/21/2016] [Indexed: 01/20/2023] Open
Abstract
Explaining trait differences between individuals is a core and challenging aim of life sciences. Here, we introduce a powerful framework for complete decomposition of trait variation into its underlying genetic causes in diploid model organisms. We sequence and systematically pair the recombinant gametes of two intercrossed natural genomes into an array of diploid hybrids with fully assembled and phased genomes, termed Phased Outbred Lines (POLs). We demonstrate the capacity of this approach by partitioning fitness traits of 6,642 Saccharomyces cerevisiae POLs across many environments, achieving near complete trait heritability and precisely estimating additive (73%), dominance (10%), second (7%) and third (1.7%) order epistasis components. We map quantitative trait loci (QTLs) and find nonadditive QTLs to outnumber (3:1) additive loci, dominant contributions to heterosis to outnumber overdominant, and extensive pleiotropy. The POL framework offers the most complete decomposition of diploid traits to date and can be adapted to most model organisms.
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Affiliation(s)
- Johan Hallin
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
| | - Kaspar Märtens
- Institute of Computer Science, University of Tartu, 50090 Tartu, Estonia
| | - Alexander I. Young
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Martin Zackrisson
- Department of Chemistry and Molecular Biology, Gothenburg University, 405 30 Gothenburg, Sweden
| | - Francisco Salinas
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
| | - Leopold Parts
- Institute of Computer Science, University of Tartu, 50090 Tartu, Estonia
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, Gothenburg University, 405 30 Gothenburg, Sweden
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Gianni Liti
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
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11
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Louis EJ. Historical Evolution of Laboratory Strains of Saccharomyces cerevisiae. Cold Spring Harb Protoc 2016; 2016:2016/7/pdb.top077750. [PMID: 27371602 DOI: 10.1101/pdb.top077750] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Budding yeast strains used in the laboratory have had a checkered past. Historically, the choice of strain for any particular experiment depended on the suitability of the strain for the topic of study (e.g., cell cycle vs. meiosis). Many laboratory strains had poor fermentation properties and were not representative of the robust strains used for domestic purposes. Most strains were related to each other, but investigators usually had only vague notions about the extent of their relationships. Isogenicity was difficult to confirm before the advent of molecular genetic techniques. However, their ease of growth and manipulation in laboratory conditions made them "the model" model organism, and they still provided a great deal of fundamental knowledge. Indeed, more than one Nobel Prize has been won using them. Most of these strains continue to be powerful tools, and isogenic derivatives of many of them-including entire collections of deletions, overexpression constructs, and tagged gene products-are now available. Furthermore, many of these strains are now sequenced, providing intimate knowledge of their relationships. Recent collections, new isolates, and the creation of genetically tractable derivatives have expanded the available strains for experiments. But even still, these laboratory strains represent a small fraction of the diversity of yeast. The continued development of new laboratory strains will broaden the potential questions that can be posed. We are now poised to take advantage of this diversity, rather than viewing it as a detriment to controlled experiments.
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Affiliation(s)
- Edward J Louis
- Centre for Genetic Architecture of Complex Traits, Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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12
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Abstract
Elucidating the underlying rules that govern the phenotypic diversity observed in natural populations is an old but still unaccomplished goal in biology. In 1865, Gregor Mendel paved the way for the dissection of the underlying genetic basis of traits by setting out to understand the principles of heredity. To date, we still lack a global overview of the spectrum and continuum existing between Mendelian and complex traits within any natural population. In this respect, we recently performed a species-wide survey of Mendelian traits across a large population of isolates using the yeast Saccharomyces cerevisiae. By analyzing the distribution and the inheritance patterns of the trait, we have clearly shown that monogenic mutations can display a significant, variable, and continuous expressivity across different genetic backgrounds. Our study also demonstrated that combining the elegancy of both classical genetics and high-throughput genomics is more than valuable to dissect the genotype-phenotype relationship in natural populations.
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Affiliation(s)
- Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, Université de Strasbourg, CNRS, UMR7156, Strasbourg, France.
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13
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Abstract
Although prions were first discovered through their link to severe brain degenerative diseases in animals, the emergence of prions as regulators of the phenotype of the yeast Saccharomyces cerevisiae and the filamentous fungus Podospora anserina has revealed a new facet of prion biology. In most cases, fungal prions are carried without apparent detriment to the host cell, representing a novel form of epigenetic inheritance. This raises the question of whether or not yeast prions are beneficial survival factors or actually gives rise to a "disease state" that is selected against in nature. To date, most studies on the impact of fungal prions have focused on laboratory-cultivated "domesticated" strains of S. cerevisiae. At least eight prions have now been described in this species, each with the potential to impact on a wide range of cellular processes. The discovery of prions in nondomesticated strains of S. cerevisiae and P. anserina has confirmed that prions are not simply an artifact of "domestication" of this species. In this review, I describe what we currently know about the phenotypic impact of fungal prions. I then describe how the interplay between host genotype and the prion-mediated changes can generate a wide array of phenotypic diversity. How such prion-generated diversity may be of benefit to the host in survival in a fluctuating, often hazardous environment is then outlined. Prion research has now entered a new phase in which we must now consider their biological function and evolutionary significance in the natural world.
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Affiliation(s)
- Mick F Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom.
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14
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Hou J, Schacherer J. Negative epistasis: a route to intraspecific reproductive isolation in yeast? Curr Genet 2016; 62:25-9. [PMID: 26164016 PMCID: PMC4710551 DOI: 10.1007/s00294-015-0505-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 01/14/2023]
Abstract
Exploring the molecular bases of intraspecific reproductive isolation captures the ongoing phenotypic consequences of genetic divergence and provides insights into the early onset of speciation. Recent species-wide surveys using natural populations of yeasts demonstrated that intrinsic post-zygotic reproductive isolation segregates readily within the same species, and revealed the multiplicity of the genetic mechanisms underlying such processes. These advances deepened our current understandings and opened further perspectives regarding the complete picture of molecular and evolutionary origins driving the onset of intraspecific reproductive isolation in yeasts.
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Affiliation(s)
- Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg / CNRS, UMR7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg / CNRS, UMR7156, Strasbourg, France.
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15
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Freel KC, Friedrich A, Sarilar V, Devillers H, Neuvéglise C, Schacherer J. Whole-Genome Sequencing and Intraspecific Analysis of the Yeast Species Lachancea quebecensis. Genome Biol Evol 2016; 8:733-41. [PMID: 26733577 PMCID: PMC4823976 DOI: 10.1093/gbe/evv262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The gold standard in yeast population genomics has been the model organism Saccharomyces cerevisiae. However, the exploration of yeast species outside the Saccharomyces genus is essential to broaden the understanding of genome evolution. Here, we report the analyses of whole-genome sequences of nineisolates from the recently described yeast species Lachancea quebecensis. The genome of one isolate was assembled and annotated, and the intraspecific variability within L. quebecensis was surveyed by comparing the sequences from the eight other isolates to this reference sequence. Our study revealed that these strains harbor genomes with an average nucleotide diversity of π = 2 × 10−3 which is slightly lower, although on the same order of magnitude, as that previously determined for S. cerevisiae (π = 4 × 10−3). Our results show that even though these isolates were all obtained from a relatively isolated geographic location, the same ecological source, and represent a smaller sample size than is available for S. cerevisiae, the levels of divergence are similar to those observed in this model species. This divergence is essentially linked to the presence of two distinct clusters delineated according to geographic location. However, even with relatively similar ranges of genome divergence, L. quebecensis has an extremely low global phenotypic variance of 0.062 compared with 0.59 previously determined in S. cerevisiae.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Véronique Sarilar
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Hugo Devillers
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
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16
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Franco-Duarte R, Bigey F, Carreto L, Mendes I, Dequin S, Santos MAS, Pais C, Schuller D. Intrastrain genomic and phenotypic variability of the commercialSaccharomyces cerevisiaestrain Zymaflore VL1 reveals microevolutionary adaptation to vineyard environments. FEMS Yeast Res 2015; 15:fov063. [DOI: 10.1093/femsyr/fov063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2015] [Indexed: 11/13/2022] Open
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17
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Friedrich A, Jung P, Reisser C, Fischer G, Schacherer J. Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast. Mol Biol Evol 2014; 32:184-92. [PMID: 25349286 PMCID: PMC4271529 DOI: 10.1093/molbev/msu295] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Yeast species represent an ideal model system for population genomic studies but large-scale polymorphism surveys have only been reported for species of the Saccharomyces genus so far. Hence, little is known about intraspecific diversity and evolution in yeast. To obtain a new insight into the evolutionary forces shaping natural populations, we sequenced the genomes of an expansive worldwide collection of isolates from a species distantly related to Saccharomyces cerevisiae: Lachancea kluyveri (formerly S. kluyveri). We identified 6.5 million single nucleotide polymorphisms and showed that a large introgression event of 1 Mb of GC-rich sequence in the chromosomal arm probably occurred in the last common ancestor of all L. kluyveri strains. Our population genomic data clearly revealed that this 1-Mb region underwent a molecular evolution pattern very different from the rest of the genome. It is characterized by a higher recombination rate, with a dramatically elevated A:T → G:C substitution rate, which is the signature of an increased GC-biased gene conversion. In addition, the predicted base composition at equilibrium demonstrates that the chromosome-scale compositional heterogeneity will persist after the genome has reached mutational equilibrium. Altogether, the data presented herein clearly show that distinct recombination and substitution regimes can coexist and lead to different evolutionary patterns within a single genome.
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Affiliation(s)
- Anne Friedrich
- Department of Genetics, Genomics and Microbiology, Université de Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Paul Jung
- Department of Genetics, Genomics and Microbiology, Université de Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Cyrielle Reisser
- Department of Genetics, Genomics and Microbiology, Université de Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Gilles Fischer
- Sorbonne Universités, UPMC Université Paris 06, UMR 7238, Biologie Computationnelle et Quantitative, Paris, France CNRS, UMR7238, Biologie Computationnelle et Quantitative, Paris, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, Université de Strasbourg/CNRS, UMR7156, Strasbourg, France
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18
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Franco-Duarte R, Mendes I, Umek L, Drumonde-Neves J, Zupan B, Schuller D. Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae. Yeast 2014; 31:265-77. [PMID: 24752995 DOI: 10.1002/yea.3016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 11/11/2022] Open
Abstract
Genome sequencing is essential to understand individual variation and to study the mechanisms that explain relations between genotype and phenotype. The accumulated knowledge from large-scale genome sequencing projects of Saccharomyces cerevisiae isolates is being used to study the mechanisms that explain such relations. Our objective was to undertake genetic characterization of 172 S. cerevisiae strains from different geographical origins and technological groups, using 11 polymorphic microsatellites, and computationally relate these data with the results of 30 phenotypic tests. Genetic characterization revealed 280 alleles, with the microsatellite ScAAT1 contributing most to intrastrain variability, together with alleles 20, 9 and 16 from the microsatellites ScAAT4, ScAAT5 and ScAAT6. These microsatellite allelic profiles are characteristic for both the phenotype and origin of yeast strains. We confirm the strength of these associations by construction and cross-validation of computational models that can predict the technological application and origin of a strain from the microsatellite allelic profile. Associations between microsatellites and specific phenotypes were scored using information gain ratios, and significant findings were confirmed by permutation tests and estimation of false discovery rates. The phenotypes associated with higher number of alleles were the capacity to resist to sulphur dioxide (tested by the capacity to grow in the presence of potassium bisulphite) and the presence of galactosidase activity. Our study demonstrates the utility of computational modelling to estimate a strain technological group and phenotype from microsatellite allelic combinations as tools for preliminary yeast strain selection.
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Affiliation(s)
- Ricardo Franco-Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
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19
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Zarin T, Moses AM. Insights into molecular evolution from yeast genomics. Yeast 2014; 31:233-41. [PMID: 24760744 DOI: 10.1002/yea.3018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 12/13/2022] Open
Abstract
Enabled by comparative genomics, yeasts have increasingly developed into a powerful model system for molecular evolution. Here we survey several areas in which yeast studies have made important contributions, including regulatory evolution, gene duplication and divergence, evolution of gene order and evolution of complexity. In each area we highlight key studies and findings based on techniques ranging from statistical analysis of large datasets to direct laboratory measurements of fitness. Future work will combine traditional evolutionary genetics analysis and experimental evolution with tools from systems biology to yield mechanistic insight into complex phenotypes.
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Affiliation(s)
- Taraneh Zarin
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
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Tofalo R, Perpetuini G, Fasoli G, Schirone M, Corsetti A, Suzzi G. Biodiversity study of wine yeasts belonging to the “terroir” of Montepulciano d'Abruzzo “Colline Teramane” revealed Saccharomyces cerevisiae strains exhibiting atypical and unique 5.8S-ITS restriction patterns. Food Microbiol 2014; 39:7-12. [DOI: 10.1016/j.fm.2013.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 09/24/2013] [Accepted: 10/01/2013] [Indexed: 11/28/2022]
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22
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Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G. A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol 2014; 31:872-88. [PMID: 24425782 PMCID: PMC3969562 DOI: 10.1093/molbev/msu037] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies.
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Affiliation(s)
- Anders Bergström
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | | | - Francisco Salinas
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | - Benjamin Barré
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | - Leopold Parts
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Amin Zia
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine
| | - Alex N. Nguyen Ba
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alan M. Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Edward J. Louis
- Centre of Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Ville Mustonen
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Durbin
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Gianni Liti
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
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Duitama J, Sánchez-Rodríguez A, Goovaerts A, Pulido-Tamayo S, Hubmann G, Foulquié-Moreno MR, Thevelein JM, Verstrepen KJ, Marchal K. Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast. BMC Genomics 2014; 15:207. [PMID: 24640961 PMCID: PMC4003806 DOI: 10.1186/1471-2164-15-207] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 03/10/2014] [Indexed: 12/21/2022] Open
Abstract
Background Bulk segregant analysis (BSA) coupled to high throughput sequencing is a powerful method to map genomic regions related with phenotypes of interest. It relies on crossing two parents, one inferior and one superior for a trait of interest. Segregants displaying the trait of the superior parent are pooled, the DNA extracted and sequenced. Genomic regions linked to the trait of interest are identified by searching the pool for overrepresented alleles that normally originate from the superior parent. BSA data analysis is non-trivial due to sequencing, alignment and screening errors. Results To increase the power of the BSA technology and obtain a better distinction between spuriously and truly linked regions, we developed EXPLoRA (EXtraction of over-rePresented aLleles in BSA), an algorithm for BSA data analysis that explicitly models the dependency between neighboring marker sites by exploiting the properties of linkage disequilibrium through a Hidden Markov Model (HMM). Reanalyzing a BSA dataset for high ethanol tolerance in yeast allowed reliably identifying QTLs linked to this phenotype that could not be identified with statistical significance in the original study. Experimental validation of one of the least pronounced linked regions, by identifying its causative gene VPS70, confirmed the potential of our method. Conclusions EXPLoRA has a performance at least as good as the state-of-the-art and it is robust even at low signal to noise ratio’s i.e. when the true linkage signal is diluted by sampling, screening errors or when few segregants are available.
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Affiliation(s)
| | | | | | | | | | | | - Johan M Thevelein
- VIB Laboratory of Systems Biology & Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics, KU Leuven, Gaston Geenslaan 1, Leuven B-3001, Belgium.
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Revisiting Mortimer's Genome Renewal Hypothesis: heterozygosity, homothallism, and the potential for adaptation in yeast. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:37-48. [PMID: 24277294 DOI: 10.1007/978-94-007-7347-9_3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In diploid organisms, the frequency and nature of sexual cycles have a major impact on genome-wide patterns of heterozygosity. Recent population genomic surveys in the budding yeast, Saccharomyces cerevisiae, have revealed surprising levels of genomic heterozygosity in what has been traditionally considered a highly inbred organism. I review evidence and hypotheses regarding the generation, maintenance, and evolutionary consequences of genomic heterozygosity in S. cerevisiae. I propose that high levels of heterozygosity in S. cerevisiae, arising from population admixture due to human domestication, coupled with selfing during rare sexual cycles, can facilitate rapid adaptation to novel environments.
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Udatha DBRKG, Rasmussen S, Sicheritz-Pontén T, Panagiotou G. Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs). Methods Mol Biol 2013; 985:409-428. [PMID: 23417815 DOI: 10.1007/978-1-62703-299-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The non-synonymous SNPs, the so-called non-silent SNPs, which are single-nucleotide variations in the coding regions that give "birth" to amino acid mutations, are often involved in the modulation of protein function. Understanding the effect of individual amino acid mutations on a protein/enzyme function or stability is useful for altering its properties for a wide variety of engineering studies. Since measuring the effects of amino acid mutations experimentally is a laborious process, a variety of computational methods have been discussed here that aid to extract direct genotype to phenotype information.
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Affiliation(s)
- D B R K Gupta Udatha
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
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Morales L, Dujon B. Evolutionary role of interspecies hybridization and genetic exchanges in yeasts. Microbiol Mol Biol Rev 2012; 76:721-39. [PMID: 23204364 PMCID: PMC3510521 DOI: 10.1128/mmbr.00022-12] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Forced interspecific hybridization has been used in yeasts for many years to study speciation or to construct artificial strains with novel fermentative and metabolic properties. Recent genome analyses indicate that natural hybrids are also generated spontaneously between yeasts belonging to distinct species, creating lineages with novel phenotypes, varied genetic stability, or altered virulence in the case of pathogens. Large segmental introgressions from evolutionarily distant species are also visible in some yeast genomes, suggesting that interspecific genetic exchanges occur during evolution. The origin of this phenomenon remains unclear, but it is likely based on weak prezygotic barriers, limited Dobzhansky-Muller (DM) incompatibilities, and rapid clonal expansions. Newly formed interspecies hybrids suffer rapid changes in the genetic contribution of each parent, including chromosome loss or aneuploidy, translocations, and loss of heterozygosity, that, except in a few recently studied cases, remain to be characterized more precisely at the genomic level by use of modern technologies. We review here known cases of natural or artificially formed interspecies hybrids between yeasts and discuss their potential importance in terms of genome evolution. Problems of meiotic fertility, ploidy constraint, gene and gene product compatibility, and nucleomitochondrial interactions are discussed and placed in the context of other known mechanisms of yeast genome evolution as a model for eukaryotes.
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Affiliation(s)
- Lucia Morales
- Institut Pasteur, Unité de Génétique Moléculaire des Levures CNRS UMR3525, University Pierre and Marie Curie UFR927, Paris, France.
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Invertase SUC2 Is the key hydrolase for inulin degradation in Saccharomyces cerevisiae. Appl Environ Microbiol 2012; 79:403-6. [PMID: 23104410 DOI: 10.1128/aem.02658-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Specific Saccharomyces cerevisiae strains were recently found to be capable of efficiently utilizing inulin, but genetic mechanisms of inulin hydrolysis in yeast remain unknown. Here we report functional characteristics of invertase SUC2 from strain JZ1C and demonstrate that SUC2 is the key enzyme responsible for inulin metabolism in S. cerevisiae.
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Riccombeni A, Butler G. Role of Genomics and RNA-seq in Studies of Fungal Virulence. CURRENT FUNGAL INFECTION REPORTS 2012. [DOI: 10.1007/s12281-012-0104-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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