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Pinto J, Tavakolian N, Li CB, Stelkens R. The relationship between cell density and cell count differs among Saccharomyces yeast species. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001215. [PMID: 38863984 PMCID: PMC11165304 DOI: 10.17912/micropub.biology.001215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/07/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
There is a recent push to develop wild and non-domesticated Saccharomyces yeast strains into useful model systems for research in ecology and evolution. Yet, the variation between species and strains in important population parameters remains largely undescribed. Here, we investigated the relationship between two commonly used measures in microbiology to estimate growth rate - cell density and cell count - in 23 strains across all eight Saccharomyces species . We found that the slope of this relationship significantly differs among species and a given optical density (OD) does not translate into the same number of cells across species. We provide a cell number calculator based on our OD measurements for each strain used in this study. Surprisingly, we found a slightly positive relationship between cell size and the slope of the cell density-cell count relationship. Our results show that the strain- and species-specificity of the cell density and cell count relationship should be taken into account, for instance when running competition experiments requiring equal starting population sizes or when estimating the fitness of strains with different genetic backgrounds in experimental evolution studies.
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Affiliation(s)
- Javier Pinto
- Zoology Department, Stockholm University, Stockholm, Sweden
| | - Nik Tavakolian
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | - Chun-Biu Li
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | - Rike Stelkens
- Zoology Department, Stockholm University, Stockholm, Sweden
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2
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Tengölics R, Szappanos B, Mülleder M, Kalapis D, Grézal G, Sajben C, Agostini F, Mokochinski JB, Bálint B, Nagy LG, Ralser M, Papp B. The metabolic domestication syndrome of budding yeast. Proc Natl Acad Sci U S A 2024; 121:e2313354121. [PMID: 38457520 PMCID: PMC10945815 DOI: 10.1073/pnas.2313354121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/11/2023] [Indexed: 03/10/2024] Open
Abstract
Cellular metabolism evolves through changes in the structure and quantitative states of metabolic networks. Here, we explore the evolutionary dynamics of metabolic states by focusing on the collection of metabolite levels, the metabolome, which captures key aspects of cellular physiology. Using a phylogenetic framework, we profiled metabolites in 27 populations of nine budding yeast species, providing a graduated view of metabolic variation across multiple evolutionary time scales. Metabolite levels evolve more rapidly and independently of changes in the metabolic network's structure, providing complementary information to enzyme repertoire. Although metabolome variation accumulates mainly gradually over time, it is profoundly affected by domestication. We found pervasive signatures of convergent evolution in the metabolomes of independently domesticated clades of Saccharomyces cerevisiae. Such recurring metabolite differences between wild and domesticated populations affect a substantial part of the metabolome, including rewiring of the TCA cycle and several amino acids that influence aroma production, likely reflecting adaptation to human niches. Overall, our work reveals previously unrecognized diversity in central metabolism and the pervasive influence of human-driven selection on metabolite levels in yeasts.
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Affiliation(s)
- Roland Tengölics
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Szappanos
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Department of Biotechnology, University of Szeged, Szeged6726, Hungary
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility High-Throughput Mass Spectrometry, Berlin10117, Germany
| | - Dorottya Kalapis
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Gábor Grézal
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Csilla Sajben
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
| | - João Benhur Mokochinski
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Bálint
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - László G. Nagy
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, LondonNW11AT, United Kingdom
| | - Balázs Papp
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- National Laboratory for Health Security, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
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3
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Hannon-Hatfield JA, Chen J, Bergman CM, Garfinkel DJ. Evolution of a Restriction Factor by Domestication of a Yeast Retrotransposon. Mol Biol Evol 2024; 41:msae050. [PMID: 38442736 PMCID: PMC10951436 DOI: 10.1093/molbev/msae050] [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: 11/21/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024] Open
Abstract
Transposable elements drive genome evolution in all branches of life. Transposable element insertions are often deleterious to their hosts and necessitate evolution of control mechanisms to limit their spread. The long terminal repeat retrotransposon Ty1 prime (Ty1'), a subfamily of the Ty1 family, is present in many Saccharomyces cerevisiae strains, but little is known about what controls its copy number. Here, we provide evidence that a novel gene from an exapted Ty1' sequence, domesticated restriction of Ty1' relic 2 (DRT2), encodes a restriction factor that inhibits Ty1' movement. DRT2 arose through domestication of a Ty1' GAG gene and contains the C-terminal domain of capsid, which in the related Ty1 canonical subfamily functions as a self-encoded restriction factor. Bioinformatic analysis reveals the widespread nature of DRT2, its evolutionary history, and pronounced structural variation at the Ty1' relic 2 locus. Ty1' retromobility analyses demonstrate DRT2 restriction factor functionality, and northern blot and RNA-seq analysis indicate that DRT2 is transcribed in multiple strains. Velocity cosedimentation profiles indicate an association between Drt2 and Ty1' virus-like particles or assembly complexes. Chimeric Ty1' elements containing DRT2 retain retromobility, suggesting an ancestral role of productive Gag C-terminal domain of capsid functionality is present in the sequence. Unlike Ty1 canonical, Ty1' retromobility increases with copy number, suggesting that C-terminal domain of capsid-based restriction is not limited to the Ty1 canonical subfamily self-encoded restriction factor and drove the endogenization of DRT2. The discovery of an exapted Ty1' restriction factor provides insight into the evolution of the Ty1 family, evolutionary hot-spots, and host-transposable element interactions.
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Affiliation(s)
- J Adam Hannon-Hatfield
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Jingxuan Chen
- Institute of Bioinformatics, 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
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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5
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Kobayashi Y, Kayamori A, Aoki K, Shiwa Y, Matsutani M, Fujita N, Sugita T, Iwasaki W, Tanaka N, Takashima M. Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny. BMC Genomics 2023; 24:609. [PMID: 37821828 PMCID: PMC10568926 DOI: 10.1186/s12864-023-09718-2] [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: 06/15/2023] [Accepted: 10/05/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Since DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided fungal identification; however, a barcode sequence alone is often insufficient. Thus, multi-gene- or whole-genome-based methods were developed. We previously isolated Basidiomycota yeasts classified in the Trichosporonales. Some strains were described as Cutaneotrichosporon cavernicola and C. spelunceum, whereas strain HIS471 remained unidentified. We analysed the genomes of these strains to elucidate their taxonomic relationship and genetic diversity. RESULTS The long-read-based assembly resulted in chromosome-level draft genomes consisting of seven chromosomes and one mitochondrial genome. The genome of strain HIS471 has more than ten chromosome inversions or translocations compared to the type strain of C. cavernicola despite sharing identical ITS barcode sequences and displaying an average nucleotide identity (ANI) above 93%. Also, the chromosome synteny between C. cavernicola and the related species, C. spelunceum, showed significant rearrangements, whereas the ITS sequence identity exceeds 98.6% and the ANI is approximately 82%. Our results indicate that the relative evolutionary rates of barcode sequences, whole-genome nucleotide sequences, and chromosome synteny in Cutaneotrichosporon significantly differ from those in the model yeast Saccharomyces. CONCLUSIONS Our results revealed that the relative evolutionary rates of nucleotide sequences and chromosome synteny are different among fungal clades, likely because different clades have diverse mutation/repair rates and distinct selection pressures on their genomic sequences and syntenic structures. Because diverse syntenic structures can be a barrier to meiotic recombination and may lead to speciation, the non-linear relationships between nucleotide and synteny diversification indicate that sequence-level distances at the barcode or whole-genome level are not sufficient for delineating species boundaries.
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Affiliation(s)
- Yuuki Kobayashi
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
| | - Ayane Kayamori
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Keita Aoki
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Nobuyuki Fujita
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Masako Takashima
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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6
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Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Tanifuji G, Kamikawa R, Nakamura Y. A practical assembly guideline for genomes with various levels of heterozygosity. Brief Bioinform 2023; 24:bbad337. [PMID: 37798248 PMCID: PMC10555665 DOI: 10.1093/bib/bbad337] [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: 05/17/2023] [Revised: 08/06/2023] [Accepted: 09/03/2023] [Indexed: 10/07/2023] Open
Abstract
Although current long-read sequencing technologies have a long-read length that facilitates assembly for genome reconstruction, they have high sequence errors. While various assemblers with different perspectives have been developed, no systematic evaluation of assemblers with long reads for diploid genomes with varying heterozygosity has been performed. Here, we evaluated a series of processes, including the estimation of genome characteristics such as genome size and heterozygosity, de novo assembly, polishing, and removal of allelic contigs, using six genomes with various heterozygosity levels. We evaluated five long-read-only assemblers (Canu, Flye, miniasm, NextDenovo and Redbean) and five hybrid assemblers that combine short and long reads (HASLR, MaSuRCA, Platanus-allee, SPAdes and WENGAN) and proposed a concrete guideline for the construction of haplotype representation according to the degree of heterozygosity, followed by polishing and purging haplotigs, using stable and high-performance assemblers: Redbean, Flye and MaSuRCA.
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Affiliation(s)
| | - Mika Sakamoto
- Genome Informatics Laboratory, National Institute of Genetics
| | | | - Takuro Nakayama
- Division of Life Sciences Center for Computational Sciences, University of Tsukuba, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science
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7
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O'Donnell S, Yue JX, Saada OA, Agier N, Caradec C, Cokelaer T, De Chiara M, Delmas S, Dutreux F, Fournier T, Friedrich A, Kornobis E, Li J, Miao Z, Tattini L, Schacherer J, Liti G, Fischer G. Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae. Nat Genet 2023; 55:1390-1399. [PMID: 37524789 PMCID: PMC10412453 DOI: 10.1038/s41588-023-01459-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
Pangenomes provide access to an accurate representation of the genetic diversity of species, both in terms of sequence polymorphisms and structural variants (SVs). Here we generated the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing the species' phylogenetic and ecological diversity. The ScRAP includes phased haplotype assemblies for several heterozygous diploid and polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that provide a broad view of the genomic diversity, including the dynamics of telomere length and transposable elements. We uncovered frequent cases of complex aneuploidies where large chromosomes underwent large deletions and translocations. We found that SVs can impact gene expression near the breakpoints and substantially contribute to gene repertoire evolution. We also discovered that horizontally acquired regions insert at chromosome ends and can generate new telomeres. Overall, the ScRAP demonstrates the benefit of a pangenome in understanding genome evolution at population scale.
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Affiliation(s)
- Samuel O'Donnell
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Nicolas Agier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Thomas Cokelaer
- Biomics Technological Platform, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
- Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, Paris, France
| | | | - Stéphane Delmas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Téo Fournier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Etienne Kornobis
- Biomics Technological Platform, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
- Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, Paris, France
| | - Jing Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Zepu Miao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | | | | | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
| | - Gilles Fischer
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France.
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8
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Weller CA, Andreev I, Chambers MJ, Park M, Bloom JS, Sadhu MJ. Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity. Genome Res 2023; 33:729-740. [PMID: 37127330 PMCID: PMC10317115 DOI: 10.1101/gr.277515.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
Understanding the genetic causes of trait variation is a primary goal of genetic research. One way that individuals can vary genetically is through variable pangenomic genes: genes that are only present in some individuals in a population. The presence or absence of entire genes could have large effects on trait variation. However, variable pangenomic genes can be missed in standard genotyping workflows, owing to reliance on aligning short-read sequencing to reference genomes. A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the genome that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting myriad yeast phenotypes. To enable the resolution of QTLs caused by variable pangenomic genes, we used long-read sequencing to generate highly complete de novo genome assemblies of 16 diverse yeast isolates. With these assemblies, we resolved QTLs for growth on maltose, sucrose, raffinose, and oxidative stress to specific genes that are absent from the reference genome but present in the broader yeast population at appreciable frequency. Copies of genes also duplicate onto chromosomes where they are absent in the reference genome, and we found that these copies generate additional QTLs whose resolution requires pangenome characterization. Our findings show the need for highly complete genome assemblies to identify the genetic basis of trait variation.
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Affiliation(s)
- Cory A Weller
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ilya Andreev
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael J Chambers
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Morgan Park
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
- Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Meru J Sadhu
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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9
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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: 11] [Impact Index Per Article: 11.0] [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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10
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Villarreal P, Villarroel CA, O'Donnell S, Agier N, Quintero-Galvis JF, Peña TA, Nespolo RF, Fischer G, Varela C, Cubillos FA. Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri. Environ Microbiol 2022; 24:5615-5629. [PMID: 35769023 DOI: 10.1111/1462-2920.16103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 01/12/2023]
Abstract
Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles. Lachancea cidri is an ideal yeast model for exploring the interplay between genetics, ecological function and evolution. Lachancea cidri diverged from the Saccharomyces lineage before the whole-genome duplication and is distributed across the South Hemisphere, displaying an important ecological success. We applied phylogenomics to investigate the genetic variation of L. cidri isolates obtained from Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggests that SoAm and Aus lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA). Interestingly, we found that the French reference strain is closely related to the Australian strains, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, we identified different lineages within the South American population, revealing that Patagonia contains a similar genetic diversity comparable to that of other lineages in S. cerevisiae. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favoured the extensive distribution of L. cidri in Patagonia.
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Affiliation(s)
- Pablo Villarreal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Carlos A Villarroel
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile
| | - Sam O'Donnell
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Julian F Quintero-Galvis
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Tomas A Peña
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Roberto F Nespolo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago, Chile.,Millenium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Cristian Varela
- The Australian Wine Research Institute, Glen Osmond, Adelaide, South Australia, Australia.,Department of Wine and Food Science, University of Adelaide, Glen Osmond, Adelaide, South Australia, Australia
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Millenium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
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11
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Salzberg LI, Martos AAR, Lombardi L, Jermiin LS, Blanco A, Byrne KP, Wolfe KH. A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family. PLoS Genet 2022; 18:e1010525. [PMID: 36441813 PMCID: PMC9731477 DOI: 10.1371/journal.pgen.1010525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/08/2022] [Accepted: 11/12/2022] [Indexed: 11/29/2022] Open
Abstract
Saccharomyces genomes are highly collinear and show relatively little structural variation, both within and between species of this yeast genus. We investigated the only common inversion polymorphism known in S. cerevisiae, which affects a 24-kb 'flip/flop' region containing 15 genes near the centromere of chromosome XIV. The region exists in two orientations, called reference (REF) and inverted (INV). Meiotic recombination in this region is suppressed in crosses between REF and INV orientation strains such as the BY x RM cross. We find that the inversion polymorphism is at least 17 million years old because it is conserved across the genus Saccharomyces. However, the REF and INV isomers are not ancient alleles but are continually being re-created by re-inversion of the region within each species. Inversion occurs due to continual homogenization of two almost identical 4-kb sequences that form an inverted repeat (IR) at the ends of the flip/flop region. The IR consists of two pairs of genes that are specifically and strongly expressed during the late stages of sporulation. We show that one of these gene pairs, YNL018C/YNL034W, codes for a protein that is essential for spore formation. YNL018C and YNL034W are the founder members of a gene family, Centroid, whose members in other Saccharomycetaceae species evolve fast, duplicate frequently, and are preferentially located close to centromeres. We tested the hypothesis that Centroid genes are a meiotic drive system, but found no support for this idea.
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Affiliation(s)
- Letal I. Salzberg
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Alexandre A. R. Martos
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Lisa Lombardi
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Lars S. Jermiin
- School of Medicine, University College Dublin, Dublin, Ireland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Alfonso Blanco
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Kevin P. Byrne
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H. Wolfe
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
- * E-mail:
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12
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Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Riffo FC, Dashko S, Dimitrov R, Fisher KJ, Gibson BR, Gouliamova D, Greig D, Heistinger L, Hittinger CT, Jecmenica M, Koufopanou V, Landry CR, Mašínová T, Naumova ES, Opulente D, Peña JJ, Petrovič U, Tsai IJ, Turchetti B, Villarreal P, Yurkov A, Liti G, Boynton P. Yeasts from temperate forests. Yeast 2022; 39:4-24. [PMID: 35146791 DOI: 10.1002/yea.3699] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.
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Affiliation(s)
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Graham Bell
- Biology Department and Redpath Museum, McGill University, Québec, Canada
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Neža Čadež
- Biotechnical Faculty, Food Science and Technology Department, University of Ljubljana, Ljubljana, Slovenia
| | - Francisco Cubillos Riffo
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sofia Dashko
- DSM Food Specialties, Center for Food Innovation, AX, Delft, The Netherlands
| | - Roumen Dimitrov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kaitlin J Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian R Gibson
- Technische Universität Berlin, Institute of Food Technology and Food Chemistry, Chair of Brewing and Beverage Technology, Berlin, Germany
| | - Dilnora Gouliamova
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Duncan Greig
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Lina Heistinger
- ETH Zurich, Department of Biology, Institute of Biochemistry, Switzerland
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Canada.,PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Canada.,Centre de Recherche sur les Données Massives, Université Laval, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Canada
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dana Opulente
- Department of Biology, Villanova University, Villanova, Pennsylvania, USA
| | | | - Uroš Petrovič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia.,Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Ljubljana, Slovenia
| | | | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Pablo Villarreal
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
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13
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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:genes13020230. [PMID: 35205274 PMCID: PMC8871604 DOI: 10.3390/genes13020230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [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
- Correspondence: ; Tel.: +86-10-6480-7406
| | - 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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14
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He PY, Shao XQ, Duan SF, Han DY, Li K, Shi JY, Zhang RP, Han PJ, Wang QM, Bai FY. Highly diverged lineages of Saccharomyces paradoxus in temperate to subtropical climate zones in China. Yeast 2021; 39:69-82. [PMID: 34961959 DOI: 10.1002/yea.3688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/06/2022] Open
Abstract
The wild yeast Saccharomyces paradoxus has become a new model in ecology and evolutionary biology. Different lineages of S. paradoxus have been recognized across the world, but the distribution and genetic diversity of the species remain unknown in China, where the origin of its sibling species S. cerevisiae lies. In this study, we investigated the ecological and geographic distribution of S. paradoxus through an extensive field survey in China and performed population genomic analysis on a set of S. paradoxus strains, including 27 strains, representing different geographic and ecological origins within China, and 59 strains representing all the known lineages of the species recognized in the other regions of the world so far. We found two distinct lineages of S. paradoxus in China. The majority of the Chinese strains studied belong to the Far East lineage, and six strains belong to a novel highly diverged lineage. The distribution of these two lineages overlaps ecologically and geographically in temperate to subtropical climate zones in China. With the addition of the new China lineage, the Eurasian population of S. paradoxus exhibits higher genetic diversity than the American population. We observed more possible lineage-specific introgression events from the Eurasian lineages than from the American lineages. Our results expand the knowledge on ecology, genetic diversity, biogeography, and evolution of S. paradoxus.
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Affiliation(s)
- Peng-Yu He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Qian Shao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Genetic Engineering Division, China National Intellectual Property Administration (CNIPA), Beijing, China
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun-Yan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ri-Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Pei-Jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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15
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Bendixsen DP, Frazão JG, Stelkens R. Saccharomyces yeast hybrids on the rise. Yeast 2021; 39:40-54. [PMID: 34907582 DOI: 10.1002/yea.3684] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/19/2021] [Accepted: 12/08/2021] [Indexed: 12/23/2022] Open
Abstract
Saccharomyces hybrid yeasts are receiving increasing attention as a powerful model system to understand adaptation to environmental stress and speciation mechanisms, using experimental evolution and omics techniques. We compiled all genomic resources available from public repositories of the eight recognized Saccharomyces species and their interspecific hybrids. We present the newest numbers on genomes sequenced, assemblies, annotations, and sequencing runs, and an updated species phylogeny using orthogroup inference. While genomic resources are highly skewed towards Saccharomyces cerevisiae, there is a noticeable movement to use wild, recently discovered yeast species in recent years. To illustrate the degree and potential causes of reproductive isolation, we reanalyzed published data on hybrid spore viabilities across the entire genus and tested for the role of genetic, geographic, and ecological divergence within and between species (28 cross types and 371 independent crosses). Hybrid viability generally decreased with parental genetic distance likely due to antirecombination and negative epistasis, but notable exceptions emphasize the importance of strain-specific structural variation and ploidy differences. Surprisingly, the viability of crosses within species varied widely, from near reproductive isolation to near-perfect viability. Geographic and ecological origins of the parents predicted cross viability to an extent, but with certain caveats. Finally, we highlight publication trends in the field and point out areas of special interest, where hybrid yeasts are particularly promising for innovation through research and development, and experimental evolution and fermentation.
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Affiliation(s)
- Devin P Bendixsen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - João G Frazão
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
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16
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Bendixsen DP, Peris D, Stelkens R. Patterns of Genomic Instability in Interspecific Yeast Hybrids With Diverse Ancestries. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:742894. [PMID: 37744091 PMCID: PMC10512264 DOI: 10.3389/ffunb.2021.742894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 09/26/2023]
Abstract
The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains, and losses. This plastic genomic architecture generates phenotypic diversity, potentially giving hybrids access to new ecological niches. It is however unclear if there are any generalizable patterns and predictability in the type and prevalence of genomic variation and instability across hybrids with different genetic and ecological backgrounds. Here, we analyzed the genomic architecture of 204 interspecific Saccharomyces yeast hybrids isolated from natural, industrial fermentation, clinical, and laboratory environments. Synchronous mapping to all eight putative parental species showed significant variation in read depth indicating frequent aneuploidy, affecting 44% of all hybrid genomes and particularly smaller chromosomes. Early generation hybrids with largely equal genomic content from both parent species were more likely to contain aneuploidies than introgressed genomes with an older hybridization history, which presumably stabilized the genome. Shared k-mer analysis showed that the degree of genomic diversity and variability varied among hybrids with different parent species. Interestingly, more genetically distant crosses produced more similar hybrid genomes, which may be a result of stronger negative epistasis at larger genomic divergence, putting constraints on hybridization outcomes. Mitochondrial genomes were typically inherited from the species also contributing the majority nuclear genome, but there were clear exceptions to this rule. Together, we find reliable genomic predictors of instability in hybrids, but also report interesting cross- and environment-specific idiosyncrasies. Our results are an important step in understanding the factors shaping divergent hybrid genomes and their role in adaptive evolution.
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Affiliation(s)
- Devin P. Bendixsen
- Population Genetics Division, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Health, Valencian International University, Valencia, Spain
| | - Rike Stelkens
- Population Genetics Division, Department of Zoology, Stockholm University, Stockholm, Sweden
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17
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Bleykasten-Grosshans C, Fabrizio R, Friedrich A, Schacherer J. Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host. Mol Biol Evol 2021; 38:4334-4345. [PMID: 34115140 PMCID: PMC8476168 DOI: 10.1093/molbev/msab171] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Transposable elements (TE) are an important source of genetic variation with a dynamic and content that greatly differ in a wide range of species. The origin of the intraspecific content variation is not always clear and little is known about the precise nature of it. Here, we surveyed the species-wide content of the Ty LTR-retrotransposons in a broad collection of 1,011 Saccharomyces cerevisiae natural isolates to understand what can stand behind the variation of the repertoire that is the type and number of Ty elements. We have compiled an exhaustive catalog of all the TE sequence variants present in the S. cerevisiae species by identifying a large set of new sequence variants. The characterization of the TE content in each isolate clearly highlighted that each subpopulation exhibits a unique and specific repertoire, retracing the evolutionary history of the species. Most interestingly, we have shown that ancient interspecific hybridization events had a major impact in the birth of new sequence variants and therefore in the shaping of the TE repertoires. We also investigated the transpositional activity of these elements in a large set of natural isolates, and we found a broad variability related to the level of ploidy as well as the genetic background. Overall, our results pointed out that the evolution of the Ty content is deeply impacted by clade-specific events such as introgressions and therefore follows the population structure. In addition, our study lays the foundation for future investigations to better understand the transpositional regulation and more broadly the TE–host interactions.
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Affiliation(s)
| | - Romeo Fabrizio
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF)
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Gorkovskiy A, Verstrepen KJ. The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. Genes (Basel) 2021; 12:699. [PMID: 34066718 PMCID: PMC8150848 DOI: 10.3390/genes12050699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.
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Affiliation(s)
- Anton Gorkovskiy
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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