1
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Seike T, Niki H. Pheromone Response and Mating Behavior in Fission Yeast. Microbiol Mol Biol Rev 2022; 86:e0013022. [PMID: 36468849 PMCID: PMC9769774 DOI: 10.1128/mmbr.00130-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Most ascomycete fungi, including the fission yeast Schizosaccharomyces pombe, secrete two peptidyl mating pheromones: C-terminally modified and unmodified peptides. S. pombe has two mating types, plus and minus, which secrete two different pheromones, P-factor (unmodified) and M-factor (modified), respectively. These pheromones are specifically recognized by receptors on the cell surface of cells of opposite mating types, which trigger a pheromone response. Recognition between pheromones and their corresponding receptors is important for mate discrimination; therefore, genetic changes in pheromone or receptor genes affect mate recognition and cause reproductive isolation that limits gene flow between populations. Such genetic variation in recognition via the pheromone/receptor system may drive speciation. Our recent studies reported that two pheromone receptors in S. pombe might have different stringencies in pheromone recognition. In this review, we focus on the molecular mechanism of pheromone response and mating behavior, emphasizing pheromone diversification and its impact on reproductive isolation in S. pombe and closely related fission yeast species. We speculate that the "asymmetric" system might allow flexible adaptation to pheromone mutational changes while maintaining stringent recognition of mating partners. The loss of pheromone activity results in the extinction of an organism's lineage. Therefore, genetic changes in pheromones and their receptors may occur gradually and/or coincidently before speciation. Our findings suggest that the M-factor plays an important role in partner discrimination, whereas P-factor communication allows flexible adaptation to create variations in S. pombe. Our inferences provide new insights into the evolutionary mechanisms underlying pheromone diversification.
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Affiliation(s)
- Taisuke Seike
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
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2
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Chou JY, Hsu PC, Leu JY. Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. Microbiol Mol Biol Rev 2022; 86:e0009822. [PMID: 36098649 PMCID: PMC9769731 DOI: 10.1128/mmbr.00098-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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3
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Wang Y, Wang Q, Wu Z, Han GZ. Segregating Complete Tf2 Elements Are Largely Neutral in Fission Yeast. Genome Biol Evol 2021; 13:6430117. [PMID: 34791222 PMCID: PMC8634392 DOI: 10.1093/gbe/evab254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2021] [Indexed: 11/14/2022] Open
Abstract
Transposable elements (TEs) comprise a large proportion of the eukaryote genomes. Yet it remains poorly understood how TEs influence the fitness of the hosts carrying them. Here, we empirically test the impact of TEs on the host fitness in the fission yeast Schizosaccharomyces pombe. We find that two families of TEs (Tf1 and Tf2 elements), both of which belong to long terminal repeat retrotransposons, are highly polymorphic among individual S. pombe strains. Only 13 complete Tf2 elements are identified in S. pombe laboratory strain 972. These 13 Tf2 elements integrated into host genomes in very recent time and are segregating within the S. pombe population. Through knocking out each of the 13 Tf2 elements in S. pombe strain 972, we find Tf2 knockout does not affect the host fitness, and Tf2 elements do not alter the expression of nearby genes. Challenged by diverse forms of stress, the Tf2 knockout strains do not exhibit different growth rates from wild-type strain. Together, we conclude that segregating complete Tf2 elements insertions are largely neutral to host fitness in the fission yeast. Our study provides genome-wide empirical support for the selfish nature of TEs in fission yeast.
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Affiliation(s)
- Yan Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qin Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhiwei Wu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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4
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Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection. J Fungi (Basel) 2021; 7:jof7100864. [PMID: 34682285 PMCID: PMC8537764 DOI: 10.3390/jof7100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Our results provided evidence that the structural and sequence evolution of the fission yeasts were correlated. Moreover, we revealed ancestral locally collinear blocks (aLCBs), which could have been inherited from their last common ancestor. These aLCBs proved to be the most conserved regions of the genomes as the aLCBs contain almost eight genes/blocks on average in the same orientation and order across the species. Gene order of the aLCBs is mainly fission-yeast-specific but supports the idea of filamentous ancestors. Nevertheless, the sequences and gene structures within the aLCBs are as mutable as any sequences in other parts of the genomes. Although genes of certain Gene Ontology (GO) categories tend to cluster at the aLCBs, those GO enrichments are not related to biological functions or high co-expression rates, they are, rather, determined by the density of essential genes and Rec12 cleavage sites. These data and our simulations indicated that aLCBs might not only be remnants of ancestral gene order but are also maintained by natural selection.
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5
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Variables Influencing Differences in Sequence Conservation in the Fission Yeast Schizosaccharomyces pombe. J Mol Evol 2021; 89:601-610. [PMID: 34436628 PMCID: PMC8599406 DOI: 10.1007/s00239-021-10028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Which variables determine the constraints on gene sequence evolution is one of the most central questions in molecular evolution. In the fission yeast Schizosaccharomyces pombe, an important model organism, the variables influencing the rate of sequence evolution have yet to be determined. Previous studies in other single celled organisms have generally found gene expression levels to be most significant, with numerous other variables such as gene length and functional importance identified as having a smaller impact. Using publicly available data, we used partial least squares regression, principal components regression, and partial correlations to determine the variables most strongly associated with sequence evolution constraints. We identify centrality in the protein–protein interactions network, amino acid composition, and cellular location as the most important determinants of sequence conservation. However, each factor only explains a small amount of variance, and there are numerous variables having a significant or heterogeneous influence. Our models explain more than half of the variance in dN, raising the possibility that future refined models could quantify the role of stochastics in evolutionary rate variation.
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6
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Hanson SJ, Cinnéide EÓ, Salzberg LI, Wolfe KH, McGowan J, Fitzpatrick DA, Matlin K. Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex. G3 (BETHESDA, MD.) 2021; 11:jkab211. [PMID: 34849824 PMCID: PMC8496258 DOI: 10.1093/g3journal/jkab211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022]
Abstract
The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.
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Affiliation(s)
- Sara J Hanson
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Eoin Ó Cinnéide
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Letal I Salzberg
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Kate Matlin
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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7
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Gounot JS, Neuvéglise C, Freel KC, Devillers H, Piškur J, Friedrich A, Schacherer J. High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population. Genome Biol Evol 2021; 12:795-807. [PMID: 32302403 PMCID: PMC7313668 DOI: 10.1093/gbe/evaa077] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype–phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to characterize at the population level the Brettanomyces bruxellensis yeast species, which is a major cause of wine spoilage and can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.
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Affiliation(s)
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Kelle C Freel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jure Piškur
- Department of Biology, Lund University, Sweden
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF)
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8
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The rate and molecular spectrum of mutation are selectively maintained in yeast. Nat Commun 2021; 12:4044. [PMID: 34193872 PMCID: PMC8245649 DOI: 10.1038/s41467-021-24364-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022] Open
Abstract
What determines the rate (μ) and molecular spectrum of mutation is a fundamental question. The prevailing hypothesis asserts that natural selection against deleterious mutations has pushed μ to the minimum achievable in the presence of genetic drift, or the drift barrier. Here we show that, contrasting this hypothesis, μ substantially exceeds the drift barrier in diverse organisms. Random mutation accumulation (MA) in yeast frequently reduces μ, and deleting the newly discovered mutator gene PSP2 nearly halves μ. These results, along with a comparison between the MA and natural yeast strains, demonstrate that μ is maintained above the drift barrier by stabilizing selection. Similar comparisons show that the mutation spectrum such as the universal AT mutational bias is not intrinsic but has been selectively preserved. These findings blur the separation of mutation from selection as distinct evolutionary forces but open the door to alleviating mutagenesis in various organisms by genome editing. How natural selection shapes the rate and molecular spectrum of mutations is debated. Yeast mutation accumulation experiments identify a gene promoting mutagenesis and show stabilizing selection maintaining the mutation rate above the drift barrier. Selection also preserves the mutation spectrum.
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9
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Kovár M, Navrátilová A, Trakovická A, Požgajová M. Ascorbic acid supplementation suppresses cadmium-derived alterations in the fission yeast Schizosaccharomyces pombe. POTRAVINARSTVO 2021. [DOI: 10.5219/1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cadmium (Cd) a highly toxic environmental pollutant, that does not have any physiological function in the organism, represents a great concern for human health as it can be easily transported from its environmental sources to the food chain. Food, water, and air are the major sources of Cd exposure to the population. Cd-mediated impairments of the basic cellular properties largely depend on its ability to enhance the formation of reactive oxygen species (ROS) and thus triggers oxidative stress to the cell. With the use of fission yeast Schizosaccharomyces pombe (S. pombe) as the model organism, we have analyzed the impact of Cd on the cell growth intensity, as it represents the fundamental feature of all living organisms. Cells were incubated with different Cd concentrations for 3, 6, and 9 hours to investigate the effect of Cd on cell growth in a time and dose-dependent manner. Further possible Cd-derived alterations, as the peroxidation of membrane lipids or the functional impairment of the enzymatic antioxidant protection mechanisms, were investigated by determination of the MDA content and via catalase (CAT) activity detection. Moreover, ascorbic acid (AsA) pre-treatment was subjected to investigate the assumed positive effect of AsA against Cd toxicity. We show here on one hand that cells suffer under the influence of Cd, but on the other hand, they substantially profit from AsA supplementation. Because S. pombe is known to shares many molecular, and biochemical similarities with higher organisms, the effect of AsA in cadmium toxicity elimination might be expected to a similar extent also in other cell types.
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10
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Basile A, De Pascale F, Bianca F, Rossi A, Frizzarin M, De Bernardini N, Bosaro M, Baldisseri A, Antoniali P, Lopreiato R, Treu L, Campanaro S. Large-scale sequencing and comparative analysis of oenological Saccharomyces cerevisiae strains supported by nanopore refinement of key genomes. Food Microbiol 2021; 97:103753. [PMID: 33653526 DOI: 10.1016/j.fm.2021.103753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/09/2020] [Accepted: 01/27/2021] [Indexed: 12/30/2022]
Abstract
Saccharomyces cerevisiae has long been part of human activities related to the production of food and wine. The industrial demand for fermented beverages with well-defined and stable characteristics boosted the isolation and selection of strains conferring a distinctive aroma profile to the final product. To uncover variants characterizing oenological strains, the sequencing of 65 new S. cerevisiae isolates, and the comparison with other 503 publicly available genomes were performed. A hybrid approach based on short Illumina and long Oxford Nanopore reads allowed the in-depth investigation of eleven genomes and the identification of putative laterally transferred regions and structural variants. A comparative analysis between clusters of strains belonging to different datasets allowed the identification of novel relevant genetic features including single nucleotide polymorphisms, insertions and structural variants. Detection of oenological single nucleotide variants shed light on the existence of different levels of modulation for the mevalonate pathway relevant for the biosynthesis of aromatic compounds.
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Affiliation(s)
- Arianna Basile
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Fabio De Pascale
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Federico Bianca
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Alessandro Rossi
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Martina Frizzarin
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy; Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | | | - Matteo Bosaro
- Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | - Anna Baldisseri
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy
| | - Paolo Antoniali
- Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | - Raffaele Lopreiato
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, 35131, Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, 35131, Padova, Italy; CRIBI Biotechnology Center, University of Padua, 35121, Padova, Italy
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11
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Sidorova A, Tverdislov V, Levashova N, Garaeva A. A model of autowave self-organization as a hierarchy of active media in the biological evolution. Biosystems 2020; 198:104234. [PMID: 32889101 DOI: 10.1016/j.biosystems.2020.104234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 11/28/2022]
Abstract
Within the framework of the active media concept, we develop a biophysical model of autowave self-organization which is treated as a hierarchy of active media in the evolution of the biosphere. We also propose a mathematical model of the autowave process of speciation in a flow of mutations for the three main taxonometric groups (prokaryotes, unicellular and multicellular eukaryotes) with a naturally determined lower boundary of living matter (the appearance of prokaryotes) and an open upper boundary for the formation of new species. It is shown that the fluctuation-bifurcation description of the evolution for the formation of new taxonometric groups as a trajectory of transformation of small fluctuations into giant ones adequately reflects the process of self-organization during the formation of taxa. The major concepts of biological evolution, conditions of hierarchy formation as a fundamental manifestation of self-organization and complexity in the evolution of biological systems are considered.
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Affiliation(s)
- Alla Sidorova
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Vsevolod Tverdislov
- Head of the Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Natalia Levashova
- Department of Mathematics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Anastasia Garaeva
- Postgraduate Student of the Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
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12
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Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum. G3-GENES GENOMES GENETICS 2020; 10:3445-3452. [PMID: 32732307 PMCID: PMC7466956 DOI: 10.1534/g3.120.401578] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium discoideum, a key model organism in molecular, cellular, evolutionary and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10−11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in D. discoideum are highly A/T biased. This bias likely contributes both to the high genomic AT content and to the formation of simple sequence repeats in the AT-rich genome of Dictyostelium discoideum. In contrast to the situation in other surveyed unicellular eukaryotes, indel rates far exceed the base-substitution mutation rate in this organism with a high proportion of 3n indels, particularly in regions without simple sequence repeats. Like ciliates, D. discoideum has a large effective population size, reducing the power of random genetic drift, magnifying the effect of selection on replication fidelity, in principle allowing D. discoideum to evolve an extremely low base-substitution mutation rate.
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13
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Bravo Núñez MA, Sabbarini IM, Eide LE, Unckless RL, Zanders SE. Atypical meiosis can be adaptive in outcrossed Schizosaccharomyces pombe due to wtf meiotic drivers. eLife 2020; 9:57936. [PMID: 32790622 PMCID: PMC7426094 DOI: 10.7554/elife.57936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
Killer meiotic drivers are genetic parasites that destroy ‘sibling’ gametes lacking the driver allele. The fitness costs of drive can lead to selection of unlinked suppressors. This suppression could involve evolutionary tradeoffs that compromise gametogenesis and contribute to infertility. Schizosaccharomyces pombe, an organism containing numerous gamete (spore)-killing wtf drivers, offers a tractable system to test this hypothesis. Here, we demonstrate that in scenarios analogous to outcrossing, wtf drivers generate a fitness landscape in which atypical spores, such as aneuploids and diploids, are advantageous. In this context, wtf drivers can decrease the fitness costs of mutations that disrupt meiotic fidelity and, in some circumstances, can even make such mutations beneficial. Moreover, we find that S. pombe isolates vary greatly in their ability to make haploid spores, with some isolates generating up to 46% aneuploid or diploid spores. This work empirically demonstrates the potential for meiotic drivers to shape the evolution of gametogenesis.
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Affiliation(s)
| | | | - Lauren E Eide
- Stowers Institute for Medical Research, Kansas City, United States.,University of Missouri-Kansas City, Kansas City, United States
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, United States
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14
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Adaptation to Industrial Stressors Through Genomic and Transcriptional Plasticity in a Bioethanol Producing Fission Yeast Isolate. G3-GENES GENOMES GENETICS 2020; 10:1375-1391. [PMID: 32086247 PMCID: PMC7144085 DOI: 10.1534/g3.119.400986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Schizosaccharomyces pombe is a model unicellular eukaryote with ties to the basic research, oenology and industrial biotechnology sectors. While most investigations into S. pombe cell biology utilize Leupold’s 972h- laboratory strain background, recent studies have described a wealth of genetic and phenotypic diversity within wild populations of S. pombe including stress resistance phenotypes which may be of interest to industry. Here we describe the genomic and transcriptomic characterization of Wilmar-P, an S. pombe isolate used for bioethanol production from sugarcane molasses at industrial scale. Novel sequences present in Wilmar-P but not in the laboratory S. pombe genome included multiple coding sequences with near-perfect nucleotide identity to Schizosaccharomyces octosporus sequences. Wilmar-P also contained a ∼100kb duplication in the right arm of chromosome III, a region harboring ght5+, the predominant hexose transporter encoding gene. Transcriptomic analysis of Wilmar-P grown in molasses revealed strong downregulation of core environmental stress response genes and upregulation of hexose transporters and drug efflux pumps compared to laboratory S. pombe. Finally, examination of the regulatory network of Scr1, which is involved in the regulation of several genes differentially expressed on molasses, revealed expanded binding of this transcription factor in Wilmar-P compared to laboratory S. pombe in the molasses condition. Together our results point to both genomic plasticity and transcriptomic adaptation as mechanisms driving phenotypic adaptation of Wilmar-P to the molasses environment and therefore adds to our understanding of genetic diversity within industrial fission yeast strains and the capacity of this strain for commercial scale bioethanol production.
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15
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Tao YT, Suo F, Tusso S, Wang YK, Huang S, Wolf JBW, Du LL. Intraspecific Diversity of Fission Yeast Mitochondrial Genomes. Genome Biol Evol 2020; 11:2312-2329. [PMID: 31364709 PMCID: PMC6736045 DOI: 10.1093/gbe/evz165] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.
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Affiliation(s)
- Yu-Tian Tao
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Science for Life Laboratories, Department of Evolutionary Biology, Uppsala University, Sweden
| | - Yan-Kai Wang
- National Institute of Biological Sciences, Beijing, China
| | - Song Huang
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Science for Life Laboratories, Department of Evolutionary Biology, Uppsala University, Sweden
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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16
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Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast. Mol Biol Evol 2019; 36:1975-1989. [PMID: 31225876 PMCID: PMC6736153 DOI: 10.1093/molbev/msz126] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.
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Affiliation(s)
- Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - John W Davey
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Daniel C Jeffares
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute (YBRI), University of York, York, United Kingdom
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
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17
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Grech L, Jeffares DC, Sadée CY, Rodríguez-López M, Bitton DA, Hoti M, Biagosch C, Aravani D, Speekenbrink M, Illingworth CJR, Schiffer PH, Pidoux AL, Tong P, Tallada VA, Allshire R, Levin HL, Bähler J. Fitness Landscape of the Fission Yeast Genome. Mol Biol Evol 2019; 36:1612-1623. [PMID: 31077324 PMCID: PMC6657727 DOI: 10.1093/molbev/msz113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The relationship between DNA sequence, biochemical function, and molecular evolution is relatively well-described for protein-coding regions of genomes, but far less clear in noncoding regions, particularly, in eukaryote genomes. In part, this is because we lack a complete description of the essential noncoding elements in a eukaryote genome. To contribute to this challenge, we used saturating transposon mutagenesis to interrogate the Schizosaccharomyces pombe genome. We generated 31 million transposon insertions, a theoretical coverage of 2.4 insertions per genomic site. We applied a five-state hidden Markov model (HMM) to distinguish insertion-depleted regions from insertion biases. Both raw insertion-density and HMM-defined fitness estimates showed significant quantitative relationships to gene knockout fitness, genetic diversity, divergence, and expected functional regions based on transcription and gene annotations. Through several analyses, we conclude that transposon insertions produced fitness effects in 66-90% of the genome, including substantial portions of the noncoding regions. Based on the HMM, we estimate that 10% of the insertion depleted sites in the genome showed no signal of conservation between species and were weakly transcribed, demonstrating limitations of comparative genomics and transcriptomics to detect functional units. In this species, 3'- and 5'-untranslated regions were the most prominent insertion-depleted regions that were not represented in measures of constraint from comparative genomics. We conclude that the combination of transposon mutagenesis, evolutionary, and biochemical data can provide new insights into the relationship between genome function and molecular evolution.
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Affiliation(s)
- Leanne Grech
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Daniel C Jeffares
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Biology and York Biomedical Research Institute, University of York, United Kingdom
| | - Christoph Y Sadée
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - María Rodríguez-López
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Danny A Bitton
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Mimoza Hoti
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Carolina Biagosch
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Dimitra Aravani
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | | | | | - Philipp H Schiffer
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alison L Pidoux
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Pin Tong
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Victor A Tallada
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Robin Allshire
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Henry L Levin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jürg Bähler
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
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18
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Abstract
Natural selection works best when the two alleles in a diploid organism are transmitted to offspring at equal frequencies. Despite this, selfish loci known as meiotic drivers that bias their own transmission into gametes are found throughout eukaryotes. Drive is thought to be a powerful evolutionary force, but empirical evolutionary analyses of drive systems are limited by low numbers of identified meiotic drive genes. Here, we analyze the evolution of the wtf gene family of Schizosaccharomyces pombe that contains both killer meiotic drive genes and suppressors of drive. We completed assemblies of all wtf genes for two S. pombe isolates, as well as a subset of wtf genes from over 50 isolates. We find that wtf copy number can vary greatly between isolates and that amino acid substitutions, expansions and contractions of DNA sequence repeats, and nonallelic gene conversion between family members all contribute to dynamic wtf gene evolution. This work demonstrates the power of meiotic drive to foster rapid evolution and identifies a recombination mechanism through which transposons can indirectly mobilize meiotic drivers.
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Affiliation(s)
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS
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19
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Seike T. The evolution of peptide mating pheromones in fission yeast. Curr Genet 2019; 65:1107-1111. [DOI: 10.1007/s00294-019-00968-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 11/30/2022]
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20
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Seike T, Shimoda C, Niki H. Asymmetric diversification of mating pheromones in fission yeast. PLoS Biol 2019; 17:e3000101. [PMID: 30668560 PMCID: PMC6342294 DOI: 10.1371/journal.pbio.3000101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/19/2018] [Indexed: 01/25/2023] Open
Abstract
In fungi, mating between partners depends on the molecular recognition of two peptidyl mating pheromones by their respective receptors. The fission yeast Schizosaccharomyces pombe (Sp) has two mating types, Plus (P) and Minus (M). The mating pheromones P-factor and M-factor, secreted by P and M cells, are recognized by the receptors mating type auxiliary minus 2 (Mam2) and mating type auxiliary plus 3 (Map3), respectively. Our recent study demonstrated that a few mutations in both M-factor and Map3 can trigger reproductive isolation in S. pombe. Here, we explored the mechanism underlying reproductive isolation through genetic changes of pheromones/receptors in nature. We investigated the diversity of genes encoding the pheromones and their receptor in 150 wild S. pombe strains. Whereas the amino acid sequences of M-factor and Map3 were completely conserved, those of P-factor and Mam2 were very diverse. In addition, the P-factor gene contained varying numbers of tandem repeats of P-factor (4–8 repeats). By exploring the recognition specificity of pheromones between S. pombe and its close relative Schizosaccharomyces octosporus (So), we found that So-M-factor did not have an effect on S. pombe P cells, but So-P-factor had a partial effect on S. pombe M cells. Thus, recognition of M-factor seems to be stringent, whereas that of P-factor is relatively relaxed. We speculate that asymmetric diversification of the two pheromones might be facilitated by the distinctly different specificities of the two receptors. Our findings suggest that M-factor communication plays an important role in defining the species, whereas P-factor communication is able to undergo a certain degree of flexible adaptation–perhaps as a first step toward prezygotic isolation in S. pombe. An asymmetric pheromone/receptor system in the fission yeast Schizosaccharomyces pombe might allow flexible adaptation of pheromones to mutational changes while maintaining stringent recognition for mating partners, perhaps as a first step toward prezygotic mating isolation. The emergence of a new species might occur when two groups can no longer mate. Although such reproductive isolation is considered a key evolutionary process, the mechanisms by which it actually occurs have been confined to conjecture. The two sexes (Plus [P] and Minus [M]) of S. pombe each secrete a pheromone (P-factor and M-factor), which binds to a corresponding receptor (mating type auxiliary minus 2 [Mam2] and mating type auxiliary plus 3 [Map3]) on cells of the opposite sex. The interaction between a pheromone and its receptor is essential for successful mating. Here, we explored conservation of the mating pheromone communication system among 150 wild S. pombe strains of different geographical origins and the closely related species S. octosporus. We found that 1) the M-factor/Map3 interaction was completely conserved, whereas the P-factor/Mam2 interaction was very diverse in the strains investigated, and 2) most of the P-factor variants were functional across species. Thus, we have revealed an asymmetric pheromone/receptor system in fungal mating: namely, whereas M-factor communication operates extremely stringently, P-factor communication has the flexibility to create variations, perhaps facilitating prezygotic isolation in S. pombe.
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Affiliation(s)
- Taisuke Seike
- Genetics Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
| | - Chikashi Shimoda
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Hironori Niki
- Genetics Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
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21
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Fairhead C, Fischer G, Liti G, Neuvéglise C, Schacherer J. André Goffeau's imprinting on second generation yeast "genomologists". Yeast 2019; 36:167-175. [PMID: 30645763 DOI: 10.1002/yea.3377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/21/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022] Open
Abstract
All authors of the present paper have worked in labs that participated to the sequencing effort of the Saccharomyces cerevisiae reference genome, and we owe to this the fact that we have all chosen to work on genomics of yeasts. S. cerevisiae has been a popular model species for genetics since the 20th century as well as being a model for general eukaryotic cellular processes. Although it has also been used empirically in fermentation for millennia, there was until recently, a lack of knowledge about the natural and evolutionary history of this yeast. The achievement of the international effort to sequence its genome was the foundation for understanding many eukaryotic biological processes but also represented the first step towards the study of the genome and ecological diversity of yeast populations worldwide. We will describe recent advances in yeast comparative and population genomics that find their origins in the S. cerevisiae genome project initiated and pursued by André Goffeau.
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Affiliation(s)
- Cécile Fairhead
- UMR Génétique Quantitative et Evolution - Le Moulon, INRA - Université Paris-Sud - CNRS - AgroParisTech, Orsay, France
| | - Gilles Fischer
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Paris, France
| | - Gianni Liti
- INSERM, IRCAN, Université Côte d'Azur, CNRS, Nice, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Joseph Schacherer
- UMR 7156 Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, CNRS, Strasbourg, France
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22
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Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells. Genetics 2018; 210:733-744. [PMID: 30072377 PMCID: PMC6216586 DOI: 10.1534/genetics.118.301262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/31/2018] [Indexed: 01/24/2023] Open
Abstract
Chronological lifespan of non-dividing yeast cells is a quantitative trait that reflects cellular aging. By monitoring allele frequencies in aging segregant pools, Ellis et al. uncover regulatory variants in the 5'-untranslated regions of two genes... Quantitative traits often show large variation caused by multiple genetic factors . One such trait is the chronological lifespan of non-dividing yeast cells, serving as a model for cellular aging. Screens for genetic factors involved in aging typically assay mutants of protein-coding genes. To identify natural genetic variants contributing to cellular aging, we exploited two strains of the fission yeast, Schizosaccharomyces pombe, that differ in chronological lifespan. We generated segregant pools from these strains and subjected them to advanced intercrossing over multiple generations to break up linkage groups. We chronologically aged the intercrossed segregant pool, followed by genome sequencing at different times to detect genetic variants that became reproducibly enriched as a function of age. A region on Chromosome II showed strong positive selection during aging. Based on expected functions, two candidate variants from this region in the long-lived strain were most promising to be causal: small insertions and deletions in the 5′-untranslated regions of ppk31 and SPBC409.08. Ppk31 is an ortholog of Rim15, a conserved kinase controlling cell proliferation in response to nutrients, while SPBC409.08 is a predicted spermine transmembrane transporter. Both Rim15 and the spermine-precursor, spermidine, are implicated in aging as they are involved in autophagy-dependent lifespan extension. Single and double allele replacement suggests that both variants, alone or combined, have subtle effects on cellular longevity. Furthermore, deletion mutants of both ppk31 and SPBC409.08 rescued growth defects caused by spermidine. We propose that Ppk31 and SPBC409.08 may function together to modulate lifespan, thus linking Rim15/Ppk31 with spermidine metabolism.
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23
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Repeated evolution of self-compatibility for reproductive assurance. Nat Commun 2018; 9:1639. [PMID: 29691402 PMCID: PMC5915400 DOI: 10.1038/s41467-018-04054-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/29/2018] [Indexed: 01/22/2023] Open
Abstract
Sexual reproduction in eukaryotes requires the fusion of two compatible gametes of opposite sexes or mating types. To meet the challenge of finding a mating partner with compatible gametes, evolutionary mechanisms such as hermaphroditism and self-fertilization have repeatedly evolved. Here, by combining the insights from comparative genomics, computer simulations and experimental evolution in fission yeast, we shed light on the conditions promoting separate mating types or self-compatibility by mating-type switching. Analogous to multiple independent transitions between switchers and non-switchers in natural populations mediated by structural genomic changes, novel switching genotypes readily evolved under selection in the experimental populations. Detailed fitness measurements accompanied by computer simulations show the benefits and costs of switching during sexual and asexual reproduction, governing the occurrence of both strategies in nature. Our findings illuminate the trade-off between the benefits of reproductive assurance and its fitness costs under benign conditions facilitating the evolution of self-compatibility. Mating-type switching enables self-compatible reproduction in fungi, but switching ability is variable even within species. Here, the authors find de novo evolution of switching genotypes in experimentally evolved fission yeast populations and show a trade-off between mating success and growth.
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24
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Jeffares DC. The natural diversity and ecology of fission yeast. Yeast 2018; 35:253-260. [PMID: 29084364 DOI: 10.1002/yea.3293] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 12/17/2022] Open
Abstract
While the fission yeast is a powerful model of eukaryote biology, there have been few studies of quantitative genetics, phenotypic or genetic diversity. Here I survey the small collection of fission yeast diversity research. I discuss what we can infer about the ecology and origins of Schizosaccharomyces pombe from microbiology field studies and the few strains that have been collected.
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Affiliation(s)
- Daniel C Jeffares
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
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25
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High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing. G3-GENES GENOMES GENETICS 2017; 7:3243-3250. [PMID: 28983066 PMCID: PMC5633375 DOI: 10.1534/g3.117.300128] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any nonmodel organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is to obtain the complete sequence and high-quality assembly of a reference genome. Here, we sequenced and assembled a reference genome of the nonconventional Dekkera bruxellensis yeast. While this species is a major cause of wine spoilage, it paradoxically contributes to the specific flavor profile of some Belgium beers. In addition, an extreme karyotype variability is observed across natural isolates, highlighting that D. bruxellensis genome is very dynamic. The whole genome of the D. bruxellensis UMY321 isolate was sequenced using a combination of Nanopore long-read and Illumina short-read sequencing data. We generated the most complete and contiguous de novo assembly of D. bruxellensis to date and obtained a first glimpse into the genomic variability within this species by comparing the sequences of several isolates. This genome sequence is therefore of high value for population genomic surveys and represents a reference to study genome dynamic in this yeast species.
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26
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Johri P, Krenek S, Marinov GK, Doak TG, Berendonk TU, Lynch M. Population Genomics of Paramecium Species. Mol Biol Evol 2017; 34:1194-1216. [PMID: 28204679 DOI: 10.1093/molbev/msx074] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium.
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Affiliation(s)
- Parul Johri
- Department of Biology, Indiana University, Bloomington, IN
| | - Sascha Krenek
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | | | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN.,National Center for Genome Analysis Support, Indiana University, Bloomington, IN
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
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27
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Liti G, Warringer J, Blomberg A. Budding Yeast Strains and Genotype-Phenotype Mapping. Cold Spring Harb Protoc 2017; 2017:pdb.top077735. [PMID: 28765302 DOI: 10.1101/pdb.top077735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A small number of well-studied laboratory strains of Saccharomyces cerevisiae, mostly derived from S288C, are used in yeast research. Although powerful, studies for understanding S288C do not always capture the phenotypic essence or the genetic complexity of S. cerevisiae biology. This is particularly problematic for multilocus phenotypes identified in laboratory strains because these loci have never been jointly exposed to natural selection and the corresponding phenotypes do not represent optimization for any particular purpose or environment. Isolation and sequencing of new natural yeast strains also reveal that the total sequence diversity of the S. cerevisiae global population is poorly sampled in common laboratory strains. Here we discuss methodologies required for using the natural genetic variation in yeast to complete a genotype-phenotype map.
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Affiliation(s)
- Gianni Liti
- IRCAN, CNRS UMR 6267, INSERM U998, University of Nice, 06107 Nice, France
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), 1432 Ås, Norway
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden;
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28
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Abstract
Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data.
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29
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Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun 2017; 8:14061. [PMID: 28117401 DOI: 10.1038/ncomms14061] [Citation(s) in RCA: 359] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/24/2016] [Indexed: 02/08/2023] Open
Abstract
Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalogue of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) show a variety of genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits, most notably intracellular amino acid concentrations, growth under stress and sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases.
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Affiliation(s)
- Daniel C Jeffares
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Clemency Jolly
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Mimoza Hoti
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Doug Speed
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Liam Shaw
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Charalampos Rallis
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Francois Balloux
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Christophe Dessimoz
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,Department of Computer Science, University College London, London WC1E 6BT, UK.,Department of Ecology and Evolution and Center for Integrative Genomics, University of Lausanne, Biophore, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Biophore, Lausanne 1015, Switzerland
| | - Jürg Bähler
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Fritz J Sedlazeck
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
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30
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Hou J, Schacherer J. Negative epistasis: a route to intraspecific reproductive isolation in yeast? Curr Genet 2016; 62:25-9. [PMID: 26164016 PMCID: PMC4710551 DOI: 10.1007/s00294-015-0505-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 01/14/2023]
Abstract
Exploring the molecular bases of intraspecific reproductive isolation captures the ongoing phenotypic consequences of genetic divergence and provides insights into the early onset of speciation. Recent species-wide surveys using natural populations of yeasts demonstrated that intrinsic post-zygotic reproductive isolation segregates readily within the same species, and revealed the multiplicity of the genetic mechanisms underlying such processes. These advances deepened our current understandings and opened further perspectives regarding the complete picture of molecular and evolutionary origins driving the onset of intraspecific reproductive isolation in yeasts.
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Affiliation(s)
- Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg / CNRS, UMR7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg / CNRS, UMR7156, Strasbourg, France.
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Peter J, Schacherer J. Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale. Yeast 2016; 33:73-81. [PMID: 26592376 DOI: 10.1002/yea.3142] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/08/2022] Open
Abstract
With the advent of high-throughput technologies for sequencing, the complete description of the genetic variation that occurs in populations, also known as population genomics, is foreseeable but far from being reached. Explaining the forces that govern patterns of genetic variation is essential to elucidate the evolutionary history of species. Genetic variation results from a wide assortment of evolutionary forces, among which mutation, selection, recombination and drift play major roles in shaping genomes. In addition, exploring the genetic variation within a population also corresponds to the first step towards dissecting the genotype-phenotype relationship. In this context, yeast species are of particular interest because they represent a unique resource for studying the evolution of intraspecific genetic diversity in a phylum spanning a broad evolutionary scale. Here, we briefly review recent progress in yeast population genomics and provide some perspective on this rapidly evolving field. In fact, we truly believe that it is of interest to supplement comparative and early population genomic studies with the deep sequencing of more extensive sets of individuals from the same species. In parallel, it would be more than valuable to uncover the intraspecific variation of a large number of unexplored species, including those that are closely and more distantly related. Altogether, these data would enable substantially more powerful genomic scans for functional dissection.
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Affiliation(s)
- Jackson Peter
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
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Hu W, Suo F, Du LL. Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast. Genome Biol Evol 2015; 7:3496-510. [PMID: 26615217 PMCID: PMC4700965 DOI: 10.1093/gbe/evv238] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although the fission yeast Schizosaccharomyces pombe is a well-established model organism, studies of natural trait variations in this species remain limited. To assess the feasibility of segregant-pool-based mapping of phenotype-causing genes in natural strains of fission yeast, we investigated the cause of a maltose utilization defect (Mal(-)) of the S. pombe strain CBS5557 (originally known as Schizosaccharomyces malidevorans). Analyzing the genome sequence of CBS5557 revealed 955 nonconservative missense substitutions, and 61 potential loss-of-function variants including 47 frameshift indels, 13 early stop codons, and 1 splice site mutation. As a side benefit, our analysis confirmed 146 sequence errors in the reference genome and improved annotations of 27 genes. We applied bulk segregant analysis to map the causal locus of the Mal(-) phenotype. Through sequencing the segregant pools derived from a cross between CBS5557 and the laboratory strain, we located the locus to within a 2.23-Mb chromosome I inversion found in most S. pombe isolates including CBS5557. To map genes within the inversion region that occupies 18% of the genome, we created a laboratory strain containing the same inversion. Analyzing segregants from a cross between CBS5557 and the inversion-containing laboratory strain narrowed down the locus to a 200-kb interval and led us to identify agl1, which suffers a 5-bp deletion in CBS5557, as the causal gene. Interestingly, loss of agl1 through a 34-kb deletion underlies the Mal(-) phenotype of another S. pombe strain CGMCC2.1628. This work adapts and validates the bulk segregant analysis method for uncovering trait-gene relationship in natural fission yeast strains.
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Affiliation(s)
- Wen Hu
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
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33
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The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe. Genetics 2015; 201:737-44. [PMID: 26265703 DOI: 10.1534/genetics.115.177329] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/30/2015] [Indexed: 02/07/2023] Open
Abstract
The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an ∼1700-generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 insertion-deletion mutations (indels) across the 96 replicates. This equates to a base-substitution mutation rate of 2.00 × 10(-10) mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT-biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in shaping the nucleotide composition of the S. pombe genome and suggest that the mechanisms of DNA maintenance may have diverged significantly between fission and budding yeasts. Unexpectedly, CpG sites appear to be excessively liable to mutation in both species despite the likely absence of DNA methylation.
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Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O’Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet 2015; 47:235-41. [PMID: 25665008 PMCID: PMC4645456 DOI: 10.1038/ng.3215] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/14/2015] [Indexed: 12/14/2022]
Abstract
Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates. We sequenced the genomes of all strains, finding moderate genetic diversity (π = 3 × 10(-3) substitutions/site) and weak global population structure. We estimate that dispersal of S. pombe began during human antiquity (∼340 BCE), and ancestors of these strains reached the Americas at ∼1623 CE. We quantified 74 traits, finding substantial heritable phenotypic diversity. We conducted 223 genome-wide association studies, with 89 traits showing at least one association. The most significant variant for each trait explained 22% of the phenotypic variance on average, with indels having larger effects than SNPs. This analysis represents a rich resource to examine genotype-phenotype relationships in a tractable model.
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Affiliation(s)
- Daniel C. Jeffares
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Charalampos Rallis
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Adrien Rieux
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Doug Speed
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Martin Převorovský
- Department of Cell Biology, Charles University in Prague, Prague, Czech Republic
| | - Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Winston Lau
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Tammy M.K. Cheng
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Rodrigo Pracana
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Michael Mülleder
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonathan L.D. Lawson
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Anatole Chessel
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sendu Bala
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | | | | | - Leanne Bischof
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Bartlomiej Tomiczek
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Danny A. Bitton
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Theodora Sideri
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Sandra Codlin
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | | | - Laurent van Trigt
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Linda Jeffery
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Juan-Juan Li
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Sophie Atkinson
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Malte Thodberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Melanie Febrer
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Kirsten McLay
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Nizar Drou
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - William Brown
- Centre for Genetics and Genomics, The University of Nottingham, Nottingham, UK
| | - Jacqueline Hayles
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Rafael E. Carazo Salas
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Division of Physiology and Metabolism, MRC National Institute for Medical Research, London, UK
| | - Nikolas Maniatis
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - David J. Balding
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Francois Balloux
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | - Jürg Bähler
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
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