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Long H, Johri P, Gout JF, Ni J, Hao Y, Licknack T, Wang Y, Pan J, Jiménez-Marín B, Lynch M. Paramecium Genetics, Genomics, and Evolution. Annu Rev Genet 2023; 57:391-410. [PMID: 38012024 DOI: 10.1146/annurev-genet-071819-104035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.
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Affiliation(s)
- Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
| | - Parul Johri
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Timothy Licknack
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Berenice Jiménez-Marín
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
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2
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Mani S, Tlusty T. Gene birth in a model of non-genic adaptation. BMC Biol 2023; 21:257. [PMID: 37957718 PMCID: PMC10644530 DOI: 10.1186/s12915-023-01745-5] [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: 09/18/2022] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Over evolutionary timescales, genomic loci can switch between functional and non-functional states through processes such as pseudogenization and de novo gene birth. Particularly, de novo gene birth is a widespread process, and many examples continue to be discovered across diverse evolutionary lineages. However, the general mechanisms that lead to functionalization are poorly understood, and estimated rates of de novo gene birth remain contentious. Here, we address this problem within a model that takes into account mutations and structural variation, allowing us to estimate the likelihood of emergence of new functions at non-functional loci. RESULTS Assuming biologically reasonable mutation rates and mutational effects, we find that functionalization of non-genic loci requires the realization of strict conditions. This is in line with the observation that most de novo genes are localized to the vicinity of established genes. Our model also provides an explanation for the empirical observation that emerging proto-genes are often lost despite showing signs of adaptation. CONCLUSIONS Our work elucidates the properties of non-genic loci that make them fertile for adaptation, and our results offer mechanistic insights into the process of de novo gene birth.
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Affiliation(s)
- Somya Mani
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea.
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Departments of Physics and Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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3
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Pflughaupt P, Sahakyan AB. Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule. Nucleic Acids Res 2023; 51:7409-7423. [PMID: 37293966 PMCID: PMC10415130 DOI: 10.1093/nar/gkad477] [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] [Received: 12/23/2022] [Revised: 05/05/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Chargaff's second parity rule (PR-2), where the complementary base and k-mer contents are matching within the same strand of a double stranded DNA (dsDNA), is a phenomenon that invited many explanations. The strict compliance of nearly all nuclear dsDNA to PR-2 implies that the explanation should also be similarly adamant. In this work, we revisited the possibility of mutation rates driving PR-2 compliance. Starting from the assumption-free approach, we constructed kinetic equations for unconstrained simulations. The results were analysed for their PR-2 compliance by employing symbolic regression and machine learning techniques. We arrived to a generalised set of mutation rate interrelations in place in most species that allow for their full PR-2 compliance. Importantly, our constraints explain PR-2 in genomes out of the scope of the prior explanations based on the equilibration under mutation rates with simpler no-strand-bias constraints. We thus reinstate the role of mutation rates in PR-2 through its molecular core, now shown, under our formulation, to be tolerant to previously noted strand biases and incomplete compositional equilibration. We further investigate the time for any genome to reach PR-2, showing that it is generally earlier than the compositional equilibrium, and well within the age of life on Earth.
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Affiliation(s)
- Patrick Pflughaupt
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Aleksandr B Sahakyan
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
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4
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Melde RH, Bao K, Sharp NP. Recent insights into the evolution of mutation rates in yeast. Curr Opin Genet Dev 2022; 76:101953. [PMID: 35834945 PMCID: PMC9491374 DOI: 10.1016/j.gde.2022.101953] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 02/08/2023]
Abstract
Mutation is the origin of all genetic variation, good and bad. The mutation process can evolve in response to mutations, positive or negative selection, and genetic drift, but how these forces contribute to mutation-rate variation is an unsolved problem at the heart of genetics research. Mutations can be challenging to measure, but genome sequencing and other tools have allowed for the collection of larger and more detailed datasets, particularly in the yeast-model system. We review key hypotheses for the evolution of mutation rates and describe recent advances in understanding variation in mutational properties within and among yeast species. The multidimensional spectrum of mutations is increasingly recognized as holding valuable clues about how this important process evolves.
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Affiliation(s)
- Robert H Melde
- Department of Genetics, University of Wisconsin-Madison, USA.
| | - Kevin Bao
- Department of Genetics, University of Wisconsin-Madison, USA
| | - Nathaniel P Sharp
- Department of Genetics, University of Wisconsin-Madison, USA. https://twitter.com/@sharpnath
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5
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Pan J, Li W, Ni J, Wu K, Konigsberg I, Rivera CE, Tincher C, Gregory C, Zhou X, Doak TG, Lee H, Wang Y, Gao X, Lynch M, Long H. Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica. Mol Biol Evol 2022; 39:msac081. [PMID: 35446958 PMCID: PMC9040049 DOI: 10.1093/molbev/msac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.
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Affiliation(s)
- Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Iain Konigsberg
- Division of Biomedical Informatics & Personalized Medicine, Department of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Caitlyn E. Rivera
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Clayton Tincher
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Thomas G. Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Heewook Lee
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85281, USA
| | - Yan Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, No. 72 Binhai Road, Qingdao, Shandong Province 266237, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Angst P, Ebert D, Fields PD. Demographic history shapes genomic variation in an intracellular parasite with a wide geographic distribution. Mol Ecol 2022; 31:2528-2544. [DOI: 10.1111/mec.16419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Peter D. Fields
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
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7
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Chen Z, Wang X, Song Y, Zeng Q, Zhang Y, Luo H. Prochlorococcus have low global mutation rate and small effective population size. Nat Ecol Evol 2022; 6:183-194. [PMID: 34949817 DOI: 10.1038/s41559-021-01591-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/14/2021] [Indexed: 12/27/2022]
Abstract
Prochlorococcus are the most abundant free-living photosynthetic carbon-fixing organisms in the ocean. Prochlorococcus show small genome sizes, low genomic G+C content, reduced DNA repair gene pool and fast evolutionary rates, which are typical features of endosymbiotic bacteria. Nevertheless, their evolutionary mechanisms are believed to be different. Evolution of endosymbiotic bacteria is dominated by genetic drift owing to repeated population bottlenecks, whereas Prochlorococcus are postulated to have extremely large effective population sizes (Ne) and thus drift has rarely been considered. However, accurately extrapolating Ne requires measuring an unbiased global mutation rate through mutation accumulation, which is challenging for Prochlorococcus. Here, we managed this experiment over 1,065 days using Prochlorococcus marinus AS9601, sequenced genomes of 141 mutant lines and determined its mutation rate to be 3.50 × 10-10 per site per generation. Extrapolating Ne additionally requires identifying population boundaries, which we defined using PopCOGenT and over 400 genomes related to AS9601. Accordingly, we calculated its Ne to be 1.68 × 107, which is only reasonably greater than that of endosymbiotic bacteria but surprisingly smaller than that of many free-living bacteria extrapolated using the same approach. Our results therefore suggest that genetic drift is a key driver of Prochlorococcus evolution.
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Affiliation(s)
- Zhuoyu Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaojun Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Clear Water Bay, Hong Kong SAR
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China. .,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Clear Water Bay, Hong Kong SAR.
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8
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Development of Monascus purpureus monacolin K-hyperproducing mutant strains by synchrotron light irradiation and their comparative genome analysis. J Biosci Bioeng 2022; 133:362-368. [DOI: 10.1016/j.jbiosc.2021.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022]
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9
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Barbosa AC, Xu Z, Karari K, Williams W, Hauf S, Brown WRA. Mutation and selection explain why many eukaryotic centromeric DNA sequences are often A + T rich. Nucleic Acids Res 2021; 50:579-596. [PMID: 34928384 PMCID: PMC8754631 DOI: 10.1093/nar/gkab1219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/16/2021] [Accepted: 11/30/2021] [Indexed: 01/10/2023] Open
Abstract
We have used chromosome engineering to replace native centromeric DNA with different test sequences at native centromeres in two different strains of the fission yeast Schizosaccharomyces pombe and have discovered that A + T rich DNA, whether synthetic or of bacterial origin, will function as a centromere in this species. Using genome size as a surrogate for the inverse of effective population size (Ne) we also show that the relative A + T content of centromeric DNA scales with Ne across 43 animal, fungal and yeast (Opisthokonta) species. This suggests that in most of these species the A + T content of the centromeric DNA is determined by a balance between selection and mutation. Combining the experimental results and the evolutionary analyses allows us to conclude that A + T rich DNA of almost any sequence will function as a centromere in most Opisthokonta species. The fact that many G/C to A/T substitutions are unlikely to be selected against may contribute to the rapid evolution of centromeric DNA. We also show that a neo-centromere sequence is not simply a weak version of native centromeric DNA and suggest that neo-centromeres require factors either for their propagation or establishment in addition to those required by native centromeres.
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Affiliation(s)
- Anne C Barbosa
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Zhengyao Xu
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Kazhal Karari
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Wendi Williams
- Virginia Tech, Department of Biological Sciences, Fralin Life Sciences Institute, 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Silke Hauf
- Virginia Tech, Department of Biological Sciences, Fralin Life Sciences Institute, 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - William R A Brown
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
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10
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Papaioannou IA, Dutreux F, Peltier FA, Maekawa H, Delhomme N, Bardhan A, Friedrich A, Schacherer J, Knop M. Sex without crossing over in the yeast Saccharomycodes ludwigii. Genome Biol 2021; 22:303. [PMID: 34732243 PMCID: PMC8567612 DOI: 10.1186/s13059-021-02521-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution. Previous studies of the budding yeast species Saccharomycodes ludwigii suggested that meiotic crossing over might be absent from its sexual life cycle, which is predominated by fertilization within the meiotic tetrad. RESULTS We demonstrate that recombination is extremely suppressed during meiosis in Sd. ludwigii. DNA double-strand break formation by the conserved transesterase Spo11, processing and repair involving interhomolog interactions are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers in its genome. A strong AT bias of spontaneous mutations and the absence of recombination are likely responsible for its unusually low genomic GC level. CONCLUSIONS Sd. ludwigii has followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent mating between products of the same meiotic event with the extreme suppression of meiotic recombination. This life style ensures preservation of heterozygosity throughout its genome and may enable the species to adapt to its environment and survive with only minimal levels of rare meiotic recombination. We propose Sd. ludwigii as an excellent natural forum for the study of genome evolution and recombination rates.
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Affiliation(s)
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - France A. Peltier
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Hiromi Maekawa
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Current affiliation: Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Amit Bardhan
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - 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), Paris, France
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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11
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Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus. Nat Commun 2021; 12:5869. [PMID: 34620872 PMCID: PMC8497519 DOI: 10.1038/s41467-021-26108-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Mutations are the source of genetic variation and the substrate for evolution. Genome-wide mutation rates appear to be affected by selection and are probably adaptive. Mutation rates are also known to vary along genomes, possibly in response to epigenetic modifications, but causality is only assumed. In this study we determine the direct impact of epigenetic modifications and temperature stress on mitotic mutation rates in a fungal pathogen using a mutation accumulation approach. Deletion mutants lacking epigenetic modifications confirm that histone mark H3K27me3 increases whereas H3K9me3 decreases the mutation rate. Furthermore, cytosine methylation in transposable elements (TE) increases the mutation rate 15-fold resulting in significantly less TE mobilization. Also accessory chromosomes have significantly higher mutation rates. Finally, we find that temperature stress substantially elevates the mutation rate. Taken together, we find that epigenetic modifications and environmental conditions modify the rate and the location of spontaneous mutations in the genome and alter its evolutionary trajectory.
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12
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Pears CJ, Brustel J, Lakin ND. Dictyostelium discoideum as a Model to Assess Genome Stability Through DNA Repair. Front Cell Dev Biol 2021; 9:752175. [PMID: 34692705 PMCID: PMC8529158 DOI: 10.3389/fcell.2021.752175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/20/2021] [Indexed: 11/25/2022] Open
Abstract
Preserving genome integrity through repair of DNA damage is critical for human health and defects in these pathways lead to a variety of pathologies, most notably cancer. The social amoeba Dictyostelium discoideum is remarkably resistant to DNA damaging agents and genome analysis reveals it contains orthologs of several DNA repair pathway components otherwise limited to vertebrates. These include the Fanconi Anemia DNA inter-strand crosslink and DNA strand break repair pathways. Loss of function of these not only results in malignancy, but also neurodegeneration, immune-deficiencies and congenital abnormalities. Additionally, D. discoideum displays remarkable conservations of DNA repair factors that are targets in cancer and other therapies, including poly(ADP-ribose) polymerases that are targeted to treat breast and ovarian cancers. This, taken together with the genetic tractability of D. discoideum, make it an attractive model to assess the mechanistic basis of DNA repair to provide novel insights into how these pathways can be targeted to treat a variety of pathologies. Here we describe progress in understanding the mechanisms of DNA repair in D. discoideum, and how these impact on genome stability with implications for understanding development of malignancy.
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Affiliation(s)
- Catherine J. Pears
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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13
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Campbell CR, Tiley GP, Poelstra JW, Hunnicutt KE, Larsen PA, Lee HJ, Thorne JL, Dos Reis M, Yoder AD. Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. Heredity (Edinb) 2021; 127:233-244. [PMID: 34272504 PMCID: PMC8322134 DOI: 10.1038/s41437-021-00446-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation-rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprises nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (Microcebus murinus), we estimated the mutation rate to be among the highest calculated for a mammal at 1.52 × 10-8 (95% credible interval: 1.28 × 10-8-1.78 × 10-8) mutations/site/generation. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false-negative and false-positive rate for our data and show that any point estimate of a de novo mutation rate should be considered with a large degree of uncertainty. For validation, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which de novo mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution-rate analyses for all species compared.
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Affiliation(s)
- C Ryan Campbell
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | | | - Kelsie E Hunnicutt
- Department of Biology, Duke University, Durham, NC, USA
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Peter A Larsen
- Department of Biology, Duke University, Durham, NC, USA
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | - Hui-Jie Lee
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA.
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14
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Bergero R, Ellis P, Haerty W, Larcombe L, Macaulay I, Mehta T, Mogensen M, Murray D, Nash W, Neale MJ, O'Connor R, Ottolini C, Peel N, Ramsey L, Skinner B, Suh A, Summers M, Sun Y, Tidy A, Rahbari R, Rathje C, Immler S. Meiosis and beyond - understanding the mechanistic and evolutionary processes shaping the germline genome. Biol Rev Camb Philos Soc 2021; 96:822-841. [PMID: 33615674 PMCID: PMC8246768 DOI: 10.1111/brv.12680] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.
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Affiliation(s)
- Roberta Bergero
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3JTU.K.
| | - Peter Ellis
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
| | | | - Lee Larcombe
- Applied Exomics LtdStevenage Bioscience CatalystStevenageSG1 2FXU.K.
| | - Iain Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Tarang Mehta
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Mette Mogensen
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
| | - David Murray
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
| | - Will Nash
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexBrightonBN1 9RHU.K.
| | | | | | - Ned Peel
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Luke Ramsey
- The James Hutton InstituteInvergowrieDundeeDD2 5DAU.K.
| | - Ben Skinner
- School of Life SciencesUniversity of EssexColchesterCO4 3SQU.K.
| | - Alexander Suh
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
- Department of Organismal BiologyUppsala UniversityNorbyvägen 18DUppsala752 36Sweden
| | - Michael Summers
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
- The Bridge Centre1 St Thomas Street, London BridgeLondonSE1 9RYU.K.
| | - Yu Sun
- Norwich Medical SchoolUniversity of East AngliaNorwich Research Park, Colney LnNorwichNR4 7UGU.K.
| | - Alison Tidy
- School of BiosciencesUniversity of Nottingham, Plant Science, Sutton Bonington CampusSutton BoningtonLE12 5RDU.K.
| | | | - Claudia Rathje
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
| | - Simone Immler
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
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15
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Nguyen DT, Wu B, Long H, Zhang N, Patterson C, Simpson S, Morris K, Thomas WK, Lynch M, Hao W. Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast. Mol Biol Evol 2021; 37:3118-3130. [PMID: 33219379 DOI: 10.1093/molbev/msaa150] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mutation and recombination are the primary sources of genetic variation. To better understand the evolution of genetic variation, it is crucial to comprehensively investigate the processes involving mutation accumulation and recombination. In this study, we performed mutation accumulation experiments on four heterozygous diploid yeast species in the Saccharomycodaceae family to determine spontaneous mutation rates, mutation spectra, and losses of heterozygosity (LOH). We observed substantial variation in mutation rates and mutation spectra. We also observed high LOH rates (1.65-11.07×10-6 events per heterozygous site per cell division). Biases in spontaneous mutation and LOH together with selection ultimately shape the variable genome-wide nucleotide landscape in yeast species.
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Affiliation(s)
- Duong T Nguyen
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Baojun Wu
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Nan Zhang
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | | | | | | | | | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI
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16
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Pan J, Williams E, Sung W, Lynch M, Long H. The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:20-27. [PMID: 33791681 PMCID: PMC8009600 DOI: 10.1007/s42995-020-00060-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Mutation is a primary source of genetic variation that is used to power evolution. Many studies, however, have shown that most mutations are deleterious and, as a result, extremely low mutation rates might be beneficial for survival. Using a mutation accumulation experiment, an unbiased method for mutation study, we found an extremely low base-substitution mutation rate of 5.94 × 10-11 per nucleotide site per cell division (95% Poisson confidence intervals: 4.65 × 10-11, 7.48 × 10-11) and indel mutation rate of 8.25 × 10-12 per site per cell division (95% confidence intervals: 3.96 × 10-12, 1.52 × 10-11) in the bacterium Photorhabdus luminescens ATCC29999. The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction. It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the effective population size (drift-barrier hypothesis) and we found that the effective population size of this bacterium is significantly greater than most other bacteria. This finding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fidelity can evolve within organisms that maintain large effective population sizes.
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Affiliation(s)
- Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Emily Williams
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85281 USA
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223 USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
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17
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Song K. Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas. Genome Biol Evol 2020; 12:1943-1952. [PMID: 32722758 PMCID: PMC7674689 DOI: 10.1093/gbe/evaa160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
Mutation is a driving force of evolution that has been shaped by natural selection and is universally biased. Previous studies determined genome-wide mutational patterns for several species and investigated the heterogeneity of mutational patterns at fine-scale levels. However, little evidence of the heterogeneity of mutation rates over large genomic regions was shown. Hence, the mutational patterns of different large-scale genomic regions and their association with selective pressures still need to be explored. As the second most species-rich animal phylum, little is known about the mutational patterns in Mollusca, especially oysters. In this study, the mutational bias patterns are characterized by using whole-genome resequencing data in the Crassostrea gigas genome. I studied the genome-wide relative rates of the pair mutations and found that the predominant mutation is GC -> AT, irrespective of the genomic regions. This analysis reveals that mutational biases were associated with gene expression levels across the C. gigas genome. Genes with higher expression levels and breadth expression patterns, longer coding length, and more exon numbers had relatively higher GC -> AT rates. I also found that genes with larger dN/dS values had relatively higher GC -> AT rates. This work represents the first comprehensive research on the mutational biases in Mollusca species. Here, I comprehensively investigated the relationships between mutational biases with some intrinsic genetic factors and evolutionary indicators and proposed that selective pressures are important forces shaping the mutational biases across the C. gigas genome.
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Affiliation(s)
- Kai Song
- School of Mathematics and Statistics, Qingdao University, Shandong, China
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18
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Nguyen DT, Wu B, Xiao S, Hao W. Evolution of a Record-Setting AT-Rich Genome: Indel Mutation, Recombination, and Substitution Bias. Genome Biol Evol 2020; 12:2344-2354. [PMID: 32986811 PMCID: PMC7846184 DOI: 10.1093/gbe/evaa202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 12/16/2022] Open
Abstract
Genome-wide nucleotide composition varies widely among species. Despite extensive research, the source of genome-wide nucleotide composition diversity remains elusive. Yeast mitochondrial genomes (mitogenomes) are highly A + T rich, and they provide a unique opportunity to study the evolution of AT-biased landscape. In this study, we sequenced ten complete mitogenomes of the Saccharomycodes ludwigii yeast with 8% G + C content, the lowest genome-wide %(G + C) in all published genomes to date. The S. ludwigii mitogenomes have high densities of short tandem repeats but severely underrepresented mononucleotide repeats. Comparative population genomics of these record-setting A + T-rich genomes shows dynamic indel mutations and strong mutation bias toward A/T. Indel mutations play a greater role in genomic variation among very closely related strains than nucleotide substitutions. Indels have resulted in presence–absence polymorphism of tRNAArg (ACG) among S. ludwigii mitogenomes. Interestingly, these mitogenomes have undergone recombination, a genetic process that can increase G + C content by GC-biased gene conversion. Finally, the expected equilibrium G + C content under mutation pressure alone is higher than observed G + C content, suggesting existence of mechanisms other than AT-biased mutation operating to increase A/T. Together, our findings shed new lights on mechanisms driving extremely AT-rich genomes.
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Affiliation(s)
- Duong T Nguyen
- Department of Biological Sciences, Wayne State University
| | - Baojun Wu
- Department of Biological Sciences, Wayne State University
| | - Shujie Xiao
- Department of Biological Sciences, Wayne State University
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University
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19
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Desnos-Ollivier M, Maufrais C, Pihet M, Aznar C, Dromer F. Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing. Mycoses 2020; 63:942-951. [PMID: 32506754 DOI: 10.1111/myc.13126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Trichosporonosis is a rare invasive infection in humans mainly due to Trichosporon asahii, and especially recovered from patients having haematological malignancy. Since 2012, IGS1 region sequencing is used as a genotyping method to distinguish isolates, with high frequency of one haplotype worldwide and a geographic specificity for some haplotypes. OBJECTIVES We compared the IGS1 genotyping method and whole genome sequencing (WGS) to study the relationship between clinical isolates involved in two grouped cases in France. METHODS IGS1 sequencing and antifungal susceptibility testing were performed for 54 clinical isolates. Clinical data for 28 isolates included in surveillance programs were analysed. Whole genome was sequenced for 32 clinical isolates and the type strain. RESULTS All isolates were intrinsically resistant to flucytosine, while voriconazole had the most potent in vitro activity. The majority of the isolates was recovered from patients with haematological malignancies (42.86%), with a high proportion of children (<15 yrs-old, 32.14%) and a high mortality rate at three months (46.15%). Based on the WGS analysis, isolates exhibiting IGS1 haplotype 1, 3 and 7 belonged to different clades. Five isolates recovered during the first grouped cases had the same IGS1 haplotype and shared 99% of SNPs similarity. For the second grouped cases, four isolates had 98.7% of SNPs similarity while the isolate recovered 4 years earlier was totally unlinked. CONCLUSIONS We confirmed the usefulness of IGS1 sequencing for grouped cases infection of T. asahii. We underlined its limitation for the study of population structure and the utility of WGS analysis for the study of epidemiologically unrelated isolates.
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Affiliation(s)
- Marie Desnos-Ollivier
- Molecular Mycology Unit, UMR2000, Institut Pasteur, CNRS, National Reference Center for Invasive Mycoses & Antifungals, Paris, France
| | - Corinne Maufrais
- Center of Bioinformatics for Biology, Institut Pasteur, Paris, France
| | - Marc Pihet
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Christine Aznar
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier de Cayenne, Cayenne, France
| | - Françoise Dromer
- Molecular Mycology Unit, UMR2000, Institut Pasteur, CNRS, National Reference Center for Invasive Mycoses & Antifungals, Paris, France
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20
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Xue CX, Zhang H, Lin HY, Sun Y, Luo D, Huang Y, Zhang XH, Luo H. Ancestral niche separation and evolutionary rate differentiation between sister marine flavobacteria lineages. Environ Microbiol 2020; 22:3234-3247. [PMID: 32390223 DOI: 10.1111/1462-2920.15065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022]
Abstract
Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive. Here, genomic analyses and physiological assays indicate that the sister flavobacteria lineages Leeuwenhoekiella and Nonlabens likely explore polysaccharide-rich macroalgae and polysaccharide-poor pelagic niches respectively. Phylogenomic analyses inferred that the niche separation likely occurred anciently and coincided with increased sequence evolutionary rate in Nonlabens compared with Leeuwenhoekiella. Further analyses ruled out the known mechanisms likely driving evolutionary rate acceleration, including reduced selection efficiency, decreased generation time and increased mutation rate. In particular, the mutation rates were determined using an unbiased experimental method, which measures the present-day populations and may not reflect ancestral populations. These data collectively lead to a new hypothesis that an ancestral and transient mutation rate increase resulted in evolutionary rate increase in Nonlabens. This hypothesis was supported by inferring that gains and losses of genes involved in SOS response, a mechanism known to drive transiently increased mutation rate, coincided with evolutionary rate acceleration. Our analyses highlight the evolutionary mechanisms underlying niche differentiation of flavobacteria lineages.
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Affiliation(s)
- Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.,Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - He-Yu Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Danli Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Yongjie Huang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
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21
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Satoh Y, Asakawa JI, Nishimura M, Kuo T, Shinkai N, Cullings HM, Minakuchi Y, Sese J, Toyoda A, Shimada Y, Nakamura N, Uchimura A. Characteristics of induced mutations in offspring derived from irradiated mouse spermatogonia and mature oocytes. Sci Rep 2020; 10:37. [PMID: 31913321 PMCID: PMC6949229 DOI: 10.1038/s41598-019-56881-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/18/2019] [Indexed: 01/07/2023] Open
Abstract
The exposure of germ cells to radiation introduces mutations in the genomes of offspring, and a previous whole-genome sequencing study indicated that the irradiation of mouse sperm induces insertions/deletions (indels) and multisite mutations (clustered single nucleotide variants and indels). However, the current knowledge on the mutation spectra is limited, and the effects of radiation exposure on germ cells at stages other than the sperm stage remain unknown. Here, we performed whole-genome sequencing experiments to investigate the exposure of spermatogonia and mature oocytes. We compared de novo mutations in a total of 24 F1 mice conceived before and after the irradiation of their parents. The results indicated that radiation exposure, 4 Gy of gamma rays, induced 9.6 indels and 2.5 multisite mutations in spermatogonia and 4.7 indels and 3.1 multisite mutations in mature oocytes in the autosomal regions of each F1 individual. Notably, we found two types of deletions, namely, small deletions (mainly 1~12 nucleotides) in non-repeat sequences, many of which showed microhomology at the breakpoint junction, and single-nucleotide deletions in mononucleotide repeat sequences. The results suggest that these deletions and multisite mutations could be a typical signature of mutations induced by parental irradiation in mammals.
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Affiliation(s)
- Yasunari Satoh
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan.
| | - Jun-Ichi Asakawa
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan
| | - Mayumi Nishimura
- Department of Radiation Effects Research, National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST), Chiba, 263-8555, Japan
| | - Tony Kuo
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Real World Big-Data Computation Open Innovation Laboratory, AIST-Tokyo Tech, 2-12-1 Okayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Norio Shinkai
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Harry M Cullings
- Department of Statistics, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Real World Big-Data Computation Open Innovation Laboratory, AIST-Tokyo Tech, 2-12-1 Okayama, Meguro-ku, Tokyo, 152-8550, Japan.,Humanome Lab, Inc., L-HUB 3F, 1-4, Shumomiyabi-cho, Sinjuku-ku, Tokyo, 162-0822, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Yoshiya Shimada
- Department of Radiological Sciences, Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, 116-8551, Japan.,Executive Director, QST, Chiba, 263-8555, Japan
| | - Nori Nakamura
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan
| | - Arikuni Uchimura
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan.
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22
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Endemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing. Heredity (Edinb) 2019; 124:397-409. [PMID: 31863032 DOI: 10.1038/s41437-019-0288-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 11/08/2022] Open
Abstract
The wheat leaf rust fungus, Puccinia triticina, is found in the major wheat growing regions of the world and is a leading cause of yield loss in wheat. Populations of P. triticina are highly variable for virulence to resistance genes in wheat and adapt quickly to resistance genes in wheat cultivars. The objectives of this study were to determine the genetic relatedness of worldwide collections of P. triticina using restriction site associated genotyping by sequencing. A total of 558 isolates of P. triticina from wheat producing regions in North America, South America, Europe, the Middle East, Ethiopia, Russia, Pakistan, Central Asia, China, New Zealand, and South Africa were characterized at 6745 single nucleotide loci. Isolates were also tested for virulence to 20 near-isogenic lines that differ for leaf rust resistance genes. Populations that were geographically proximal were also more closely related for genotypes. In addition, groups of isolates within regions that varied for genotype were similar to groups from other regions, which indicated past and recent migration across regions. Isolates from tetraploid durum wheat in five different regions were highly related with distinct genotypes compared to isolates from hexaploid common wheat. Based on a molecular clock, isolates from durum wheat found only in Ethiopia were the first to diverge from a common ancestor form of P. triticina that is found on the wild wheat relative Aegilops speltoides, followed by the divergence of isolates found worldwide that are virulent to durum wheat, and then by isolates found on common wheat.
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23
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Álvarez-Escribano I, Sasse C, Bok JW, Na H, Amirebrahimi M, Lipzen A, Schackwitz W, Martin J, Barry K, Gutiérrez G, Cea-Sánchez S, Marcos AT, Grigoriev IV, Keller NP, Braus GH, Cánovas D. Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants. BMC Biol 2019; 17:88. [PMID: 31711484 PMCID: PMC6844060 DOI: 10.1186/s12915-019-0702-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/19/2019] [Indexed: 01/19/2023] Open
Abstract
Background Aspergillus spp. comprises a very diverse group of lower eukaryotes with a high relevance for industrial applications and clinical implications. These multinucleate species are often cultured for many generations in the laboratory, which can unknowingly propagate hidden genetic mutations. To assess the likelihood of such events, we studied the genome stability of aspergilli by using a combination of mutation accumulation (MA) lines and whole genome sequencing. Results We sequenced the whole genomes of 30 asexual and 10 sexual MA lines of three Aspergillus species (A. flavus, A. fumigatus and A. nidulans) and estimated that each MA line accumulated mutations for over 4000 mitoses during asexual cycles. We estimated mutation rates of 4.2 × 10−11 (A. flavus), 1.1 × 10−11 (A. fumigatus) and 4.1 × 10−11 (A. nidulans) per site per mitosis, suggesting that the genomes are very robust. Unexpectedly, we found a very high rate of GC → TA transversions only in A. flavus. In parallel, 30 asexual lines of the non-homologous end-joining (NHEJ) mutants of the three species were also allowed to accumulate mutations for the same number of mitoses. Sequencing of these NHEJ MA lines gave an estimated mutation rate of 5.1 × 10−11 (A. flavus), 2.2 × 10−11 (A. fumigatus) and 4.5 × 10−11 (A. nidulans) per base per mitosis, which is slightly higher than in the wild-type strains and some ~ 5–6 times lower than in the yeasts. Additionally, in A. nidulans, we found a NHEJ-dependent interference of the sexual cycle that is independent of the accumulation of mutations. Conclusions We present for the first time direct counts of the mutation rate of filamentous fungal species and find that Aspergillus genomes are very robust. Deletion of the NHEJ machinery results in a slight increase in the mutation rate, but at a rate we suggest is still safe to use for biotechnology purposes. Unexpectedly, we found GC→TA transversions predominated only in the species A. flavus, which could be generated by the hepatocarcinogen secondary metabolite aflatoxin. Lastly, a strong effect of the NHEJ mutation in self-crossing was observed and an increase in the mutations of the asexual lines was quantified.
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Affiliation(s)
- Isidro Álvarez-Escribano
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.,Present Address: Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
| | - Christoph Sasse
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Göttingen, Germany
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Gabriel Gutiérrez
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
| | - Sara Cea-Sánchez
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
| | - Ana T Marcos
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.,Present Address: Instituto para el Estudio de la Reproducción Humana (Inebir), Avda de la Cruz Roja 1, 41009, Sevilla, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Göttingen, Germany
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.
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Saxena AS, Salomon MP, Matsuba C, Yeh SD, Baer CF. Evolution of the Mutational Process under Relaxed Selection in Caenorhabditis elegans. Mol Biol Evol 2019; 36:239-251. [PMID: 30445510 DOI: 10.1093/molbev/msy213] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mutational process varies at many levels, from within genomes to among taxa. Many mechanisms have been linked to variation in mutation, but understanding of the evolution of the mutational process is rudimentary. Physiological condition is often implicated as a source of variation in microbial mutation rate and may contribute to mutation rate variation in multicellular organisms.Deleterious mutations are an ubiquitous source of variation in condition. We test the hypothesis that the mutational process depends on the underlying mutation load in two groups of Caenorhabditis elegans mutation accumulation (MA) lines that differ in their starting mutation loads. "First-order MA" (O1MA) lines maintained under minimal selection for ∼250 generations were divided into high-fitness and low-fitness groups and sets of "second-order MA" (O2MA) lines derived from each O1MA line were maintained for ∼150 additional generations. Genomes of 48 O2MA lines and their progenitors were sequenced. There is significant variation among O2MA lines in base-substitution rate (µbs), but no effect of initial fitness; the indel rate is greater in high-fitness O2MA lines. Overall, µbs is positively correlated with recombination and proximity to short tandem repeats and negatively correlated with 10 bp and 1 kb GC content. However, probability of mutation is sufficiently predicted by the three-nucleotide motif alone. Approximately 90% of the variance in standing nucleotide variation is explained by mutability. Total mutation rate increased in the O2MA lines, as predicted by the "drift barrier" model of mutation rate evolution. These data, combined with experimental estimates of fitness, suggest that epistasis is synergistic.
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Affiliation(s)
| | - Matthew P Salomon
- Department of Biology, University of Florida, Gainesville, FL
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, CA
| | - Chikako Matsuba
- Department of Biology, University of Florida, Gainesville, FL
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, CA
| | - Shu-Dan Yeh
- Department of Biology, University of Florida, Gainesville, FL
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute
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25
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Derbyshire MC, Denton-Giles M, Hane JK, Chang S, Mousavi-Derazmahalleh M, Raffaele S, Buchwaldt L, Kamphuis LG. A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum. PLoS One 2019; 14:e0214201. [PMID: 30921376 PMCID: PMC6438532 DOI: 10.1371/journal.pone.0214201] [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: 05/14/2018] [Accepted: 03/10/2019] [Indexed: 01/08/2023] Open
Abstract
The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking. We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents–Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps. Among the 25 isolates, there was evidence for two major population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), and the other consisted of nine isolates from Australia and one from Morocco (population 2). The rest of the isolates were genotypic outliers. We found that there was evidence of outcrossing in these two populations based on linkage disequilibrium decay. However, only a single candidate selective sweep was observed, and it was present in population 2. This sweep was close to a Major Facilitator Superfamily transporter gene, and we speculate that this gene may have a role in nutrient uptake from the host. The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens. This may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction.
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Affiliation(s)
- Mark Charles Derbyshire
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
- * E-mail:
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Steven Chang
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Micro-organismes (LIPM), Université de Toulouse, INRA, Toulouse, France
| | - Lone Buchwaldt
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatchewan, Saskatoon, Canada
| | - Lars G. Kamphuis
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
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26
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A Novel, Drug Resistance-Independent, Fluorescence-Based Approach To Measure Mutation Rates in Microbial Pathogens. mBio 2019; 10:mBio.00120-19. [PMID: 30808701 PMCID: PMC6391916 DOI: 10.1128/mbio.00120-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Measurements of mutation rates—i.e., how often proliferating cells acquire mutations in their DNA—are essential for understanding cellular processes that maintain genome stability. Many traditional mutation rate measurement assays are based on detecting mutations that cause resistance to a particular drug. Such assays typically work well for laboratory strains but have significant limitations when comparing clinical or environmental isolates that have various intrinsic levels of drug tolerance, which confounds the interpretation of results. Here we report the development and validation of a novel method of measuring mutation rates, which detects mutations that cause loss of fluorescence rather than acquisition of drug resistance. Using this method, we measured the mutation rates of clinical isolates of fungal pathogen Candida glabrata. This assay can be adapted to other organisms and used to compare mutation rates in contexts where unequal drug sensitivity is anticipated. All evolutionary processes are underpinned by a cellular capacity to mutate DNA. To identify factors affecting mutagenesis, it is necessary to compare mutation rates between different strains and conditions. Drug resistance-based mutation reporters are used extensively to measure mutation rates, but they are suitable only when the compared strains have identical drug tolerance levels—a condition that is not satisfied under many “real-world” circumstances, e.g., when comparing mutation rates among a series of environmental or clinical isolates. Candida glabrata is a fungal pathogen that shows a high degree of genetic diversity and fast emergence of antifungal drug resistance. To enable meaningful comparisons of mutation rates among C. glabrata clinical isolates, we developed a novel fluorescence-activated cell sorting-based approach to measure the mutation rate of a chromosomally integrated GFP gene. We found that in Saccharomyces cerevisiae this approach recapitulated the reported mutation rate of a wild-type strain and the mutator phenotype of a shu1Δ mutant. In C. glabrata, the GFP reporter captured the mutation rate increases caused either by a genotoxic agent or by deletion of DNA mismatch repair gene MSH2, as well as the specific mutational signature associated with msh2Δ. Finally, the reporter was used to measure the mutation rates of C. glabrata clinical isolates carrying different alleles of MSH2. Together, these results show that fluorescence-based mutation reporters can be used to measure mutation rates in microbes under conditions of unequal drug susceptibility to reveal new insights about drivers of mutagenesis.
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27
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Spontaneous mutation rate as a source of diversity for improving desirable traits in cultured microalgae. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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28
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Limited Mutation-Rate Variation Within the Paramecium aurelia Species Complex. G3-GENES GENOMES GENETICS 2018; 8:2523-2526. [PMID: 29794165 PMCID: PMC6027866 DOI: 10.1534/g3.118.200420] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mutation is one of the most fundamental evolutionary forces. Studying variation in the mutation rate within and among closely-related species can help reveal mechanisms of genome divergence, but such variation is unstudied in the vast majority of organisms. Previous studies on ciliated protozoa have found extremely low mutation rates. In this study, using mutation-accumulation techniques combined with deep whole-genome sequencing, we explore the germline base-substitution mutation-rate variation of three cryptic species in the Paramecium aurelia species complex—P. biaurelia, P. sexaurelia, and P. tetraurelia. We find that there is extremely limited variation of the mutation rate and spectrum in the three species and confirm the extremely low mutation rate of ciliates.
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29
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Burkholder AB, Lujan SA, Lavender CA, Grimm SA, Kunkel TA, Fargo DC. Muver, a computational framework for accurately calling accumulated mutations. BMC Genomics 2018; 19:345. [PMID: 29743009 PMCID: PMC5944071 DOI: 10.1186/s12864-018-4753-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/02/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Identification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impart significant phenotypic consequences on cells but are harder to call than substitution mutations from whole genome mutation accumulation experiments. To overcome these difficulties, we present muver, a computational framework that integrates established bioinformatics tools with novel analytical methods to generate mutation calls with the extremely low false positive rates and high sensitivity required for accurate mutation rate determination and comparison. RESULTS Muver uses statistical comparison of ancestral and descendant allelic frequencies to identify variant loci and assigns genotypes with models that include per-sample assessments of sequencing errors by mutation type and repeat context. Muver identifies maximally parsimonious mutation pathways that connect these genotypes, differentiating potential allelic conversion events and delineating ambiguities in mutation location, type, and size. Benchmarking with a human gold standard father-son pair demonstrates muver's sensitivity and low false positive rates. In DNA mismatch repair (MMR) deficient Saccharomyces cerevisiae, muver detects multi-base deletions in homopolymers longer than the replicative polymerase footprint at rates greater than predicted for sequential single-base deletions, implying a novel multi-repeat-unit slippage mechanism. CONCLUSIONS Benchmarking results demonstrate the high accuracy and sensitivity achieved with muver, particularly for indels, relative to available tools. Applied to an MMR-deficient Saccharomyces cerevisiae system, muver mutation calls facilitate mechanistic insights into DNA replication fidelity.
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Affiliation(s)
- Adam B Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Scott A Lujan
- Laboratory of Genomic Integrity and Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Christopher A Lavender
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Sara A Grimm
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Thomas A Kunkel
- Laboratory of Genomic Integrity and Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA.
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30
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Long H, Sung W, Kucukyildirim S, Williams E, Miller SF, Guo W, Patterson C, Gregory C, Strauss C, Stone C, Berne C, Kysela D, Shoemaker WR, Muscarella ME, Luo H, Lennon JT, Brun YV, Lynch M. Evolutionary determinants of genome-wide nucleotide composition. Nat Ecol Evol 2018; 2:237-240. [PMID: 29292397 PMCID: PMC6855595 DOI: 10.1038/s41559-017-0425-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022]
Abstract
One of the long-standing mysteries of evolutionary genomics is the source of the wide phylogenetic diversity in genome nucleotide composition (G + C versus A + T), which must be a consequence of interspecific differences in mutation bias, the efficiency of selection for different nucleotides or a combination of the two. We demonstrate that although genomic G + C composition is strongly driven by mutation bias, it is also substantially modified by direct selection and/or as a by-product of biased gene conversion. Moreover, G + C composition at fourfold redundant sites is consistently elevated above the neutral expectation-more so than for any other class of sites.
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Affiliation(s)
- Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
| | | | - Emily Williams
- Center for Mechanisms of Evolution, Arizona State University, PO Box 877701, Tempe, AZ, USA
| | - Samuel F Miller
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Wanfeng Guo
- Center for Mechanisms of Evolution, Arizona State University, PO Box 877701, Tempe, AZ, USA
| | | | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Chloe Strauss
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Casey Stone
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Cécile Berne
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - David Kysela
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Mario E Muscarella
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Champaign, IL, USA
| | - Haiwei Luo
- School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, PO Box 877701, Tempe, AZ, USA.
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31
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Gangloff S, Achaz G, Francesconi S, Villain A, Miled S, Denis C, Arcangioli B. Quiescence unveils a novel mutational force in fission yeast. eLife 2017; 6. [PMID: 29252184 PMCID: PMC5734874 DOI: 10.7554/elife.27469] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 12/02/2017] [Indexed: 12/18/2022] Open
Abstract
To maintain life across a fluctuating environment, cells alternate between phases of cell division and quiescence. During cell division, the spontaneous mutation rate is expressed as the probability of mutations per generation (Luria and Delbrück, 1943; Lea and Coulson, 1949), whereas during quiescence it will be expressed per unit of time. In this study, we report that during quiescence, the unicellular haploid fission yeast accumulates mutations as a linear function of time. The novel mutational landscape of quiescence is characterized by insertion/deletion (indels) accumulating as fast as single nucleotide variants (SNVs), and elevated amounts of deletions. When we extended the study to 3 months of quiescence, we confirmed the replication-independent mutational spectrum at the whole-genome level of a clonally aged population and uncovered phenotypic variations that subject the cells to natural selection. Thus, our results support the idea that genomes continuously evolve under two alternating phases that will impact on their size and composition.
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Affiliation(s)
- Serge Gangloff
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Guillaume Achaz
- ISYEB UMR7505 CNRS MNHN UPMC EPHE CIRB UMR 7241 CNRS Collège de France INSERM, UPMC, Paris, France
| | - Stefania Francesconi
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | | | - Samia Miled
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Claire Denis
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Benoit Arcangioli
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
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