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She H, Liu Z, Xu Z, Zhang H, Wu J, Wang X, Cheng F, Charlesworth D, Qian W. Insights into spinach domestication from genome sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra. THE NEW PHYTOLOGIST 2024; 243:477-494. [PMID: 38715078 DOI: 10.1111/nph.19799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/18/2024] [Indexed: 06/07/2024]
Abstract
Cultivated spinach (Spinacia oleracea) is a dioecious species. We report high-quality genome sequences for its two closest wild relatives, Spinacia turkestanica and Spinacia tetrandra, which are also dioecious, and are used to study the genetics of spinach domestication. Using a combination of genomic approaches, we assembled genomes of both these species and analyzed them in comparison with the previously assembled S. oleracea genome. These species diverged c. 6.3 million years ago (Ma), while cultivated spinach split from S. turkestanica 0.8 Ma. In all three species, all six chromosomes include very large gene-poor, repeat-rich regions, which, in S. oleracea, are pericentromeric regions with very low recombination rates in both male and female genetic maps. We describe population genomic evidence that the similar regions in the wild species also recombine rarely. We characterized 282 structural variants (SVs) that have been selected during domestication. These regions include genes associated with leaf margin type and flowering time. We also describe evidence that the downy mildew resistance loci of cultivated spinach are derived from introgression from both wild spinach species. Collectively, this study reveals the genome architecture of spinach assemblies and highlights the importance of SVs during the domestication of cultivated spinach.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Hinch R, Donnelly P, Hinch AG. Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line. Science 2023; 382:eadh2531. [PMID: 38033082 PMCID: PMC7615360 DOI: 10.1126/science.adh2531] [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: 02/20/2023] [Accepted: 09/29/2023] [Indexed: 12/02/2023]
Abstract
Meiotic recombination commences with hundreds of programmed DNA breaks; however, the degree to which they are accurately repaired remains poorly understood. We report that meiotic break repair is eightfold more mutagenic for single-base substitutions than was previously understood, leading to de novo mutation in one in four sperm and one in 12 eggs. Its impact on indels and structural variants is even higher, with 100- to 1300-fold increases in rates per break. We uncovered new mutational signatures and footprints relative to break sites, which implicate unexpected biochemical processes and error-prone DNA repair mechanisms, including translesion synthesis and end joining in meiotic break repair. We provide evidence that these mechanisms drive mutagenesis in human germ lines and lead to disruption of hundreds of genes genome wide.
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Affiliation(s)
- Robert Hinch
- Big Data Institute, University of Oxford; Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford; Oxford, UK
- Genomics plc; Oxford, UK
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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Rimbault M, Legeai F, Peccoud J, Mieuzet L, Call E, Nouhaud P, Defendini H, Mahéo F, Marande W, Théron N, Tagu D, Le Trionnaire G, Simon JC, Jaquiéry J. Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid. Genome Biol Evol 2023; 15:evad168. [PMID: 37717171 PMCID: PMC10538257 DOI: 10.1093/gbe/evad168] [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] [Received: 05/23/2022] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Although asexual lineages evolved from sexual lineages in many different taxa, the genetics of sex loss remains poorly understood. We addressed this issue in the pea aphid Acyrthosiphon pisum, whose natural populations encompass lineages performing cyclical parthenogenesis (CP) and producing one sexual generation per year, as well as obligate parthenogenetic (OP) lineages that can no longer produce sexual females but can still produce males. An SNP-based, whole-genome scan of CP and OP populations sequenced in pools (103 individuals from 6 populations) revealed that an X-linked region is associated with the variation in reproductive mode. This 840-kb region is highly divergent between CP and OP populations (FST = 34.9%), with >2,000 SNPs or short Indels showing a high degree of association with the phenotypic trait. In OP populations specifically, this region also shows reduced diversity and Tajima's D, consistent with the OP phenotype being a derived trait in aphids. Interestingly, the low genetic differentiation between CP and OP populations at the rest of the genome (FST = 2.5%) suggests gene flow between them. Males from OP lineages thus likely transmit their op allele to new genomic backgrounds. These genetic exchanges, combined with the selection of the OP and CP reproductive modes under different climates, probably contribute to the long-term persistence of the cp and op alleles.
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Affiliation(s)
- Maud Rimbault
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- University of Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, Poitiers CEDEX 9, France
| | - Lucie Mieuzet
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Elsa Call
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Pierre Nouhaud
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Hélène Defendini
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Frédérique Mahéo
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - William Marande
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Nicolas Théron
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Denis Tagu
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Gaël Le Trionnaire
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Christophe Simon
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Julie Jaquiéry
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
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Zhuk AS, Shiriaeva AA, Andreychuk YV, Kochenova OV, Tarakhovskaya ER, Bure VM, Pavlov YI, Inge-Vechtomov SG, Stepchenkova EI. Detection of Primary DNA Lesions by Transient Changes in Mating Behavior in Yeast Saccharomyces cerevisiae Using the Alpha-Test. Int J Mol Sci 2023; 24:12163. [PMID: 37569542 PMCID: PMC10418631 DOI: 10.3390/ijms241512163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Spontaneous or induced DNA lesions can result in stable gene mutations and chromosomal aberrations due to their inaccurate repair, ultimately resulting in phenotype changes. Some DNA lesions per se may interfere with transcription, leading to temporary phenocopies of mutations. The direct impact of primary DNA lesions on phenotype before their removal by repair is not well understood. To address this question, we used the alpha-test, which allows for detecting various genetic events leading to temporary or hereditary changes in mating type α→a in heterothallic strains of yeast Saccharomyces cerevisiae. Here, we compared yeast strains carrying mutations in DNA repair genes, mismatch repair (pms1), base excision repair (ogg1), and homologous recombination repair (rad52), as well as mutagens causing specific DNA lesions (UV light and camptothecin). We found that double-strand breaks and UV-induced lesions have a stronger effect on the phenotype than mismatches and 8-oxoguanine. Moreover, the loss of the entire chromosome III leads to an immediate mating type switch α→a and does not prevent hybridization. We also evaluated the ability of primary DNA lesions to persist through the cell cycle by assessing the frequency of UV-induced inherited and non-inherited genetic changes in asynchronous cultures of a wild-type (wt) strain and in a cdc28-4 mutant arrested in the G1 phase. Our findings suggest that the phenotypic manifestation of primary DNA lesions depends on their type and the stage of the cell cycle in which it occurred.
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Affiliation(s)
- Anna S. Zhuk
- Institute of Applied Computer Science, ITMO University, 191002 St. Petersburg, Russia
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (E.R.T.); (S.G.I.-V.)
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Anna A. Shiriaeva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.A.S.); (O.V.K.)
| | - Yulia V. Andreychuk
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Olga V. Kochenova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.A.S.); (O.V.K.)
- Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - Elena R. Tarakhovskaya
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (E.R.T.); (S.G.I.-V.)
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Vladimir M. Bure
- Faculty of Applied Mathematics and Control Processes, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, the University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, the University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sergey G. Inge-Vechtomov
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (E.R.T.); (S.G.I.-V.)
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.A.S.); (O.V.K.)
| | - Elena I. Stepchenkova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (E.R.T.); (S.G.I.-V.)
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.A.S.); (O.V.K.)
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Komluski J, Habig M, Stukenbrock EH. Repeat-Induced Point Mutation and Gene Conversion Coinciding with Heterochromatin Shape the Genome of a Plant-Pathogenic Fungus. mBio 2023:e0329022. [PMID: 37093087 DOI: 10.1128/mbio.03290-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Meiosis is associated with genetic changes in the genome-via recombination, gene conversion, and mutations. The occurrence of gene conversion and mutations during meiosis may further be influenced by the chromatin conformation, similar to the effect of the chromatin conformation on the mitotic mutation rate. To date, however, the exact distribution and type of meiosis-associated changes and the role of the chromatin conformation in this context are largely unexplored. Here, we determine recombination, gene conversion, and de novo mutations using whole-genome sequencing of all meiotic products of 23 individual meioses in Zymoseptoria tritici, an important pathogen of wheat. We confirm a high genome-wide recombination rate of 65 centimorgan (cM)/Mb and see higher recombination rates on the accessory compared to core chromosomes. A substantial fraction of 0.16% of all polymorphic markers was affected by gene conversions, showing a weak GC-bias and occurring at higher frequency in regions of constitutive heterochromatin, indicated by the histone modification H3K9me3. The de novo mutation rate associated with meiosis was approximately three orders of magnitude higher than the corresponding mitotic mutation rate. Importantly, repeat-induced point mutation (RIP), a fungal defense mechanism against duplicated sequences, is active in Z. tritici and responsible for the majority of these de novo meiotic mutations. Our results indicate that the genetic changes associated with meiosis are a major source of variability in the genome of an important plant pathogen and shape its evolutionary trajectory. IMPORTANCE The impact of meiosis on the genome composition via gene conversion and mutations is mostly poorly understood, in particular, for non-model species. Here, we sequenced all four meiotic products for 23 individual meioses and determined the genetic changes caused by meiosis for the important fungal wheat pathogen Zymoseptoria tritici. We found a high rate of gene conversions and an effect of the chromatin conformation on gene conversion rates. Higher conversion rates were found in regions enriched with the H3K9me3-a mark for constitutive heterochromatin. Most importantly, meiosis was associated with a much higher frequency of de novo mutations than mitosis; 78% of the meiotic mutations were caused by repeat-induced point mutations-a fungal defense mechanism against duplicated sequences. In conclusion, the genetic changes associated with meiosis are therefore a major factor shaping the genome of this fungal pathogen.
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Affiliation(s)
- Jovan Komluski
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Michael Habig
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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Ghasemi D, Ebrahimi-Barough S, Nekoofar MH, Mohamadnia A, Lotfibakhshaiesh N, Bahrami N, Karimi R, Taghdiri Nooshabadi V, Azami M, Hasanzadeh E, Ai J. Differentiation of human endometrial stem cells encapsulated in alginate hydrogel into oocyte-like cells. BIOIMPACTS : BI 2022; 13:229-240. [PMID: 37431484 PMCID: PMC10329755 DOI: 10.34172/bi.2022.23960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/02/2021] [Accepted: 12/04/2021] [Indexed: 08/25/2023]
Abstract
INTRODUCTION Human endometrial mesenchymal stem cells (hEnMSCs) are a rich source of mesenchymal stem cells (MSCs) with multi-lineage differentiation potential, making them an intriguing tool in regenerative medicine, particularly for the treatment of reproductive and infertility issues. The specific process of germline cell-derived stem cell differentiation remains unknown, the aim is to study novel ways to achieve an effective differentiation method that produces adequate and functioning human gamete cells. METHODS We adjusted the optimum retinoic acid (RA) concentration for enhancement of germ cell-derived hEnSCs generation in 2D cell culture after 7 days in this study. Subsequently, we developed a suitable oocyte-like cell induction media including RA and bone morphogenetic protein 4 (BMP4), and studied their effects on oocyte-like cell differentiation in 2D and 3D cell culture media utilizing cells encapsulated in alginate hydrogel. RESULTS Our results from microscopy analysis, real-time PCR, and immunofluorescence tests revealed that 10 µM RA concentration was the optimal dose for inducing germ-like cells after 7 days. We examined the alginate hydrogel structural characteristics and integrity by rheology analysis and SEM microscope. We also demonstrated encapsulated cell viability and adhesion in the manufactured hydrogel. We propose that in 3D cell cultures in alginate hydrogel, an induction medium containing 10 µM RA and 50 ng/mL BMP4 can enhance hEnSC differentiation into oocyte-like cells. CONCLUSION The production of oocyte-like cells using 3D alginate hydrogel may be viable in vitro approach for replacing gonad tissues and cells.
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Affiliation(s)
- Diba Ghasemi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Ebrahimi-Barough
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Nekoofar
- Department of Endodontics, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Abdolreza Mohamadnia
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nasrin Lotfibakhshaiesh
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Naghmeh Bahrami
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Craniomaxillofacial Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Roya Karimi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Vajihe Taghdiri Nooshabadi
- Department of Tissue Engineering and Applied Cell Sciences, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Mahmoud Azami
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Hasanzadeh
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Jafar Ai
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
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da Cunha NL, Xue H, Wright SI, Barrett SCH. Genetic variation and clonal diversity in floating aquatic plants: Comparative genomic analysis of water hyacinth species in their native range. Mol Ecol 2022; 31:5307-5325. [PMID: 35984729 DOI: 10.1111/mec.16664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/24/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
Many eukaryotic organisms reproduce by sexual and asexual reproduction. Genetic diversity in populations can be strongly dependent on the relative importance of these two reproductive modes. Here, we compare the amounts and patterns of genetic diversity in related water hyacinths that differ in their propensity for clonal propagation - highly clonal Eichhornia crassipes and moderately clonal E. azurea (Pontederiaceae). Our comparisons involved genotype-by-sequencing (GBS) of 137 E. crassipes ramets from 60 locations (193,495 nucleotide sites) and 118 E. azurea ramets from 53 locations (198,343 nucleotide sites) among six hydrological basins in central South America, the native range of both species. We predicted that because of more prolific clonal propagation, E. crassipes would exhibit lower clonal diversity than E. azurea. This prediction was supported by all measures of clonal diversity that we examined. Eichhornia crassipes also had a larger excess of heterozygotes at variant sites, another signature of clonality. However, genome-wide heterozygosity was not significantly different between the species. Eichhornia crassipes had weaker spatial genetic structure and lower levels of differentiation among hydrological basins than E. azurea, probably because of higher clonality and more extensive dispersal of its free-floating life form. Our findings for E. crassipes contrast with earlier studies from the invasive range which have reported very low levels of clonal diversity and extensive geographic areas of genetic uniformity.
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Affiliation(s)
- Nicolay Leme da Cunha
- Grupo de Ecología de la Polinización, INIBIOMA, CONICET-Universidad Nacional del Comahue, San Carlos de Bariloche, Rio Negro, Argentina.,Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Haoran Xue
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Feng W, Wang J, Liu X, Wu H, Liu M, Zhang H, Zheng X, Wang P, Zhang Z. Distinctive phosphorylation pattern during mitotic exit network (MEN) regulation is important for the development and pathogenicity of Magnaporthe oryzae. STRESS BIOLOGY 2022; 2:41. [PMID: 37676543 PMCID: PMC10441846 DOI: 10.1007/s44154-022-00063-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/31/2022] [Indexed: 09/08/2023]
Abstract
The mitotic exit network (MEN) pathway is a vital kinase cascade regulating the timely and correct progress of cell division. In the rice blast fungus Magnaporthe oryzae, the MEN pathway, consisting of conserved protein kinases MoSep1 and MoMob1-MoDbf2, is important in the development and pathogenicity of the fungus. We found that deletion of MoSEP1 affects the phosphorylation of MoMob1, but not MoDbf2, in contrast to what was found in the buddy yeast Saccharomyces cerevisiae, and verified this finding by in vitro phosphorylation assay and mass spectrometry (MS) analysis. We also found that S43 residue is the critical phosphor-site of MoMob1 by MoSep1, and proved that MoSep1-dependent MoMob1 phosphorylation is essential for cell division during the development of M. oryzae. We further provided evidence demonstrating that MoSep1 phosphorylates MoMob1 to maintain the cell cycle during vegetative growth and infection. Taken together, our results revealed that the MEN pathway has both distinct and conservative functions in regulating the cell cycle during the development and pathogenesis of M. oryzae.
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Affiliation(s)
- Wanzhen Feng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiansheng Wang
- Plant Protection and Quarantine Station of Nanjing, Nanjing, 210095, China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haowen Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Wang
- Departments of Microbiology, Immunology, and Parasitology, and Pediatrics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, 70112, USA
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China.
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China.
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Hirao AS, Watanabe Y, Hasegawa Y, Takagi T, Ueno S, Kaneko S. Mutational effects of chronic gamma radiation throughout the life cycle of Arabidopsis thaliana: Insight into radiosensitivity in the reproductive stage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156224. [PMID: 35644386 DOI: 10.1016/j.scitotenv.2022.156224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Organisms living on Earth have always been exposed to natural sources of ionizing radiation, but following recent nuclear disasters, these background levels have often increased regionally due to the addition of man-made sources of radiation. To assess the mutational effects of ubiquitously present radiation on plants, we performed a whole-genome resequencing analysis of mutations induced by chronic irradiation throughout the life cycle of Arabidopsis thaliana grown under controlled conditions. We obtained resequencing data from 36 second generation post-mutagenesis (M2) progeny derived from 12 first generation (M1) lines grown under gamma-irradiation conditions, ranging from 0.0 to 2.0 Gray per day (Gy/day), to identify de novo mutations, including single base substitutions (SBSs) and small insertions/deletions (INDELs). The relationship between de novo mutation frequency and radiation dose rate from 0.0 to 2.0 Gy/day was assessed by statistical modeling. The increase in de novo mutations in response to irradiation dose fit the negative binomial model, which accounted for the high variability of mutation frequency observed. Among the different types of mutations, SBSs were more prevalent than INDELs, and deletions were more frequent than insertions. Furthermore, we observed that the mutational effects of chronic radiation were greater during the reproductive stage. These results will provide valuable insights into practical strategies for analyzing mutational effects in wild plants growing in environments with various mutagens.
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Affiliation(s)
- Akira S Hirao
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan; National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Yoshito Watanabe
- Fukushima Project Headquarters, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Yoichi Hasegawa
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, Japan
| | - Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan; Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, Japan.
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11
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Michelotti LA, Sun S, Heitman J, James TY. Clonal evolution in serially passaged Cryptococcus neoformans × deneoformans hybrids reveals a heterogenous landscape of genomic change. Genetics 2022; 220:iyab142. [PMID: 34849836 PMCID: PMC8733418 DOI: 10.1093/genetics/iyab142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/14/2022] Open
Abstract
Cryptococcus neoformans × deneoformans hybrids (also known as serotype AD hybrids) are basidiomycete yeasts that are common in a clinical setting. Like many hybrids, the AD hybrids are largely locked at the F1 stage and are mostly unable to undergo normal meiotic reproduction. However, these F1 hybrids, which display a high (∼10%) sequence divergence are known to genetically diversify through mitotic recombination and aneuploidy, and this diversification may be adaptive. In this study, we evolved a single AD hybrid genotype in six diverse environments by serial passaging and then used genome resequencing of evolved clones to determine evolutionary mechanisms of adaptation. The evolved clones generally increased fitness after passaging, accompanied by an average of 3.3 point mutations, 2.9 loss of heterozygosity (LOH) events, and 0.7 trisomic chromosomes per clone. LOH occurred through nondisjunction of chromosomes, crossing over consistent with break-induced replication, and gene conversion, in that order of prevalence. The breakpoints of these recombination events were significantly associated with regions of the genome with lower sequence divergence between the parents and clustered in sub-telomeric regions, notably in regions that had undergone introgression between the two parental species. Parallel evolution was observed, particularly through repeated homozygosity via nondisjunction, yet there was little evidence of environment-specific parallel change for either LOH, aneuploidy, or mutations. These data show that AD hybrids have both a remarkable genomic plasticity and yet are challenged in the ability to recombine through sequence divergence and chromosomal rearrangements, a scenario likely limiting the precision of adaptive evolution to novel environments.
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Affiliation(s)
- Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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12
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Lesaffre T. Population-level consequences of inheritable somatic mutations and the evolution of mutation rates in plants. Proc Biol Sci 2021; 288:20211127. [PMID: 34493080 DOI: 10.1098/rspb.2021.1127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Inbreeding depression, that is the decrease in fitness of inbred relative to outbred individuals, was shown to increase strongly as life expectancy increases in plants. Because plants are thought to not have a separated germline, it was proposed that this pattern could be generated by somatic mutations accumulating during growth, since larger and more long-lived species have more opportunities for mutations to accumulate. A key determinant of the role of somatic mutations is the rate at which they occur, which probably differs between species because mutation rates may evolve differently in species with constrasting life histories. In this paper, I study the evolution of the mutation rates in plants, and consider the population-level consequences of inheritable somatic mutations given this evolution. I show that despite substantially lower somatic and meiotic mutation rates, more long-lived species still tend to accumulate larger amounts of deleterious mutations because of the increased number of opportunities they have to acquire mutations during growth, leading to higher levels of inbreeding depression in these species. However, the magnitude of this increase depends strongly on how mutagenic meiosis is relative to growth, to the point of being close to non-existent in some situations.
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Affiliation(s)
- Thomas Lesaffre
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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13
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Yang Q, Li F, Miao Y, Luo X, Dai S, Liu J, Niu W, Sun Y. CdSe/ZnS quantum dots induced spermatogenesis dysfunction via autophagy activation. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122327. [PMID: 32454327 DOI: 10.1016/j.jhazmat.2020.122327] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/23/2020] [Accepted: 02/15/2020] [Indexed: 06/11/2023]
Abstract
Recent researches have demonstrated that many nanoparticles are harmful to spermatogenesis. However, the reported nanoparticles -elicited testicular pathologies have been mostly confined to hormone levels and sperm quality and quantity, the detail mechanism is still largely unknown and the strategies to reduce the toxicity of nanoparticles on testis are lacking. Here, we found that CdSe/ZnS quantum dots (QDs) exposure impair double-strand break (DSB) repair in spermatocyte, leading to the disruption of meiotic progression and thus cell apoptosis and decreased sperm production. Furthermore, we found that QDs exposure elevates the autophagy. Crucially, both in vitro and in vivo studies indicated that elevated autophagy could down-regulate the expression of the genes responsible for homologous recombination, which is the main pathway for DSB repair during meiosis, indicating that spermatogenesis impairment by CdSe/ZnS QDs is mediated by autophagy. Consequently, injection of autophagy inhibitor (3-MA) restore DSB repair in spermatocytes, resulting in prevention of spermatocyte apoptosis and recovery of spermatogenesis. Our studies strongly indicate that autophagy is key for eliciting the spermatogenesis dysfunction after nanoparticle exposure, and autophagy inhibition can be used as a potential clinical remedy for alleviating the male reproductive toxicity of nanoparticles.
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Affiliation(s)
- Qingling Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Fangyuan Li
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanyan Miao
- Institute of Molecular Medicine, Renjin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaoyan Luo
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanjun Dai
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinhao Liu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenbin Niu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingpu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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14
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Zhao Y, Wang Y, Upadhyay S, Xue C, Lin X. Activation of Meiotic Genes Mediates Ploidy Reduction during Cryptococcal Infection. Curr Biol 2020; 30:1387-1396.e5. [PMID: 32109388 DOI: 10.1016/j.cub.2020.01.081] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/04/2019] [Accepted: 01/28/2020] [Indexed: 12/23/2022]
Abstract
Cryptococcus neoformans is a global human fungal pathogen that causes fatal meningoencephalitis in mostly immunocompromised individuals. During pulmonary infection, cryptococcal cells form large polyploid cells that exhibit increased resistance to host immune attack and are proposed to contribute to the latency of cryptococcal infection. These polyploid titan cells can generate haploid and aneuploid progeny that may result in systemic infection. What triggers cryptococcal polyploidization and how ploidy reduction is achieved remain open questions. Here, we discovered that Cryptococcus cells polyploidize in response to genotoxic stresses that cause DNA double-strand breaks. Intriguingly, meiosis-specific genes are activated in C. neoformans and contribute to ploidy reduction, both in vitro and during infection in mice. Cryptococcal cells that activated their meiotic genes in mice were resistant to specific genotoxic stress compared to sister cells recovered from the same host tissue but without activation of meiotic genes. Our findings support the idea that meiotic genes, in addition to their conventional roles in classic sexual reproduction, contribute to adaptation of eukaryotic cells that undergo dramatic genome changes in response to genotoxic stress. The discovery has additional implications for evolution of sexual reproduction and the paradox of the presence of meiotic machinery in asexual species. Finally, our findings in this eukaryotic microbe mirror the revolutionary discoveries of the polyploidization and meiosis-like ploidy reduction process in cancer cells, suggesting that the reversible ploidy change itself could provide a general mechanism for rejuvenation to promote individual survival in response to stress.
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Affiliation(s)
- Youbao Zhao
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Yina Wang
- Public Health Research Institute Center, New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Srijana Upadhyay
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Chaoyang Xue
- Public Health Research Institute Center, New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, NJ 07103, USA.
| | - Xiaorong Lin
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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15
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Timing of appearance of new mutations during yeast meiosis and their association with recombination. Curr Genet 2020; 66:577-592. [DOI: 10.1007/s00294-019-01051-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/26/2019] [Accepted: 12/29/2019] [Indexed: 01/18/2023]
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