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Li J, Dai L, Feng Y, Cao Z, Ding Y, Xu H, Xu A, Du H. Multigenerational effects and mutagenicity of three flame retardants on germ cells in Caenorhabditis elegans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 269:115815. [PMID: 38091675 DOI: 10.1016/j.ecoenv.2023.115815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/14/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024]
Abstract
Flame retardants (FRs) have raised public concerns because of their environmental persistence and negative impacts on human health. Recent evidence has revealed that many FRs exhibit reproductive toxicities and transgenerational impacts, whereas the toxic effects of FRs on germ cells remain barely explored. Here we investigated the multigenerational effects of three flame retardants (TBBPA, TCEP and TCPP) on germ cell development in Caenorhabditis elegans, and examined the germ cell mutagenicity of these FRs by using whole genome sequencing. Parental exposure to three FRs markedly increased germ cell apoptosis, and impeded oogenesis in F1-F6 offspring. In addition, the double-increased mutation frequencies observed in progeny genomes uncover the mutagenic actions of FRs on germ cells. Analysis of mutation spectra revealed that these FRs predominantly induced point mutations at A:T base pairs, whereas both small and large indels were almost unaffected. These results revealed the long-term effects of FRs on development and genomic stability of germ cells, which may pose risks to environmental organisms and human reproductive health. Taken together, our findings suggest that germ cell mutagenicity should be carefully examined for the environmental risk assessment of FRs and other emerging pollutants.
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Affiliation(s)
- Jiali Li
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China
| | - Linglong Dai
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Science Island Branch, Graduate School of USTC, Hefei 230026, Anhui, China
| | - Yu Feng
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Science Island Branch, Graduate School of USTC, Hefei 230026, Anhui, China
| | - Zhenxiao Cao
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Yuting Ding
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Hao Xu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, Anhui, China
| | - An Xu
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China.
| | - Hua Du
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China.
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2
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Liu H, Sun M, Zhang J. Genomic estimates of mutation and substitution rates contradict the evolutionary speed hypothesis of the latitudinal diversity gradient. Proc Biol Sci 2023; 290:20231787. [PMID: 37876195 PMCID: PMC10598419 DOI: 10.1098/rspb.2023.1787] [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: 08/08/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
The latitudinal diversity gradient (LDG) refers to a decrease in biodiversity from the equator to the poles. The evolutionary speed hypothesis, backed by the metabolic theory of ecology, asserts that nucleotide mutation and substitution rates per site per year are higher and thereby speciation rates are higher at higher temperatures, generating the LDG. However, prior empirical investigations of the relationship between the temperature and mutation or substitution rate were based on a few genes and the results were mixed. We here revisit this relationship using genomic data. No significant correlation between the temperature and mutation rate is found in 13 prokaryotes or in 107 eukaryotes. An analysis of 234 diverse trios of bacterial taxa indicates that the synonymous substitution rate is not significantly associated with the growth temperature. The same data, however, reveal a significant negative association between the nonsynonymous substitution rate and temperature, which is explainable by a larger fraction of detrimental nonsynonymous mutations at higher temperatures due to a stronger demand for protein stability. We conclude that the evolutionary speed hypothesis of the LDG is unsupported by genomic data and advise that future mechanistic studies of the LDG should focus on other hypotheses.
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Affiliation(s)
- Haoxuan Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Evolutionary & Organismal Biology and the Fourth Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou 310058, People's Republic of China
| | - Mengyi Sun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
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Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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4
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Wang Y, Obbard DJ. Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis. Evol Lett 2023; 7:216-226. [PMID: 37475753 PMCID: PMC10355183 DOI: 10.1093/evlett/qrad027] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023] Open
Abstract
Mutation is the ultimate source of all genetic variation, and over the last 10 years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. In this meta-analysis, we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent-offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in the single-nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide diversity-while accounting for phylogenetic nonindependence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide diversity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply branching eukaryotic lineages-or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for amphibia and scarce for reptiles and fish.
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Affiliation(s)
- Yiguan Wang
- Corresponding author: Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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5
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Feng Y, Cao Z, Xu A, Du H. Evaluation of toxicity and mutagenicity of oxaliplatin on germ cells in an alternative in vivo model Caenorhabditis elegans. Food Chem Toxicol 2023:113902. [PMID: 37331561 DOI: 10.1016/j.fct.2023.113902] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
The platinum compound oxaliplatin is a widely used chemotherapeutic drug that shows a broad spectrum of activity in various human tumors. While the treatment-related side effects of oxaliplatin on directly treated individuals have been well-documented, little is known about the influence of oxaliplatin on germ cells and non-exposed progenies. Here we investigated the reproductive toxicity of oxaliplatin in a 3R-compliant in vivo model Caenorhabditis elegans, and evaluated the germ cell mutagenicity of oxaliplatin by using whole genome sequencing. Our results indicated that oxaliplatin treatment significantly disrupts development of spermatids and oocytes. By treating parental worms with oxaliplatin for three successive generations, sequencing data unveiled the clear mutagenic effects of oxaliplatin on germ cells. Analysis of genome-wide mutation spectra showed the preferentially induction of indels by oxaliplatin. In addition, we uncovered the involvement of translesion synthesis polymerase ζ in modulating mutagenic effects of oxaliplatin. These findings suggest that germ cell mutagenicity is worthy of consideration for the health risk assessment of chemotherapeutic drugs, while the combined use of alternative in vivo models and next generation sequencing technology appears to be a promising way for the preliminary safety assessment of various drugs.
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Affiliation(s)
- Yu Feng
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei, 230031, Anhui, PR China; Science Island Branch, Graduate School of USTC, Hefei, 230026, Anhui, PR China
| | - Zhenxiao Cao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei, 230031, Anhui, PR China; School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, 230026, Anhui, PR China
| | - An Xu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei, 230031, Anhui, PR China.
| | - Hua Du
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei, 230031, Anhui, PR China.
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6
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Huang J, Liao L, Wang G, Du Z, Wu Z. Reproductive toxicity of enrofloxacin in Caenorhabditis elegans involves oxidative stress-induced cell apoptosis. J Environ Sci (China) 2023; 127:726-737. [PMID: 36522101 DOI: 10.1016/j.jes.2022.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 06/17/2023]
Abstract
Fluoroquinolone antibiotics (FQs) that persist and bioaccumulate in the environment have aroused people's great concern. Here, we studied the adverse effects of FQs in soil animals of Caenorhabditis elegans via food-chronically exposure. The result shows C. elegans exposed to FQs exhibited reproductive toxicity with small-brood size and low-egg hatchability. To study the underlying mechanism, we conduct a deep investigation of enrofloxacin (ENR), one of the most frequently detected FQs, on nematodes which is one of commonly used animal indicator of soil sustainability. The concentration-effect curves simulated by the Hill model showed that the half effect concentrations (EC50) of ENR were (494.3 ± 272.9) µmol/kg and (107.4 ± 30.9) µmol/kg for the brood size and the hatchability, respectively. Differential gene expression between the control and the ENR-exposure group enriched with the oxidative stress and cell apoptosis pathways. The results together with the enzyme activity in oxidative stress and the cell corpses suggested that ENR-induced reproductive toxicity was related to germ cell apoptosis under oxidative stress. The risk quotients of some soil and livestock samples were calculated based on the threshold value of EC10 for the egg hatchability (2.65 µmol/kg). The results indicated that there was possible reproductive toxicity on the nematodes in certain agricultural soils for the FQs. This study suggested that chronic exposure to FQs at certain levels in environment would induce reproductive toxicity to the nematodes and might reduce the soil sustainability, alarming the environment risks of antibiotics abuse.
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Affiliation(s)
- Jiahao Huang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lizi Liao
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Guowei Wang
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China; Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Wuhan 430205, China.
| | - Zhongkun Du
- College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Zhengxing Wu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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7
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Mallard F, Noble L, Baer CF, Teotónio H. Variation in mutational (co)variances. G3 (BETHESDA, MD.) 2023; 13:jkac335. [PMID: 36548954 PMCID: PMC9911065 DOI: 10.1093/g3journal/jkac335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/10/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
Because of pleiotropy, mutations affect the expression and inheritance of multiple traits and, together with selection, are expected to shape standing genetic covariances between traits and eventual phenotypic divergence between populations. It is therefore important to find if the M matrix, describing mutational variances of each trait and covariances between traits, varies between genotypes. We here estimate the M matrix for six locomotion behavior traits in lines of two genotypes of the nematode Caenorhabditis elegans that accumulated mutations in a nearly neutral manner for 250 generations. We find significant mutational variance along at least one phenotypic dimension of the M matrices, but neither their size nor their orientation had detectable differences between genotypes. The number of generations of mutation accumulation, or the number of MA lines measured, was likely insufficient to sample enough mutations and detect potentially small differences between the two M matrices. We then tested if the M matrices were similar to one G matrix describing the standing genetic (co)variances of a population derived by the hybridization of several genotypes, including the two measured for M, and domesticated to a lab-defined environment for 140 generations. We found that the M and G were different because the genetic covariances caused by mutational pleiotropy in the two genotypes are smaller than those caused by linkage disequilibrium in the lab population. We further show that M matrices differed in their alignment with the lab population G matrix. If generalized to other founder genotypes of the lab population, these observations indicate that selection does not shape the evolution of the M matrix for locomotion behavior in the short-term of a few tens to hundreds of generations and suggests that the hybridization of C. elegans genotypes allows selection on new phenotypic dimensions of locomotion behavior.
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Affiliation(s)
- François Mallard
- Institut de Biologie de l’École Normale Supérieure, PSL Research University, CNRS UMR 8197, Inserm U1024, F-75005 Paris, France
| | - Luke Noble
- Institut de Biologie de l’École Normale Supérieure, PSL Research University, CNRS UMR 8197, Inserm U1024, F-75005 Paris, France
| | - Charles F Baer
- Department of Biology, University of Florida Genetics Institute, University of Florida, Gainsville, FL 32611, USA
| | - Henrique Teotónio
- Institut de Biologie de l’École Normale Supérieure, PSL Research University, CNRS UMR 8197, Inserm U1024, F-75005 Paris, France
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8
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Verbiest M, Maksimov M, Jin Y, Anisimova M, Gymrek M, Bilgin Sonay T. Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species. J Evol Biol 2023; 36:321-336. [PMID: 36289560 PMCID: PMC9990875 DOI: 10.1111/jeb.14106] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/29/2022] [Accepted: 08/01/2022] [Indexed: 02/03/2023]
Abstract
Short tandem repeats (STRs) are units of 1-6 bp that repeat in a tandem fashion in DNA. Along with single nucleotide polymorphisms and large structural variations, they are among the major genomic variants underlying genetic, and likely phenotypic, divergence. STRs experience mutation rates that are orders of magnitude higher than other well-studied genotypic variants. Frequent copy number changes result in a wide range of alleles, and provide unique opportunities for modulating complex phenotypes through variation in repeat length. While classical studies have identified key roles of individual STR loci, the advent of improved sequencing technology, high-quality genome assemblies for diverse species, and bioinformatics methods for genome-wide STR analysis now enable more systematic study of STR variation across wide evolutionary ranges. In this review, we explore mutation and selection processes that affect STR copy number evolution, and how these processes give rise to varying STR patterns both within and across species. Finally, we review recent examples of functional and adaptive changes linked to STRs.
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Affiliation(s)
- Max Verbiest
- Institute of Computational Life Sciences, School of Life Sciences and Facility ManagementZürich University of Applied SciencesWädenswilSwitzerland
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Mikhail Maksimov
- Department of Computer Science & EngineeringUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Ye Jin
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of BioengineeringUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Maria Anisimova
- Institute of Computational Life Sciences, School of Life Sciences and Facility ManagementZürich University of Applied SciencesWädenswilSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Melissa Gymrek
- Department of Computer Science & EngineeringUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Tugce Bilgin Sonay
- Institute of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNew YorkUSA
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9
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Cao Z, Wang M, Zhou T, Xu A, Du H. Whole-Genome Sequencing Reveals Germ Cell Mutagenicity of α-Endosulfan in Caenorhabditis elegans. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16024-16032. [PMID: 36239620 DOI: 10.1021/acs.est.2c06817] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Endosulfan is an extensively used organochlorine pesticide around the world, which was classified as a persistent organic pollutant (POP) in 2009. Although previous studies have documented the reproductive toxicity of endosulfan in a variety of organisms, little is known about the influence of endosulfan on the genome stability of germ cells and nonexposed progeny. Here we applied whole-genome sequencing to explore the germ cell mutagenicity of α-endosulfan in Caenorhabditis elegans (C. elegans). We found that, although low doses of α-endosulfan exhibited a minor effect on the reproductive capacity of C. elegans, chronic exposure to 1 μM α-endosulfan significantly increased the mutation frequencies of nonexposed progeny. Further analysis of genome-wide mutation spectra demonstrated that α-endosulfan preferentially elicited A:T → G:C substitutions and clustered mutations. By using worms deficient in DNA damage response genes, our results suggest the involvement of translesion synthesis polymerase η in modulating α-endosulfan-induced mutations in germ cells. Together, these observations reveal the germ cell mutagenicity of α-endosulfan in C. elegans and the possible underlying mechanism. In addition, our findings implicate that germ cell mutagenicity might be a necessary consideration for the health risk assessment of environmental chemicals such as POPs.
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Affiliation(s)
- Zhenxiao Cao
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, P. R. China
| | - Meimei Wang
- Department of Pathophysiology, School of Basic Medical Science, Anhui Medical University, No. 81 Mei-Shan Rd, Hefei 230032, Anhui, P. R. China
| | - Tong Zhou
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, P. R. China
| | - An Xu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, P. R. China
| | - Hua Du
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, P. R. China
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10
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Hasan AR, Lachapelle J, El-Shawa SA, Potjewyd R, Ford SA, Ness RW. Salt stress alters the spectrum of de novo mutation available to selection during experimental adaptation of Chlamydomonas reinhardtii. Evolution 2022; 76:2450-2463. [PMID: 36036481 DOI: 10.1111/evo.14604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/12/2022] [Indexed: 01/22/2023]
Abstract
The genetic basis of adaptation is driven by both selection and the spectrum of available mutations. Given that the rate of mutation is not uniformly distributed across the genome and varies depending on the environment, understanding the signatures of selection across the genome is aided by first establishing what the expectations of genetic change are from mutation. To determine the interaction between salt stress, selection, and mutation across the genome, we compared mutations observed in a selection experiment for salt tolerance in Chlamydomonas reinhardtii to those observed in mutation accumulation (MA) experiments with and without salt exposure. MA lines evolved under salt stress had a single-nucleotide mutation rate of 1.1 × 10 - 9 $1.1 \times 10^{-9}$ , similar to that of MA lines under standard conditions ( 9.6 × 10 - 10 $9.6 \times 10^{-10}$ ). However, we found that salt stress led to an increased rate of indel mutations, but that many of these mutations were removed under selection. Finally, lines adapted to salt also showed excess clustering of mutations in the genome and the co-expression network, suggesting a role for positive selection in retaining mutations in particular compartments of the genome during the evolution of salt tolerance. Our study shows that characterizing mutation rates and spectra expected under stress helps disentangle the effects of environment and selection during adaptation.
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Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Josianne Lachapelle
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Sara A El-Shawa
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.,Department of Mathematical and Computational Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Roman Potjewyd
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Scott A Ford
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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11
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Abstract
We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone-Lewontin's Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Saber S, Snyder M, Rajaei M, Baer CF. Mutation, selection, and the prevalence of the Caenorhabditis elegans heat-sensitive mortal germline phenotype. G3 (BETHESDA, MD.) 2022; 12:jkac063. [PMID: 35311992 PMCID: PMC9073675 DOI: 10.1093/g3journal/jkac063] [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] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/10/2022] [Indexed: 11/17/2022]
Abstract
Caenorhabditis elegans strains with the heat-sensitive mortal germline phenotype become progressively sterile over the course of a few tens of generations when maintained at temperatures near the upper range of C. elegans' tolerance. Mortal germline is transgenerationally heritable, and proximately under epigenetic control. Previous studies have suggested that mortal germline presents a relatively large mutational target and that mortal germline is not uncommon in natural populations of C. elegans. The mortal germline phenotype is not monolithic. Some strains exhibit a strong mortal germline phenotype, in which individuals invariably become sterile over a few generations, whereas other strains show a weaker (less penetrant) phenotype in which the onset of sterility is slower and more stochastic. We present results in which we (1) quantify the rate of mutation to the mortal germline phenotype and (2) quantify the frequency of mortal germline in a collection of 95 wild isolates. Over the course of ∼16,000 meioses, we detected one mutation to a strong mortal germline phenotype, resulting in a point estimate of the mutation rate UMrt≈ 6×10-5/genome/generation. We detected no mutations to a weak mortal germline phenotype. Six out of 95 wild isolates have a strong mortal germline phenotype, and although quantification of the weak mortal germline phenotype is inexact, the weak mortal germline phenotype is not rare in nature. We estimate a strength of selection against mutations conferring the strong mortal germline phenotype s¯≈0.1%, similar to selection against mutations affecting competitive fitness. The appreciable frequency of weak mortal germline variants in nature combined with the low mutation rate suggests that mortal germline may be maintained by balancing selection.
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Affiliation(s)
- Sayran Saber
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
| | - Michael Snyder
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
| | - Moein Rajaei
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- University of Florida Genetics Institute, Gainesville, FL 32610, USA
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Oman M, Alam A, Ness RW. How sequence context-dependent mutability drives mutation rate variation in the genome. Genome Biol Evol 2022; 14:6537538. [PMID: 35218359 PMCID: PMC8920511 DOI: 10.1093/gbe/evac032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 11/12/2022] Open
Abstract
The rate of mutations varies >100-fold across the genome, altering the rate of evolution, and susceptibility to genetic diseases. The strongest predictor of mutation rate is the sequence itself, varying 75-fold between trinucleotides. The fact that DNA sequence drives its own mutation rate raises a simple but important prediction; highly mutable sequences will mutate more frequently and eliminate themselves in favor of sequences with lower mutability, leading to a lower equilibrium mutation rate. However, purifying selection constrains changes in mutable sequences, causing higher rates of mutation. We conduct a simulation using real human mutation data to test if 1) DNA evolves to a low equilibrium mutation rate and 2) purifying selection causes a higher equilibrium mutation rate in the genome’s most important regions. We explore how this simple process affects sequence evolution in the genome, and discuss the implications for modeling evolution and susceptibility to DNA damage.
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Affiliation(s)
- Madeleine Oman
- Dept of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Dept of Biology, University of Toronto, Mississauga, Canada
| | - Aqsa Alam
- Dept of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Rob W Ness
- Dept of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Dept of Biology, University of Toronto, Mississauga, Canada.,Dept of Cell and Systems Biology, University of Toronto, Toronto, Canada
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Waneka G, Svendsen JM, Havird JC, Sloan DB. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias. Genetics 2021; 219:6346985. [PMID: 34849888 DOI: 10.1093/genetics/iyab116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/09/2021] [Indexed: 01/25/2023] Open
Abstract
Rapid mutation rates are typical of mitochondrial genomes (mtDNAs) in animals, but it is not clear why. The difficulty of obtaining measurements of mtDNA mutation that are not biased by natural selection has stymied efforts to distinguish between competing hypotheses about the causes of high mtDNA mutation rates. Several studies which have measured mtDNA mutations in nematodes have yielded small datasets with conflicting conclusions about the relative abundance of different substitution classes (i.e., the mutation spectrum). We therefore leveraged Duplex Sequencing, a high-fidelity DNA sequencing technique, to characterize de novo mtDNA mutations in Caenorhabditis elegans. This approach detected nearly an order of magnitude more mtDNA mutations than documented in any previous nematode mutation study. Despite an existing extreme AT bias in the C. elegans mtDNA (75.6% AT), we found that a significant majority of mutations increase genomic AT content. Compared to some prior studies in nematodes and other animals, the mutation spectrum reported here contains an abundance of CG→AT transversions, supporting the hypothesis that oxidative damage may be a driver of mtDNA mutations in nematodes. Furthermore, we found an excess of G→T and C→T changes on the coding DNA strand relative to the template strand, consistent with increased exposure to oxidative damage. Analysis of the distribution of mutations across the mtDNA revealed significant variation among protein-coding genes and as well as among neighboring nucleotides. This high-resolution view of mitochondrial mutations in C. elegans highlights the value of this system for understanding relationships among oxidative damage, replication error, and mtDNA mutation.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Joshua M Svendsen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
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