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Flynn JM, Yamashita YM. The implications of satellite DNA instability on cellular function and evolution. Semin Cell Dev Biol 2024; 156:152-159. [PMID: 37852904 DOI: 10.1016/j.semcdb.2023.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Abundant tandemly repeated satellite DNA is present in most eukaryotic genomes. Previous limitations including a pervasive view that it was uninteresting junk DNA, combined with challenges in studying it, are starting to dissolve - and recent studies have found important functions for satellite DNAs. The observed rapid evolution and implied instability of satellite DNA now has important significance for their functions and maintenance within the genome. In this review, we discuss the processes that lead to satellite DNA copy number instability, and the importance of mechanisms to manage the potential negative effects of instability. Satellite DNA is vulnerable to challenges during replication and repair, since it forms difficult-to-process secondary structures and its homology within tandem arrays can result in various types of recombination. Satellite DNA instability may be managed by DNA or chromatin-binding proteins ensuring proper nuclear localization and repair, or by proteins that process aberrant structures that satellite DNAs tend to form. We also discuss the pattern of satellite DNA mutations from recent mutation accumulation (MA) studies that have tracked changes in satellite DNA for up to 1000 generations with minimal selection. Finally, we highlight examples of satellite evolution from studies that have characterized satellites across millions of years of Drosophila fruit fly evolution, and discuss possible ways that selection might act on the satellite DNA composition.
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Affiliation(s)
- Jullien M Flynn
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, 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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Krasovec M, Hoshino M, Zheng M, Lipinska AP, Coelho SM. Low Spontaneous Mutation Rate in Complex Multicellular Eukaryotes with a Haploid-Diploid Life Cycle. Mol Biol Evol 2023; 40:msad105. [PMID: 37140022 PMCID: PMC10254074 DOI: 10.1093/molbev/msad105] [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: 03/09/2023] [Revised: 04/22/2023] [Accepted: 05/01/2023] [Indexed: 05/05/2023] Open
Abstract
The spontaneous mutation rate µ is a crucial parameter to understand evolution and biodiversity. Mutation rates are highly variable across species, suggesting that µ is susceptible to selection and drift and that species life cycle and life history may impact its evolution. In particular, asexual reproduction and haploid selection are expected to affect the mutation rate, but very little empirical data are available to test this expectation. Here, we sequence 30 genomes of a parent-offspring pedigree in the model brown alga Ectocarpus sp.7, and 137 genomes of an interspecific cross of the closely related brown alga Scytosiphon to have access to the spontaneous mutation rate of representative organisms of a complex multicellular eukaryotic lineage outside animals and plants, and to evaluate the potential impact of life cycle on the mutation rate. Brown algae alternate between a haploid and a diploid stage, both multicellular and free living, and utilize both sexual and asexual reproduction. They are, therefore, excellent models to empirically test expectations of the effect of asexual reproduction and haploid selection on mutation rate evolution. We estimate that Ectocarpus has a base substitution rate of µbs = 4.07 × 10-10 per site per generation, whereas the Scytosiphon interspecific cross had µbs = 1.22 × 10-9. Overall, our estimations suggest that these brown algae, despite being multicellular complex eukaryotes, have unusually low mutation rates. In Ectocarpus, effective population size (Ne) could not entirely explain the low µbs. We propose that the haploid-diploid life cycle, combined with extensive asexual reproduction, may be additional key drivers of the mutation rate in these organisms.
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Affiliation(s)
- Marc Krasovec
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Masakazu Hoshino
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Min Zheng
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
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4
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Gill SE, Chain FJJ. Very Low Rates of Spontaneous Gene Deletions and Gene Duplications in Dictyostelium discoideum. J Mol Evol 2023; 91:24-32. [PMID: 36484794 PMCID: PMC9849192 DOI: 10.1007/s00239-022-10081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
The study of spontaneous mutation rates has revealed a wide range of heritable point mutation rates across species, but there are comparatively few estimates for large-scale deletion and duplication rates. The handful of studies that have directly calculated spontaneous rates of deletion and duplication using mutation accumulation lines have estimated that genes are duplicated and deleted at orders of magnitude greater rates than the spontaneous point mutation rate. In our study, we tested whether spontaneous gene deletion and gene duplication rates are also high in Dictyostelium discoideum, a eukaryote with among the lowest point mutation rates (2.5 × 10-11 per site per generation) and an AT-rich genome (GC content of 22%). We calculated mutation rates of gene deletions and duplications using whole-genome sequencing data originating from a mutation accumulation experiment and determined the association between the copy number mutations and GC content. Overall, we estimated an average of 3.93 × 10-8 gene deletions and 1.18 × 10-8 gene duplications per gene per generation. While orders of magnitude greater than their point mutation rate, these rates are much lower compared to gene deletion and duplication rates estimated from mutation accumulation lines in other organisms (that are on the order of ~ 10-6 per gene/generation). The deletions and duplications were enriched in regions that were AT-rich even compared to the genomic background, in contrast to our expectations if low GC content was contributing to low mutation rates. The low deletion and duplication mutation rates in D. discoideum compared to other eukaryotes mirror their low point mutation rates, supporting previous work suggesting that this organism has high replication fidelity and effective molecular machinery to avoid the accumulation of mutations in their genome.
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Affiliation(s)
- Shelbi E Gill
- Department of Biology, University of Massachusetts Lowell, Lowell, MA, 01854-2874, USA.
| | - Frédéric J J Chain
- Department of Biology, University of Massachusetts Lowell, Lowell, MA, 01854-2874, USA.
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5
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Hiltunen M, Ament-Velásquez SL, Ryberg M, Johannesson H. Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades. Proc Natl Acad Sci U S A 2022; 119:e2208575119. [PMID: 36343254 PMCID: PMC9674265 DOI: 10.1073/pnas.2208575119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/02/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a Marasmius oreades fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.
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Affiliation(s)
- Markus Hiltunen
- Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | | | - Martin Ryberg
- Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
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6
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Adiba S, Forget M, De Monte S. Evolving social behaviour through selection of single-cell adhesion in Dictyostelium discoideum. iScience 2022; 25:105006. [PMID: 36105585 PMCID: PMC9464967 DOI: 10.1016/j.isci.2022.105006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
The social amoeba Dictyostelium discoideum commonly forms chimeric fruiting bodies. Genetic variants that produce a higher proportion of spores are predicted to undercut multicellular organization unless cooperators assort positively. Cell adhesion is considered a primary factor driving such assortment, but evolution of adhesion has not been experimentally connected to changes in social performance. We modified by experimental evolution the efficiency of individual cells in attaching to a surface. Surprisingly, evolution appears to have produced social cooperators irrespective of whether stronger or weaker adhesion was selected. Quantification of reproductive success, cell-cell adhesion, and developmental patterns, however, revealed two distinct social behaviors, as captured when the classical metric for social success is generalized by considering clonal spore production. Our work shows that cell mechanical interactions can constrain the evolution of development and sociality in chimeras and that elucidation of proximate mechanisms is necessary to understand the ultimate emergence of multicellular organization. Cooperative behavior evolved as a pleiotropic effect of selection for surface adhesion Multicellular development of evolved lines with the ancestor follows two different paths A metric of social behavior including clonal development differentiates these two paths
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Affiliation(s)
- Sandrine Adiba
- Institut de Biologie de l’ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Corresponding author
| | - Mathieu Forget
- Institut de Biologie de l’ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Silvia De Monte
- Institut de Biologie de l’ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
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7
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Williams FN, Scaglione KM. Insights on Microsatellite Characteristics, Evolution, and Function From the Social Amoeba Dictyostelium discoideum. Front Neurosci 2022; 16:886837. [PMID: 35769695 PMCID: PMC9234386 DOI: 10.3389/fnins.2022.886837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Microsatellites are repetitive sequences commonly found in the genomes of higher organisms. These repetitive sequences are prone to expansion or contraction, and when microsatellite expansion occurs in the regulatory or coding regions of genes this can result in a number of diseases including many neurodegenerative diseases. Unlike in humans and other organisms, the social amoeba Dictyostelium discoideum contains an unusually high number of microsatellites. Intriguingly, many of these microsatellites fall within the coding region of genes, resulting in nearly 10,000 homopolymeric repeat proteins within the Dictyostelium proteome. Surprisingly, among the most common of these repeats are polyglutamine repeats, a type of repeat that causes a class of nine neurodegenerative diseases in humans. In this minireview, we summarize what is currently known about homopolymeric repeats and microsatellites in Dictyostelium discoideum and discuss the potential utility of Dictyostelium for identifying novel mechanisms that utilize and regulate regions of repetitive DNA.
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Affiliation(s)
- Felicia N. Williams
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
| | - K. Matthew Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
- Department of Neurology, Duke University, Durham, NC, United States
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, United States
- *Correspondence: K. Matthew Scaglione,
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8
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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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9
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Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
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10
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de Oliveira JL, Morales AC, Hurst LD, Urrutia AO, Thompson CRL, Wolf JB. Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias. Mol Biol Evol 2021; 38:3247-3266. [PMID: 33871580 PMCID: PMC8321536 DOI: 10.1093/molbev/msab099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alternative synonymous codons are often used at unequal frequencies. Classically, studies of such codon usage bias (CUB) attempted to separate the impact of neutral from selective forces by assuming that deviations from a predicted neutral equilibrium capture selection. However, GC-biased gene conversion (gBGC) can also cause deviation from a neutral null. Alternatively, selection has been inferred from CUB in highly expressed genes, but the accuracy of this approach has not been extensively tested, and gBGC can interfere with such extrapolations (e.g., if expression and gene conversion rates covary). It is therefore critical to examine deviations from a mutational null in a species with no gBGC. To achieve this goal, we implement such an analysis in the highly AT rich genome of Dictyostelium discoideum, where we find no evidence of gBGC. We infer neutral CUB under mutational equilibrium to quantify "adaptive codon preference," a nontautologous genome wide quantitative measure of the relative selection strength driving CUB. We observe signatures of purifying selection consistent with selection favoring adaptive codon preference. Preferred codons are not GC rich, underscoring the independence from gBGC. Expression-associated "preference" largely matches adaptive codon preference but does not wholly capture the influence of selection shaping patterns across all genes, suggesting selective constraints associated specifically with high expression. We observe patterns consistent with effects on mRNA translation and stability shaping adaptive codon preference. Thus, our approach to quantifying adaptive codon preference provides a framework for inferring the sources of selection that shape CUB across different contexts within the genome.
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Affiliation(s)
- Janaina Lima de Oliveira
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, 40170-115, Brazil.,Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Atahualpa Castillo Morales
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Laurence D Hurst
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Araxi O Urrutia
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.,Instituto de Ecologia, UNAM, Ciudad de Mexico 04510, Mexico
| | - Christopher R L Thompson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Jason B Wolf
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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11
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Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum. G3-GENES GENOMES GENETICS 2020; 10:3445-3452. [PMID: 32732307 PMCID: PMC7466956 DOI: 10.1534/g3.120.401578] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium discoideum, a key model organism in molecular, cellular, evolutionary and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10−11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in D. discoideum are highly A/T biased. This bias likely contributes both to the high genomic AT content and to the formation of simple sequence repeats in the AT-rich genome of Dictyostelium discoideum. In contrast to the situation in other surveyed unicellular eukaryotes, indel rates far exceed the base-substitution mutation rate in this organism with a high proportion of 3n indels, particularly in regions without simple sequence repeats. Like ciliates, D. discoideum has a large effective population size, reducing the power of random genetic drift, magnifying the effect of selection on replication fidelity, in principle allowing D. discoideum to evolve an extremely low base-substitution mutation rate.
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12
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Krasovec M, Sanchez-Brosseau S, Piganeau G. First Estimation of the Spontaneous Mutation Rate in Diatoms. Genome Biol Evol 2020; 11:1829-1837. [PMID: 31218358 PMCID: PMC6604790 DOI: 10.1093/gbe/evz130] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2019] [Indexed: 12/25/2022] Open
Abstract
Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation-accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10-10 and the insertion-deletion mutation rate is μid = 1.58 × 10-11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.
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Affiliation(s)
- Marc Krasovec
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France
| | - Gwenael Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France.,Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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13
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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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14
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Katju V, Bergthorsson U. Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches. Genome Biol Evol 2019; 11:136-165. [PMID: 30476040 PMCID: PMC6330053 DOI: 10.1093/gbe/evy252] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Abstract
Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurements of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters, such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations. Rapidly emerging next-generating sequencing technology has supplanted this phenotype-dependent approach, enabling direct empirical estimates of the mutation rate and a more nuanced understanding of the relative contributions of different classes of mutations to the standing genetic variation. Whole-genome sequencing of MA lines bears immense potential to provide a unified account of the evolutionary process at multiple levels-the genetic basis of variation, and the evolutionary dynamics of mutations under the forces of selection and drift. In this review, we have attempted to synthesize key insights into the spontaneous mutation process that are rapidly emerging from the partnering of classical MA experiments with high-throughput sequencing, with particular emphasis on the spontaneous rates and molecular properties of different mutational classes in nuclear and mitochondrial genomes of diverse taxa, the contribution of mutations to the evolution of gene expression, and the rate and stability of transgenerational epigenetic modifications. Future advances in sequencing technologies will enable greater species representation to further refine our understanding of mutational parameters and their functional consequences.
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Affiliation(s)
- Vaishali Katju
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
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15
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Tang X, Zhong Z, Ren Q, Liu B, Zhang Y. A Single Transcript CRISPR-Cas9 System for Multiplex Genome Editing in Plants. Methods Mol Biol 2019; 1917:75-82. [PMID: 30610629 DOI: 10.1007/978-1-4939-8991-1_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The CRISPR-Cas9 system has been widely adopted in genome editing. By changing the 20 bp guide sequence, it can easily edit any sequence adjacent to a protospacer adjacent motif (PAM) in a genome. Multiplex genome editing could be accomplished with simultaneous expression of multiple single-guide RNAs (sgRNA). Given that sgRNAs are expressed by Pol III promoters, multiplex genome editing is conventionally done by assembly of multiple complete sgRNA expression cassettes together, which can be a challenge in vector construction. Here, we described a multiplex genome editing system based on a single transcript unit CRISPR-Cas9 (STU CRISPR-Cas9) expression system driven by a single Pol II promoter. It represents a novel approach for multiplex genome editing.
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Affiliation(s)
- Xu Tang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qiurong Ren
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Binglin Liu
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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16
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Christy SF, Wernick RI, Lue MJ, Velasco G, Howe DK, Denver DR, Estes S. Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans. Genome Biol Evol 2018; 9:3008-3022. [PMID: 29069345 PMCID: PMC5714194 DOI: 10.1093/gbe/evx222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2017] [Indexed: 12/30/2022] Open
Abstract
A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1. The original intent of the study was to assess the effect of electron transport chain dysfunction involving elevated reactive oxygen species production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared with their ancestor. Likewise, the gas-1 MA lines experienced partial recovery to wildtype reactive oxygen species levels. Whole-genome sequencing and analysis revealed that the molecular spectrum but not the overall rate of nuclear DNA mutation differed from wildtype patterns. Further analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome, and could be classified into a small number of functional-genomic categories. Characterization of a backcrossed four-mutation set isolated from one gas-1 MA line revealed this combination to be beneficial on both gas-1 mutant and wildtype genetic backgrounds. Our combined results suggest that selection favoring beneficial mutations can be powerful even under unfavorable population genetic conditions, and agree with fitness landscape theory predicting an inverse relationship between population fitness and the likelihood of adaptation.
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Affiliation(s)
| | | | | | | | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University
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17
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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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18
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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: 13] [Impact Index Per Article: 2.2] [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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19
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Abstract
Sex in social amoebae (or dictyostelids) has a number of striking features. Dictyostelid zygotes do not proliferate but grow to a large size by feeding on other cells of the same species, each zygote ultimately forming a walled structure called a macrocyst. The diploid macrocyst nucleus undergoes meiosis, after which a single meiotic product survives to restart haploid vegetative growth. Meiotic recombination is generally initiated by the Spo11 enzyme, which introduces DNA double-strand breaks. Uniquely, as far as is known among sexual eukaryotes, dictyostelids lack a SPO11 gene. Despite this, recombination occurs at high frequencies during meiosis in dictyostelids, through unknown mechanisms. The molecular processes underlying these events, and the evolutionary drivers that brought them into being, may shed light on the genetic conflicts that occur within and between genomes, and how they can be resolved.
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20
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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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21
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Tekle YI, Wood FC, Katz LA, Cerón-Romero MA, Gorfu LA. Amoebozoans Are Secretly but Ancestrally Sexual: Evidence for Sex Genes and Potential Novel Crossover Pathways in Diverse Groups of Amoebae. Genome Biol Evol 2017; 9:375-387. [PMID: 28087686 PMCID: PMC5381635 DOI: 10.1093/gbe/evx002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2017] [Indexed: 12/12/2022] Open
Abstract
Sex is beneficial in eukaryotes as it can increase genetic diversity, reshuffle their genomes, and purge deleterious mutations. Yet, its evolution remains a mystery. The eukaryotic clade supergroup Amoebozoa encompasses diverse lineages of polymorphic amoeboid forms, including both free-living and parasitic lineages. The group is generally believed to be asexual, though recent studies show that some of its members are implicated in cryptic forms of sexual cycles. In this study, we conduct a comprehensive inventory and analysis of genes involved in meiosis and related processes, in order to investigate the evolutionary history of sex in the clade. We analyzed genomic and transcriptomic data of 39 amoebozoans representing all major subclades of Amoebozoa. Our results show that Amoebozoa possess most of the genes exclusive to meiosis but lack genes encoding synaptonemal complex (SC). The absence of SC genes is discussed in the context of earlier studies that reported ultrastructural evidence of SC in some amoebae. We also find interclade and intrageneric variation in sex gene distribution, indicating diversity in sexual pathways in the group. Particularly, members of Mycetozoa engage in a novel sexual pathway independent of the universally conserved meiosis initiator gene, SPO11. Our findings strongly suggest that not only do amoebozoans possess sex genes in their genomes, but also, based on the transcriptome evidence, the present sex genes are functional. We conclude that Amoebozoa is ancestrally sexual, contrary to the long held belief that most of its members are asexual. Thus, asexuality in Amoebozoa, if confirmed to be present, is a derived-trait that appeared later in their evolution.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, Atlanta, Georgia
| | - Fiona C Wood
- Department of Biology, Spelman College, Atlanta, Georgia
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst
| | - Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst
| | - Lydia A Gorfu
- Department of Biology, Spelman College, Atlanta, Georgia
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22
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Konrad A, Thompson O, Waterston RH, Moerman DG, Keightley PD, Bergthorsson U, Katju V. Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size. Mol Biol Evol 2017; 34:1319-1334. [PMID: 28087770 DOI: 10.1093/molbev/msx051] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10, and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection. New mutations were identified by Illumina paired-end sequencing of 86 mtDNA genomes across 35 experimental lines and compared with published genomes of natural isolates. The spontaneous mitochondrial mutation rate was estimated at 1.05 × 10-7/site/generation. A strong G/C→A/T mutational bias was observed in both the MA lines and the natural isolates. This suggests that the low G + C content at synonymous sites is the product of mutation bias rather than selection as previously proposed. The mitochondrial effective population size per worm generation was estimated to be 62. Although it was previously concluded that heteroplasmy was rare in C. elegans, the vast majority of mutations in this study were heteroplasmic despite an experimental regime exceeding 400 generations. The frequencies of frameshift and nonsynonymous mutations were negatively correlated with population size, which suggests their deleterious effects on fitness and a potent role for selection in their eradication.
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Affiliation(s)
- Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Owen Thompson
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Donald G Moerman
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
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23
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Martínez-García R, Tarnita CE. Seasonality can induce coexistence of multiple bet-hedging strategies in Dictyostelium discoideum via storage effect. J Theor Biol 2017; 426:104-116. [PMID: 28536035 DOI: 10.1016/j.jtbi.2017.05.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 02/06/2023]
Abstract
The social amoeba Dictyostelium discoideum has been recently suggested as an example of bet-hedging in microbes. In the presence of resources, amoebae reproduce as unicellular organisms. Resource depletion, however, leads to a starvation phase in which the population splits between aggregators, which form a fruiting body made of a stalk and resistant spores, and non-aggregators, which remain as vegetative cells. Spores are favored when starvation periods are long, but vegetative cells can exploit resources in environments where food replenishes quickly. The investment in aggregators versus non-aggregators can therefore be understood as a bet-hedging strategy that evolves in response to stochastic starvation times. A genotype (or strategy) is defined by the balance between each type of cells. In this framework, if the ecological conditions on a patch are defined in terms of the mean starvation time (i.e. time between the onset of starvation and the arrival of a new food pulse), a single genotype dominates each environment, which is inconsistent with the huge genetic diversity observed in nature. Here we investigate whether seasonality, represented by a periodic, wet-dry alternation in the mean starvation times, allows the coexistence of several strategies in a single patch. We study this question in a non-spatial (well-mixed) setting in which different strains compete for a common pool of resources over a sequence of growth-starvation cycles. We find that seasonality induces a temporal storage effect that can promote the stable coexistence of multiple genotypes. Two conditions need to be met in our model. First, there has to be a temporal niche partitioning (two well-differentiated habitats within the year), which requires not only different mean starvation times between seasons but also low variance within each season. Second, each season's well-adapted strain has to grow and create a large enough population that permits its survival during the subsequent unfavorable season, which requires the number of growth-starvation cycles within each season to be sufficiently large. These conditions allow the coexistence of two bet-hedging strategies. Additional tradeoffs among life-history traits can expand the range of coexistence and increase the number of coexisting strategies, contributing toward explaining the genetic diversity observed in D. discoideum. Although focused on this cellular slime mold, our results are general and may be easily extended to other microbes.
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Affiliation(s)
- Ricardo Martínez-García
- Department of Ecology and Evolutionary Biology, Princeton University. Princeton NJ 08544, USA
| | - Corina E Tarnita
- Department of Ecology and Evolutionary Biology, Princeton University. Princeton NJ 08544, USA.
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24
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Zhu YO, Sherlock G, Petrov DA. Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum. PLoS Genet 2017; 13:e1006455. [PMID: 28046117 PMCID: PMC5207638 DOI: 10.1371/journal.pgen.1006455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 11/03/2016] [Indexed: 12/04/2022] Open
Abstract
The characterization of mutational spectra is usually carried out in one of three ways-by direct observation through mutation accumulation (MA) experiments, through parent-offspring sequencing, or by indirect inference from sequence data. Direct observations of spontaneous mutations with MA experiments are limited, given (i) the rarity of spontaneous mutations, (ii) applicability only to laboratory model species with short generation times, and (iii) the possibility that mutational spectra under lab conditions might be different from those observed in nature. Trio sequencing is an elegant solution, but it is not applicable in all organisms. Indirect inference, usually from divergence data, faces no such technical limitations, but rely upon critical assumptions regarding the strength of natural selection that are likely to be violated. Ideally, new mutational events would be directly observed before the biased filter of selection, and without the technical limitations common to lab experiments. One approach is to identify very young mutations from population sequencing data. Here we do so by leveraging two characteristics common to all new mutations-new mutations are necessarily rare in the population, and absent in the genomes of immediate relatives. From 132 clinical yeast strains, we were able to identify 1,425 putatively new mutations and show that they exhibit extremely low signatures of selection, as well as display a mutational spectrum that is similar to that identified by a large scale MA experiment. We verify that population sequencing data are a potential wealth of information for inferring mutational spectra, and should be considered for analysis where MA experiments are infeasible or especially tedious.
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Affiliation(s)
- Yuan O. Zhu
- Department of Genetics, Stanford University, Stanford, CA, United States of America
- Department of Biology, Stanford University, Stanford, CA, United States of America
- Genome Institute of Singapore, Singapore
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA, United States of America
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25
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Martínez-García R, Tarnita CE. Lack of Ecological and Life History Context Can Create the Illusion of Social Interactions in Dictyostelium discoideum. PLoS Comput Biol 2016; 12:e1005246. [PMID: 27977666 PMCID: PMC5157950 DOI: 10.1371/journal.pcbi.1005246] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 11/14/2016] [Indexed: 12/13/2022] Open
Abstract
Studies of social microbes often focus on one fitness component (reproductive success within the social complex), with little information about or attention to other stages of the life cycle or the ecological context. This can lead to paradoxical results. The life cycle of the social amoeba Dictyostelium discoideum includes a multicellular stage in which not necessarily clonal amoebae aggregate upon starvation to form a possibly chimeric (genetically heterogeneous) fruiting body made of dead stalk cells and spores. The lab-measured reproductive skew in the spores of chimeras indicates strong social antagonism that should result in low genotypic diversity, which is inconsistent with observations from nature. Two studies have suggested that this inconsistency stems from the one-dimensional assessment of fitness (spore production) and that the solution lies in tradeoffs between multiple life-history traits, e.g.: spore size versus viability; and spore-formation (via aggregation) versus staying vegetative (as non-aggregated cells). We develop an ecologically-grounded, socially-neutral model (i.e. no social interactions between genotypes) for the life cycle of social amoebae in which we theoretically explore multiple non-social life-history traits, tradeoffs and tradeoff-implementing mechanisms. We find that spore production comes at the expense of time to complete aggregation, and, depending on the experimental setup, spore size and viability. Furthermore, experimental results regarding apparent social interactions within chimeric mixes can be qualitatively recapitulated under this neutral hypothesis, without needing to invoke social interactions. This allows for simple potential resolutions to the previously paradoxical results. We conclude that the complexities of life histories, including social behavior and multicellularity, can only be understood in the appropriate multidimensional ecological context, when considering all stages of the life cycle. Fitness in social microbes is often measured in terms of reproductive success in the social stage, with little regard to other stages of the life cycle (e.g. solitary) or to the ecological context. This approach can lead to seemingly paradoxical results that point to complex social interactions (e.g., social cheating) among individuals in the population. However, recent experimental studies in Dictyostelium discoideum, one of the most studied social microbes, have highlighted various tradeoffs among previously ignored non-social traits that should affect fitness. We develop an ecologically-motivated socially-neutral model for the life cycle of D. discoideum that combines these proposed traits and tradeoffs and proposes new ones to determine whether existing observations can be explained without the need to invoke social interactions. We confirm this expectation and conclude that the complexities of social behavior can only be understood in the appropriate ecological context, when considering a complete description of the life cycle.
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Affiliation(s)
- Ricardo Martínez-García
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton NJ, United States of America
| | - Corina E Tarnita
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton NJ, United States of America
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26
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Long H, Winter DJ, Chang AYC, Sung W, Wu SH, Balboa M, Azevedo RBR, Cartwright RA, Lynch M, Zufall RA. Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophil. Genome Biol Evol 2016; 8:3629-3639. [PMID: 27635054 PMCID: PMC5585995 DOI: 10.1093/gbe/evw223] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2016] [Indexed: 12/28/2022] Open
Abstract
Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate. Here, we tested the generality of this result among ciliates using Tetrahymena thermophila. We sequenced the genomes of 10 lines of T. thermophila that had each undergone approximately 1,000 generations of mutation accumulation (MA). We applied an existing mutation-calling pipeline and developed a new probabilistic mutation detection approach that directly models the design of an MA experiment and accommodates the noise introduced by mismapped reads. Our probabilistic mutation-calling method provides a straightforward way of estimating the number of sites at which a mutation could have been called if one was present, providing the denominator for our mutation rate calculations. From these methods, we find that T. thermophila has a germline base-substitution mutation rate of 7.61 × 10 - 12 per-site, per cell division, which is consistent with the low base-substitution mutation rate in P. tetraurelia. Over the course of the evolution experiment, genomic exclusion lines derived from the MA lines experienced a fitness decline that cannot be accounted for by germline base-substitution mutations alone, suggesting that other genetic or epigenetic factors must be involved. Because selection can only operate to reduce mutation rates based upon the "visible" mutational load, asexual reproduction with a transcriptionally silent germline may allow ciliates to evolve extremely low germline mutation rates.
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Affiliation(s)
- Hongan Long
- Department of Biology and Biochemistry, University of Houston, Houston, TX
- Department of Biology, Indiana University, Bloomington, IN
| | - David J Winter
- The Biodesign Institute, Arizona State University, Tempe, AZ
| | - Allan Y.-C Chang
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC
| | - Steven H Wu
- The Biodesign Institute, Arizona State University, Tempe, AZ
| | - Mariel Balboa
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | | | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX
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27
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Flynn JM, Chain FJ, Schoen DJ, Cristescu ME. Spontaneous Mutation Accumulation inDaphnia pulexin Selection-Free vs. Competitive Environments. Mol Biol Evol 2016; 34:160-173. [DOI: 10.1093/molbev/msw234] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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28
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Behringer MG, Hall DW. The repeatability of genome-wide mutation rate and spectrum estimates. Curr Genet 2016; 62:507-12. [PMID: 26919990 PMCID: PMC4930417 DOI: 10.1007/s00294-016-0573-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 01/11/2023]
Abstract
Over the last decade, mutation studies have grown in popularity due to the affordability and accessibility of whole genome sequencing. As the number of species in which spontaneous mutation has been directly estimated approaches 20 across two domains of life, questions arise over the repeatability of results in such experiments. Five species were identified in which duplicate mutation studies have been performed. Across these studies the difference in estimated spontaneous mutation rate is at most, weakly significant (p < 0.01). However, a highly significant (p < 10(-5)), threefold difference in the rate of insertions/deletions (indels) exists between two recent studies in Schizosaccharomyces pombe. Upon investigation of the ancestral genome sequence for both studies, a possible anti-mutator allele was identified. The observed variation in indel rate may imply that the use of indel markers, such as microsatellites, for the investigation of genetic diversity within and among populations may be inappropriate because of the assumption of uniform mutation rate within a species.
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Affiliation(s)
- Megan G Behringer
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, 47405, IN, USA.
| | - David W Hall
- Department of Genetics, University of Georgia, Athens, 3060, Georgia
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29
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Diwan D, Masubuchi Y, Furukawa T, Nishigaki K. Ordered genome change of plant and animal body cells revealed by the genome profiling method. FEBS Lett 2016; 590:2119-26. [PMID: 27277546 DOI: 10.1002/1873-3468.12248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/14/2016] [Accepted: 05/20/2016] [Indexed: 01/30/2023]
Abstract
In the past, it was widely thought that, although epigenetically different, the genome sequences of cells are basically the same in a single body. In retrospect, the genome-uniformity idea may have been naïve, considering that DNA polymerases cannot be perfect. Here, a systemic, not sporadic, genome change was demonstrated in a single plant (Arabidopsis) and animal (zebrafish) body using genome DNAs taken in an ordered manner using the genome profiling method. This can be explained because mutations accumulate additively in progeny cells, and these results are critically significant for developmental and oncological research.
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Affiliation(s)
- Deepti Diwan
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Yuki Masubuchi
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Tatsuya Furukawa
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
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30
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Abstract
Whole-genome sequencing provides a rapid and powerful method for identifying mutations on a global scale, and has spurred a renewed enthusiasm for classical genetic screens in model organisms. The most commonly characterized category of mutation consists of monogenic, recessive traits, due to their genetic tractability. Therefore, most of the mapping methods for mutation identification by whole-genome sequencing are directed toward alleles that fulfill those criteria (i.e., single-gene, homozygous variants). However, such approaches are not entirely suitable for the characterization of a variety of more challenging mutations, such as dominant and semidominant alleles or multigenic traits. Therefore, we have developed strategies for the identification of those classes of mutations, using polymorphism mapping in Caenorhabditis elegans as our model for validation. We also report an alternative approach for mutation identification from traditional recombinant crosses, and a solution to the technical challenge of sequencing sterile or terminally arrested strains where population size is limiting. The methods described herein extend the applicability of whole-genome sequencing to a broader spectrum of mutations, including classes that are difficult to map by traditional means.
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31
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Bloomfield G. Atypical ploidy cycles, Spo11, and the evolution of meiosis. Semin Cell Dev Biol 2016; 54:158-64. [PMID: 26811992 DOI: 10.1016/j.semcdb.2016.01.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/20/2016] [Indexed: 12/14/2022]
Abstract
The Spo11 protein induces DNA double strand breaks before the first division of meiosis, enabling the formation of the chiasmata that physically link homologous chromosomes as they align. Spo11 is an ancient and well conserved protein, related in sequence and structure to a DNA topoisomerase subunit found in Archaea as well as a subset of eukaryotes. However the origins of its meiotic function are unclear. This review examines some apparent exceptions to the rule that Spo11 activity is specific to, and required for meiosis. Spo11 appears to function in the context of unusual forms of ploidy reduction in some protists and fungi. One lineage of amoebae, the dictyostelids, is thought to undergo meiosis during its sexual cycle despite having lost Spo11 entirely. Further experimental characterisation of these and other non-canonical ploidy cycling mechanisms may cast light of the evolution of meiosis.
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Affiliation(s)
- Gareth Bloomfield
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom.
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32
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Genome-Wide Estimates of Mutation Rates and Spectrum in Schizosaccharomyces pombe Indicate CpG Sites are Highly Mutagenic Despite the Absence of DNA Methylation. G3-GENES GENOMES GENETICS 2015; 6:149-60. [PMID: 26564949 PMCID: PMC4704713 DOI: 10.1534/g3.115.022129] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We accumulated mutations for 1952 generations in 79 initially identical, haploid lines of the fission yeast Schizosaccharomyces pombe, and then performed whole-genome sequencing to determine the mutation rates and spectrum. We captured 696 spontaneous mutations across the 79 mutation accumulation (MA) lines. We compared the mutation spectrum and rate to a recently published equivalent experiment on the same species, and to another model ascomycetous yeast, the budding yeast Saccharomyces cerevisiae. While the two species are approximately 600 million years diverged from each other, they share similar life histories, genome size and genomic G/C content. We found that Sc. pombe and S. cerevisiae have similar mutation rates, but Sc. pombe exhibits a stronger insertion bias. Intriguingly, we observed an increased mutation rate at cytosine nucleotides, specifically CpG nucleotides, which is also seen in S. cerevisiae. However, the absence of methylation in Sc. pombe and the pattern of mutation at these sites, primarily C → A as opposed to C → T, strongly suggest that the increased mutation rate is not caused by deamination of methylated cytosines. This result implies that the high mutability of CpG dinucleotides in other species may be caused in part by a methylation-independent mechanism. Many of our findings mirror those seen in the recent study, despite the use of different passaging conditions, indicating that MA is a reliable method for estimating mutation rates and spectra.
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33
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Dissecting genetic and environmental mutation signatures with model organisms. Trends Genet 2015; 31:465-74. [PMID: 25940384 DOI: 10.1016/j.tig.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/31/2022]
Abstract
Deep sequencing has impacted on cancer research by enabling routine sequencing of genomes and exomes to identify genetic changes associated with carcinogenesis. Researchers can now use the frequency, type, and context of all mutations in tumor genomes to extract mutation signatures that reflect the driving mutational processes. Identifying mutation signatures, however, may not immediately suggest a mechanism. Consequently, several recent studies have employed deep sequencing of model organisms exposed to discrete genetic or environmental perturbations. These studies exploit the simpler genomes and availability of powerful genetic tools in model organisms to analyze mutation signatures under controlled conditions, forging mechanistic links between mutational processes and signatures. We discuss the power of this approach and suggest that many such studies may be on the horizon.
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34
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Saxer G, Krepps MD, Merkley ED, Ansong C, Deatherage Kaiser BL, Valovska MT, Ristic N, Yeh PT, Prakash VP, Leiser OP, Nakhleh L, Gibbons HS, Kreuzer HW, Shamoo Y. Mutations in global regulators lead to metabolic selection during adaptation to complex environments. PLoS Genet 2014; 10:e1004872. [PMID: 25501822 PMCID: PMC4263409 DOI: 10.1371/journal.pgen.1004872] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 11/04/2014] [Indexed: 01/12/2023] Open
Abstract
Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. Adaptation to a new environment with abundant and varied resources can be difficult to achieve by small incremental changes if many mutations are required to achieve even modest gains in fitness. Since changing complex environments are quite common in nature, we investigated how such an epistatic bottleneck can be avoided to allow rapid adaptation. We show that adaptive mutations arise repeatedly in independently evolved populations in the context of greatly increased genetic and phenotypic diversity. We go on to show that weak selection requiring substantial metabolic reprogramming can be readily achieved by mutations in the global response regulator arcA and the stress response regulator rpoS. We identified 46 unique single-nucleotide variants of arcA and 18 mutations in rpoS, nine of which resulted in stop codons or large deletions, suggesting that subtle modulations of ArcA function and knockouts of rpoS are largely responsible for the metabolic shifts leading to adaptation. These mutations allow a higher order metabolic selection that eliminates epistatic bottlenecks, which could occur when many changes would be required. Proteomic and carbohydrate analysis of adapting E. coli populations revealed an up-regulation of enzymes associated with the TCA cycle and amino acid metabolism, and an increase in the secretion of putrescine. The overall effect of adaptation across populations is to redirect and efficiently utilize uptake and catabolism of abundant amino acids. Concomitantly, there is a pronounced spread of more ecologically limited strains that results from specialization through metabolic erosion. Remarkably, the global regulators arcA and rpoS can provide a “one-step” mechanism of adaptation to a novel environment, which highlights the importance of global resource management as a powerful strategy to adaptation. Changing environmental conditions are the norm in biology. However, understanding adaptation to complex environments presents many challenges. For example, adaptation to resource-rich environments can potentially have many successful evolutionary trajectories to increased fitness. Even in conditions of plenty, the utilization of numerous but novel resources can require multiple mutations before a benefit is accrued. We evolved two bacterial species isolated from the gut of healthy humans in two different, resource-rich media commonly used in the laboratory. We anticipated that under weak selection the population would evolve tremendous genetic diversity. Despite such a complex genetic background we were able to identify a strong degree of parallel evolution and using a combination of population proteomic and population genomic approaches we show that two global regulators, arcA and rpoS, are the principle targets of selection. Up-regulation of the different metabolic pathways that are controlled by these global regulators in combination with up-regulation of transporters that transport nutrients into the cell revealed increased use of the novel resources. Thus global regulators can provide a one-step model to shift metabolism efficiently and provide rapid a one-step reprogramming of the cell metabolic profile.
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Affiliation(s)
- Gerda Saxer
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail: (GS); (YS)
| | - Michael D. Krepps
- United States Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, United States of America
- EXCET, Inc, Springfield, Virginia, United States of America
| | - Eric D. Merkley
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Charles Ansong
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | | | | | - Nikola Ristic
- Department of Computer Science, Rice University, Houston, Texas, United States of America
| | - Ping T. Yeh
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Vittal P. Prakash
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Owen P. Leiser
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, Texas, United States of America
| | - Henry S. Gibbons
- United States Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, United States of America
| | - Helen W. Kreuzer
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail: (GS); (YS)
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35
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Ségurel L, Wyman MJ, Przeworski M. Determinants of Mutation Rate Variation in the Human Germline. Annu Rev Genomics Hum Genet 2014; 15:47-70. [DOI: 10.1146/annurev-genom-031714-125740] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Laure Ségurel
- Laboratoire Éco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle–Centre National de la Recherche Scientifique–Université Paris 7 Diderot, Paris 75231, France;
| | - Minyoung J. Wyman
- Department of Biological Sciences, Columbia University, New York, NY 10027;
| | - Molly Przeworski
- Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637;
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36
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Emergence of resistance to atovaquone-proguanil in malaria parasites: insights from computational modeling and clinical case reports. Antimicrob Agents Chemother 2014; 58:4504-14. [PMID: 24867967 DOI: 10.1128/aac.02550-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The usefulness of atovaquone-proguanil (AP) as an antimalarial treatment is compromised by the emergence of atovaquone resistance during therapy. However, the origin of the parasite mitochondrial DNA (mtDNA) mutation conferring atovaquone resistance remains elusive. Here, we report a patient-based stochastic model that tracks the intrahost emergence of mutations in the multicopy mtDNA during the first erythrocytic parasite cycles leading to the malaria febrile episode. The effect of mtDNA copy number, mutation rate, mutation cost, and total parasite load on the mutant parasite load per patient was evaluated. Computer simulations showed that almost any infected patient carried, after four to seven erythrocytic cycles, de novo mutant parasites at low frequency, with varied frequencies of parasites carrying varied numbers of mutant mtDNA copies. A large interpatient variability in the size of this mutant reservoir was found; this variability was due to the different parameters tested but also to the relaxed replication and partitioning of mtDNA copies during mitosis. We also report seven clinical cases in which AP-resistant infections were treated by AP. These provided evidence that parasiticidal drug concentrations against AP-resistant parasites were transiently obtained within days after treatment initiation. Altogether, these results suggest that each patient carries new mtDNA mutant parasites that emerge before treatment but are killed by high starting drug concentrations. However, because the size of this mutant reservoir is highly variable from patient to patient, we propose that some patients fail to eliminate all of the mutant parasites, repeatedly producing de novo AP treatment failures.
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37
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Pears CJ, Lakin ND. Emerging models for DNA repair: Dictyostelium discoideum as a model for nonhomologous end-joining. DNA Repair (Amst) 2014; 17:121-31. [DOI: 10.1016/j.dnarep.2014.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 01/09/2014] [Accepted: 01/24/2014] [Indexed: 02/03/2023]
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38
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Stoeckel S, Masson JP. The exact distributions of F(IS) under partial asexuality in small finite populations with mutation. PLoS One 2014; 9:e85228. [PMID: 24465510 PMCID: PMC3897417 DOI: 10.1371/journal.pone.0085228] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022] Open
Abstract
Reproductive systems like partial asexuality participate to shape the evolution of genetic diversity within populations, which is often quantified by the inbreeding coefficient FIS. Understanding how those mating systems impact the possible distributions of FIS values in theoretical populations helps to unravel forces shaping the evolution of real populations. We proposed a population genetics model based on genotypic states in a finite population with mutation. For populations with less than 400 individuals, we assessed the impact of the rates of asexuality on the full exact distributions of FIS, the probabilities of positive and negative FIS, the probabilities of fixation and the probabilities to observe changes in the sign of FIS over one generation. After an infinite number of generations, we distinguished three main patterns of effects of the rates of asexuality on genetic diversity that also varied according to the interactions of mutation and genetic drift. Even rare asexual events in mainly sexual populations impacted the balance between negative and positive FIS and the occurrence of extreme values. It also drastically modified the probability to change the sign of FIS value at one locus over one generation. When mutation prevailed over genetic drift, increasing rates of asexuality continuously increased the variance of FIS that reached its highest value in fully asexual populations. In consequence, even ancient asexual populations showed the entire FIS spectrum, including strong positive FIS. The prevalence of heterozygous loci only occurred in full asexual populations when genetic drift dominated.
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Affiliation(s)
- Solenn Stoeckel
- INRA, UMR1349 Institute for Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Pierre Masson
- INRA, UMR1349 Institute for Genetics, Environment and Plant Protection, Le Rheu, France
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39
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Keightley PD, Ness RW, Halligan DL, Haddrill PR. Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family. Genetics 2014; 196:313-20. [PMID: 24214343 PMCID: PMC3872194 DOI: 10.1534/genetics.113.158758] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 11/06/2013] [Indexed: 01/06/2023] Open
Abstract
We employed deep genome sequencing of two parents and 12 of their offspring to estimate the mutation rate per site per generation in a full-sib family of Drosophila melanogaster recently sampled from a natural population. Sites that were homozygous for the same allele in the parents and heterozygous in one or more offspring were categorized as candidate mutations and subjected to detailed analysis. In 1.23 × 10(9) callable sites from 12 individuals, we confirmed six single nucleotide mutations. We estimated the false negative rate in the experiment by generating synthetic mutations using the empirical distributions of numbers of nonreference bases at heterozygous sites in the offspring. The proportion of synthetic mutations at callable sites that we failed to detect was <1%, implying that the false negative rate was extremely low. Our estimate of the point mutation rate is 2.8 × 10(-9) (95% confidence interval = 1.0 × 10(-9) - 6.1 × 10(-9)) per site per generation, which is at the low end of the range of previous estimates, and suggests an effective population size for the species of ∼1.4 × 10(6). At one site, point mutations were present in two individuals, indicating that there had been a premeiotic mutation cluster, although surprisingly one individual had a G→A transition and the other a G→T transversion, possibly associated with error-prone mismatch repair. We also detected three short deletion mutations and no insertions, giving a deletion mutation rate of 1.2 × 10(-9) (95% confidence interval = 0.7 × 10(-9) - 11 × 10(-9)).
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Affiliation(s)
- Peter D. Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Rob W. Ness
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Daniel L. Halligan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Penelope R. Haddrill
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
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40
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The rate and effects of spontaneous mutation on fitness traits in the social amoeba, Dictyostelium discoideum. G3-GENES GENOMES GENETICS 2013; 3:1115-27. [PMID: 23665876 PMCID: PMC3704240 DOI: 10.1534/g3.113.005934] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We performed a mutation accumulation (MA) experiment in the social amoeba Dictyostelium discoideum to estimate the rate and distribution of effects of spontaneous mutations affecting eight putative fitness traits. We found that the per-generation mutation rate for most fitness components is 0.0019 mutations per haploid genome per generation or larger. This rate is an order of magnitude higher than estimates for fitness components in the unicellular eukaryote Saccharomyces cerevisiae, even though the base-pair substitution rate is two orders of magnitude lower. The high rate of fitness-altering mutations observed in this species may be partially explained by a large mutational target relative to S. cerevisiae. Fitness-altering mutations also may occur primarily at simple sequence repeats, which are common throughout the genome, including in coding regions, and may represent a target that is particularly likely to give fitness effects upon mutation. The majority of mutations had deleterious effects on fitness, but there was evidence for a substantial fraction, up to 40%, being beneficial for some of the putative fitness traits. Competitive ability within the multicellular slug appears to be under weak directional selection, perhaps reflecting the fact that slugs are sometimes, but not often, comprised of multiple clones in nature. Evidence for pleiotropy among fitness components across MA lines was absent, suggesting that mutations tend to act on single fitness components.
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