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Wang Y, Obbard DJ. Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis. Evol Lett 2023; 7:216-226. [PMID: 37475753 PMCID: PMC10355183 DOI: 10.1093/evlett/qrad027] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023] Open
Abstract
Mutation is the ultimate source of all genetic variation, and over the last 10 years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. In this meta-analysis, we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent-offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in the single-nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide diversity-while accounting for phylogenetic nonindependence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide diversity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply branching eukaryotic lineages-or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for amphibia and scarce for reptiles and fish.
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Affiliation(s)
- Yiguan Wang
- Corresponding author: Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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Liu J, Li W, Yao C, Yu J, Zhang H. Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts. BMC Microbiol 2022; 22:158. [PMID: 35710325 PMCID: PMC9202165 DOI: 10.1186/s12866-022-02573-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/06/2022] [Indexed: 12/08/2022] Open
Abstract
BACKGROUND The two subspecies of Bifidobacterium catenulatum, B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum, are usually from the infant and adult gut, respectively. However, the genomic analysis of their functional difference and genetic divergence has been rare. Here, 16 B. catenulatum strains, including 2 newly sequenced strains, were analysed through comparative genomics. RESULTS A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated. The comparison of genomic characteristics revealed that the two subspecies had significantly different genomic sizes (p < 0.05) but similar GC contents. The functional comparison revealed the most significant difference in genes of carbohydrate utilisation. Carbohydrate-active enzymes (CAZyme) present two clustering patterns in B. catenulatum. The B. catenulatum subsp. kashiwanohense specially including the glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51) families involved in the metabolism of human milk oligosaccharides (HMO) common in infants, also, the corresponding fucosylated HMO gene clusters were detected. Meanwhile, B. catenulatum subsp. catenulatum rich in GH3 may metabolise more plant-derived glycan in the adult intestine. CONCLUSIONS These findings provide genomic evidence of carbohydrate utilisation bias, which may be a key cause of the genetic divergence of two B. catenulatum subspecies.
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Affiliation(s)
- Jiaqi Liu
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Caiqing Yao
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China.
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Martinez-Gutierrez CA, Aylward FO. Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales. PLoS Genet 2022; 18:e1010220. [PMID: 35605022 PMCID: PMC9166353 DOI: 10.1371/journal.pgen.1010220] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/03/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022] Open
Abstract
The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel’s lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution. The evolutionary forces driving genome size in bacteria and archaea have been subject to debate during the last decades. Typically, independent comparative analyses have suggested that unique variables, such as the strength of selection, environmental complexity, and mutation rate, are the main drivers of this trait, without considering for potential biases derived from shared ancestry. Here, we applied a phylogeny-based statistical approach to assess how tightly genome size in bacteria and archaea is linked to evolutionary history. Moreover, we also evaluated the predictability of genome size from the strength of purifying selection and ecological strategy on a broad diversity of bacteria and archaea genomes under a phylogenetic comparative framework. Our approach indicates that despite the ability of bacteria and archaea to rapidly exchange genes, a strong phylogenetic signal to genome size distributions can be recovered at broad phylogenetic scales.
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Affiliation(s)
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
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Chen Z, Wang X, Song Y, Zeng Q, Zhang Y, Luo H. Prochlorococcus have low global mutation rate and small effective population size. Nat Ecol Evol 2022; 6:183-194. [PMID: 34949817 DOI: 10.1038/s41559-021-01591-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/14/2021] [Indexed: 12/27/2022]
Abstract
Prochlorococcus are the most abundant free-living photosynthetic carbon-fixing organisms in the ocean. Prochlorococcus show small genome sizes, low genomic G+C content, reduced DNA repair gene pool and fast evolutionary rates, which are typical features of endosymbiotic bacteria. Nevertheless, their evolutionary mechanisms are believed to be different. Evolution of endosymbiotic bacteria is dominated by genetic drift owing to repeated population bottlenecks, whereas Prochlorococcus are postulated to have extremely large effective population sizes (Ne) and thus drift has rarely been considered. However, accurately extrapolating Ne requires measuring an unbiased global mutation rate through mutation accumulation, which is challenging for Prochlorococcus. Here, we managed this experiment over 1,065 days using Prochlorococcus marinus AS9601, sequenced genomes of 141 mutant lines and determined its mutation rate to be 3.50 × 10-10 per site per generation. Extrapolating Ne additionally requires identifying population boundaries, which we defined using PopCOGenT and over 400 genomes related to AS9601. Accordingly, we calculated its Ne to be 1.68 × 107, which is only reasonably greater than that of endosymbiotic bacteria but surprisingly smaller than that of many free-living bacteria extrapolated using the same approach. Our results therefore suggest that genetic drift is a key driver of Prochlorococcus evolution.
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Affiliation(s)
- Zhuoyu Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaojun Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Clear Water Bay, Hong Kong SAR
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China. .,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Clear Water Bay, Hong Kong SAR.
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Unexpectedly high mutation rate of a deep-sea hyperthermophilic anaerobic archaeon. THE ISME JOURNAL 2021; 15:1862-1869. [PMID: 33452477 PMCID: PMC8163891 DOI: 10.1038/s41396-020-00888-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023]
Abstract
Deep-sea hydrothermal vents resemble the early Earth, and thus the dominant Thermococcaceae inhabitants, which occupy an evolutionarily basal position of the archaeal tree and take an obligate anaerobic hyperthermophilic free-living lifestyle, are likely excellent models to study the evolution of early life. Here, we determined that unbiased mutation rate of a representative species, Thermococcus eurythermalis, exceeded that of all known free-living prokaryotes by 1-2 orders of magnitude, and thus rejected the long-standing hypothesis that low mutation rates were selectively favored in hyperthermophiles. We further sequenced multiple and diverse isolates of this species and calculated that T. eurythermalis has a lower effective population size than other free-living prokaryotes by 1-2 orders of magnitude. These data collectively indicate that the high mutation rate of this species is not selectively favored but instead driven by random genetic drift. The availability of these unusual data also helps explore mechanisms underlying microbial genome size evolution. We showed that genome size is negatively correlated with mutation rate and positively correlated with effective population size across 30 bacterial and archaeal lineages, suggesting that increased mutation rate and random genetic drift are likely two important mechanisms driving microbial genome reduction. Future determinations of the unbiased mutation rate of more representative lineages with highly reduced genomes such as Prochlorococcus and Pelagibacterales that dominate marine microbial communities are essential to test these hypotheses.
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Gerth M, Martinez-Montoya H, Ramirez P, Masson F, Griffin JS, Aramayo R, Siozios S, Lemaitre B, Mateos M, Hurst GDD. Rapid molecular evolution of Spiroplasma symbionts of Drosophila. Microb Genom 2021; 7:000503. [PMID: 33591248 PMCID: PMC8208695 DOI: 10.1099/mgen.0.000503] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma, and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.
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Affiliation(s)
- Michael Gerth
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Present address: Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Humberto Martinez-Montoya
- Laboratorio de Genética y Genómica Comparativa, Unidad Académica Multidisciplinaria Reynosa Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Mexico
| | - Paulino Ramirez
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Florent Masson
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne), Lausanne, Switzerland
| | - Joanne S. Griffin
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne), Lausanne, Switzerland
| | - Mariana Mateos
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Gregory D. D. Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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