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Maltseva AL, Lobov AA, Pavlova PA, Panova M, Gafarova ER, Marques JP, Danilov LG, Granovitch AI. Orphan gene in Littorina: An unexpected role of symbionts in the host evolution. Gene 2022; 824:146389. [PMID: 35257790 DOI: 10.1016/j.gene.2022.146389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/29/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.
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Affiliation(s)
- A L Maltseva
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
| | - A A Lobov
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - P A Pavlova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - M Panova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Department of Marine Sciences - Tjärnö, University of Gothenburg, Sweden
| | - E R Gafarova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - J P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências do Porto, 4169-007 Porto, Portugal; ISEM, Univ Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
| | - L G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - A I Granovitch
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
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Wang J, Wang J, Zhao Z, Chen J, Lu H, Liu G, Zhou J, Guan X. PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community. Environ Pollut 2017; 231:1145-1152. [PMID: 28886881 DOI: 10.1016/j.envpol.2017.07.067] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 05/11/2023]
Abstract
Antibiotic resistance genes (ARGs) have been regarded as emerging contaminants and have attracted growing attention owing to their widespread presence in the environment. In addition to the well-documented selective pressure of antibiotics, ARGs have also become prevalent because of anthropogenic impacts. Coastal habitats are located between terrestrial and marine ecosystems, which are a hotspot for anthropogenic impacts. Excessive accumulation of polycyclic aromatic hydrocarbons (PAHs) has posed a serious threat to coastal habitats, but no information is available on the effect of PAHs on antibiotic resistance in the microbial community of coastal environments. In this study, the effect of two typical PAHs, naphthalene and phenanthrene, on antibiotic resistance propagation was investigated in a coastal microbial community. The results indicated that the presence of 100 mg/L of naphthalene or 10 mg/L of phenanthrene significantly enhanced the abundance of class I integrase gene (intI1), sulfanilamide resistance gene (sulI), and aminoglycosides resistance gene (aadA2) in the microbial community. Horizontal gene transfer experiment demonstrated that increased abundance of ARGs was primarily a result of conjugative transfer mediated by class I integrons. These findings provided direct evidence that coastal microbial community exposed to PAHs might have resulted in the dissemination of ARGs and implied that a more comprehensive risk assessment of PAHs to natural ecosystems and public health is necessary.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Zelong Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Guangfei Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaoyan Guan
- Key Lab of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
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Abstract
Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships. These types of approach have been used to elucidate the nature and extent of LGT and its physiological and ecological consequences throughout the Tree of Life. Advances in DNA sequencing technology have led to enormous increases in the number of sequenced genomes, including ultra-deep sampling of specific taxonomic groups and single cell-based sequencing of unculturable "microbial dark matter." Environmental shotgun sequencing enables the study of LGT among organisms that share the same habitat.This abundance of genomic data offers new opportunities for scientific discovery, but poses two key problems. As ever more genomes are generated, the assembly and annotation of each individual genome receives less scrutiny; and with so many genomes available it is tempting to include them all in a single analysis, but thousands of genomes and millions of genes can overwhelm key algorithms in the analysis pipeline. Identifying LGT events of interest therefore depends on choosing the right dataset, and on algorithms that appropriately balance speed and accuracy given the size and composition of the chosen set of genomes.
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Affiliation(s)
- Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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