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Gilbert C, Peccoud J, Cordaux R. Transposable Elements and the Evolution of Insects. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:355-372. [PMID: 32931312 DOI: 10.1146/annurev-ento-070720-074650] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.
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Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France;
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France
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Dunemann SM, Wasmuth JD. Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew. Mob DNA 2019; 10:24. [PMID: 31160924 PMCID: PMC6542046 DOI: 10.1186/s13100-019-0166-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/09/2019] [Indexed: 01/09/2023] Open
Abstract
Background As the genomes of more metazoan species are sequenced, reports of horizontal transposon transfers (HTT) have increased. Our understanding of the mechanisms of such events is at an early stage. The close physical relationship between a parasite and its host could facilitate horizontal transfer. To date, two studies have identified horizontal transfer of RTEs, a class of retrotransposable elements, involving parasites: ticks might act as vector for BovB between ruminants and squamates, and AviRTE was transferred between birds and parasitic nematodes. Results We searched for RTEs shared between nematode and mammalian genomes. Given their physical proximity, it was necessary to detect and remove sequence contamination from the genome datasets, which would otherwise distort the signal of horizontal transfer. We developed an approach that is based on reads instead of genomic sequences to reliably detect contamination. From comparison of 43 RTEs across 197 genomes, we identified a single putative case of horizontal transfer: we detected RTE1_Sar from Sorex araneus, the common shrew, in parasitic nematodes. From the taxonomic distribution and evolutionary analysis, we show that RTE1_Sar was horizontally transferred. Conclusion We identified a new horizontal RTE transfer in host-parasite interactions, which suggests that it is not uncommon. Further, we present and provide the workflow a read-based method to distinguish between contamination and horizontal transfer. Electronic supplementary material The online version of this article (10.1186/s13100-019-0166-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonja M Dunemann
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, T2N 4Z6 Canada
| | - James D Wasmuth
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, T2N 4Z6 Canada
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Fonseca PM, Moura RD, Wallau GL, Loreto ELS. The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies. Chromosome Res 2019; 27:203-219. [DOI: 10.1007/s10577-019-09609-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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da Silva AF, Dezordi FZ, Loreto ELS, Wallau GL. Drosophila parasitoid wasps bears a distinct DNA transposon profile. Mob DNA 2018; 9:23. [PMID: 30002736 PMCID: PMC6035795 DOI: 10.1186/s13100-018-0127-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/19/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genomic analysis and detailed characterized mobilomes only exists for model species. In this study, we used a combination of de novo and homology approaches to characterize the Mobilome of two non-model parasitoid wasp species. RESULTS The different methodologies employed for TE characterization recovered TEs with different features as TE consensus number and size. Moreover, some TEs were detected only by one or few methodologies. RepeatExplorer and dnaPipeTE estimated a low TE content of 5.86 and 4.57% for Braconidae wasp and 5.22% and 7.42% for L. boulardi species, respectively. Both mobilomes are composed by a miscellaneous of ancient and recent elements. Braconidae wasps presented a large diversity of Maverick/Polintons Class II TEs while other TE superfamilies were more equally diverse in both species. Phylogenetic analysis of reconstructed elements showed that vertical transfer is the main mode of transmission. CONCLUSION Different methodologies should be used complementarity in order to achieve better mobilome characterization. Both wasps genomes have one of the lower mobilome estimates among all Hymenoptera genomes studied so far and presented a higher proportion of Class II than Class I TEs. The large majority of superfamilies analyzed phylogenetically showed that the elements are being inherited by vertical transfer. Overall, we achieved a deep characterization of the mobilome in two non-model parasitoid wasps improving our understanding of their evolution.
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Affiliation(s)
- Alexandre Freitas da Silva
- Pós Graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães (IAM), Recife, Pernambuco Brazil
| | - Filipe Zimmer Dezordi
- Pós Graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães (IAM), Recife, Pernambuco Brazil
| | - Elgion Lucio Silva Loreto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ/PE), Recife, Pernambuco Brazil
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Wallau GL, Vieira C, Loreto ÉLS. Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome. Mob DNA 2018; 9:6. [PMID: 29422954 PMCID: PMC5791352 DOI: 10.1186/s13100-018-0112-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
Background All living species contain genetic information that was once shared by their common ancestor. DNA is being inherited through generations by vertical transmission (VT) from parents to offspring and from ancestor to descendant species. This process was considered the sole pathway by which biological entities exchange inheritable information. However, Horizontal Transfer (HT), the exchange of genetic information by other means than parents to offspring, was discovered in prokaryotes along with strong evidence showing that it is a very important process by which prokaryotes acquire new genes. Main body For some time now, it has been a scientific consensus that HT events were rare and non-relevant for evolution of eukaryotic species, but there is growing evidence supporting that HT is an important and frequent phenomenon in eukaryotes as well. Conclusion Here, we will discuss the latest findings regarding HT among eukaryotes, mainly HT of transposons (HTT), establishing HTT once and for all as an important phenomenon that should be taken into consideration to fully understand eukaryotes genome evolution. In addition, we will discuss the latest development methods to detect such events in a broader scale and highlight the new approaches which should be pursued by researchers to fill the knowledge gaps regarding HTT among eukaryotes.
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Affiliation(s)
- Gabriel Luz Wallau
- 1Entomology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE Brazil
| | - Cristina Vieira
- 2Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, F-69622 Villeurbanne, France
| | - Élgion Lúcio Silva Loreto
- 3Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS Brazil
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Drezen JM, Gauthier J, Josse T, Bézier A, Herniou E, Huguet E. Foreign DNA acquisition by invertebrate genomes. J Invertebr Pathol 2017; 147:157-168. [DOI: 10.1016/j.jip.2016.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
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Venner S, Miele V, Terzian C, Biémont C, Daubin V, Feschotte C, Pontier D. Ecological networks to unravel the routes to horizontal transposon transfers. PLoS Biol 2017; 15:e2001536. [PMID: 28199335 PMCID: PMC5331948 DOI: 10.1371/journal.pbio.2001536] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs.
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Affiliation(s)
- Samuel Venner
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Vincent Miele
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Christophe Terzian
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- UMR754 INRA, Université Claude Bernard Lyon 1, Lyon, France
- Ecole Pratique des Hautes Etudes, Paris, France
| | - Christian Biémont
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Vincent Daubin
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, Utah, United States of America
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
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Wang GH, Sun BF, Xiong TL, Wang YK, Murfin KE, Xiao JH, Huang DW. Bacteriophage WO Can Mediate Horizontal Gene Transfer in Endosymbiotic Wolbachia Genomes. Front Microbiol 2016; 7:1867. [PMID: 27965627 PMCID: PMC5126046 DOI: 10.3389/fmicb.2016.01867] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/07/2016] [Indexed: 11/26/2022] Open
Abstract
Phage-mediated horizontal gene transfer (HGT) is common in free-living bacteria, and many transferred genes can play a significant role in their new bacterial hosts. However, there are few reports concerning phage-mediated HGT in endosymbionts (obligate intracellular bacteria within animal or plant hosts), such as Wolbachia. The Wolbachia-infecting temperate phage WO can actively shift among Wolbachia genomes and has the potential to mediate HGT between Wolbachia strains. In the present study, we extend previous findings by validating that the phage WO can mediate transfer of non-phage genes. To do so, we utilized bioinformatic, phylogenetic, and molecular analyses based on all sequenced Wolbachia and phage WO genomes. Our results show that the phage WO can mediate HGT between Wolbachia strains, regardless of whether the transferred genes originate from Wolbachia or other unrelated bacteria.
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Affiliation(s)
- Guan H Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijing, China; University of Chinese Academy of SciencesBeijing, China
| | - Bao F Sun
- Disease Genomics and Individualized Medicine Laboratory, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Tuan L Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijing, China; University of Chinese Academy of SciencesBeijing, China
| | - Yan K Wang
- College of Life Sciences, Hebei University Baoding, China
| | - Kristen E Murfin
- Section of Infectious Diseases, Yale University School of Medicine New Haven, CT, USA
| | - Jin H Xiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences Beijing, China
| | - Da W Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, Hebei UniversityBaoding, China
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Oliveira DS, Gomes TMFF, Loreto ELS. The rearranged mitochondrial genome of Leptopilina boulardi (Hymenoptera: Figitidae), a parasitoid wasp of Drosophila. Genet Mol Biol 2016; 39:611-615. [PMID: 27648767 PMCID: PMC5127158 DOI: 10.1590/1678-4685-gmb-2016-0062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 08/02/2016] [Indexed: 11/22/2022] Open
Abstract
The partial mitochondrial genome sequence of Leptopilina boulardi (Hymenoptera: Figitidae) was characterized. Illumina sequencing was used yielding 35,999,679 reads, from which 102,482 were utilized in the assembly. The length of the sequenced region of this partial mitochondrial genome is 15,417 bp, consisting of 13 protein-coding, two rRNA, and 21tRNA genes (the trnaM failed to be sequenced) and a partial A+T-rich region. All protein-coding genes start with ATN codons. Eleven protein-coding genes presented TAA stop codons, whereas ND6 and COII that presented TA, and T nucleotides, respectively. The gene pattern revealed extensive rearrangements compared to the typical pattern generally observed in insects. These rearrangements involve two protein-coding and two ribosomal genes, along with the 16 tRNA genes. This gene order is different from the pattern described for Ibalia leucospoides (Ibaliidae, Cynipoidea), suggesting that this particular gene order can be variable among Cynipoidea superfamily members. A maximum likelihood phylogenetic analysis of the main groups of Apocrita was performed using amino acid sequence of 13 protein-coding genes, showing monophyly for the Cynipoidea superfamily within the Hymenoptera phylogeny.
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Affiliation(s)
- Daniel S Oliveira
- Curso Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Tiago M F F Gomes
- Curso Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Elgion L S Loreto
- Departamento de Bioquímica e Biologia Molecular (CCNE), Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
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Wallau GL, da Rosa MT, De Ré FC, Loreto ELS. Wolbachia from Drosophila incompta: just a hitchhiker shared by Drosophila in the New and Old World? INSECT MOLECULAR BIOLOGY 2016; 25:487-499. [PMID: 27122079 DOI: 10.1111/imb.12237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Wolbachia are intracellular endosymbionts that infect arthropods and filarial nematodes, occasionally causing a wide variety of modifications in host biology, such as male-killing and cytoplasmic incompatibility (CI), amongst others. This study assembled draft genomes for Wolbachia infecting Drosophila incompta, a species that uses flowers as exclusive breeding and feeding sites, in two distinct Brazilian populations. The absence of four genes involved in CI from this genome, together with literature reports of low frequencies of infected flies in wild populations that contain high mitogenome polymorphism, suggests that this bacterium does not induce CI in D. incompta. Phylogenomic analysis placed Wolbachia infecting D. incompta as closely related to the wMel strain which received such name since it was originally detected in Drosophila melanogaster. In addition, phylogenetic analysis using the Wolbachia surface protein gene and five genes used for multilocus sequence typing of Wolbachia found infecting Drosophila and other arthropod species of Old and New World displayed a complex evolutionary scenario involving recent horizontal transfer bursts in all major clades of Wolbachia pipens belonging to the supergroup A in both geographical regions.
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Affiliation(s)
- G L Wallau
- PPG Biodiversade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
- Departamento de Entomologia, Centro de Pesquisas Aggeu Magalhães - FIOCRUZ-CPqAM, Recife, PE, Brazil
| | - M T da Rosa
- PPG Biodiversade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - F C De Ré
- PPG Biodiversade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - E L S Loreto
- PPG Biodiversade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
- Departamento Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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Affiliation(s)
- Elgion Lucio Silva Loreto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Centro de Pesquisas Aggeu Magalhães-FIOCRUZ-CPqAM, Recife, PE, Brazil.
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