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Zhang L, Liu K, Liu M, Hu J, Bao Z, Wang M. Development of a real-time enzymatic recombinase amplification assay for rapid detection of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimp Penaeus vannamei. J Invertebr Pathol 2023; 201:108024. [PMID: 37992986 DOI: 10.1016/j.jip.2023.108024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/18/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023]
Abstract
Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is classified as a reportable crustacean disease by the World Organisation for Animal Health (WOAH), which causes poor growth in Penaeus vannamei. According to genome sequence alignment analysis, enzymatic recombinase amplification (ERA) primers and probe were designed based on the ORF1 region of IHHNV, and a real-time ERA assay for IHHNV detection (IHHNV-ERA) was established. The experimental results show that IHHNV-F2/IHHNV-R2 and IHHNV-Probe can effectively amplify the target gene, and the sensitivity is 1.4 × 101 copies/μL within 14.97 ± 0.19 min, while the qPCR using primers 309F/309R could reach the detection limit of 1.4 × 101 copies/μL within 21.76 ± 0.63 min, and the sensitivity results of one-step PCR could be as low as 1.4 copies/μL with expense of time and false positives. The IHHNV-ERA system can effectively amplify the target gene at 42 ℃ within 20 min, and has no cross-reaction with white spot syndrome virus (WSSV), Ecytonucleospora hepatopenaei (EHP), Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (VpAHPND), and healthy shrimp genomic DNA. Test results of practical samples showed that the detection rate of IHHNV-ERA (18/20) was better than the industrial standard qPCR assay (17/20). Compared with the existing technology, the useful results of this detection assay are: (1) get rid of the dependence on the thermal cycle instrument in the PCR process; (2) the experimental procedure is simple, time-consuming and fast; (3) the detection sensitivity is high. This study provides an ERA based detection assay for IHHNV, which can be used not only for the rapid detection of IHHNV infection, but also for the field screening of pathogens. This assay can also be applied to clinical inspection, customs detection, enterprise quality inspection and other fields, and has obvious practical application value.
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Affiliation(s)
- Lu Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
| | - Kexin Liu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
| | - Mengran Liu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China.
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Mengqiang Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China.
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2
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Rozo-Lopez P, Brewer W, Käfer S, Martin MM, Parker BJ. Untangling an insect's virome from its endogenous viral elements. BMC Genomics 2023; 24:636. [PMID: 37875824 PMCID: PMC10594914 DOI: 10.1186/s12864-023-09737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Insects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. METHODS In this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphid Macrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly for M. euphorbiae using Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome. RESULTS We found reads from two insect-specific viruses (a Flavivirus and an Ambidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the 'virome' of this insect can be attributed to EVEs in the host genome. CONCLUSION Our work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects.
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Affiliation(s)
- Paula Rozo-Lopez
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
| | - William Brewer
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Simon Käfer
- Institut Für Biologie Und Umweltwissenschaften, Carl Von Ossietzky Universität Oldenburg, 26129, Oldenburg, Germany
| | - McKayla M Martin
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Benjamin J Parker
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
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Vassilieff H, Haddad S, Jamilloux V, Choisne N, Sharma V, Giraud D, Wan M, Serfraz S, Geering ADW, Teycheney PY, Maumus F. CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes. Mob DNA 2022; 13:31. [PMID: 36463202 PMCID: PMC9719215 DOI: 10.1186/s13100-022-00288-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.
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Affiliation(s)
- Héléna Vassilieff
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Sana Haddad
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.460789.40000 0004 4910 6535Present Address: Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Véronique Jamilloux
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.507621.7Present Address: Université Paris-Saclay, INRAE, PROSE, 92160 Antony, France
| | - Nathalie Choisne
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Vikas Sharma
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.8385.60000 0001 2297 375XPresent Address: Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Delphine Giraud
- UMR AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France
| | - Mariène Wan
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Saad Serfraz
- grid.413016.10000 0004 0607 1563CABB, University of Agriculture Faisalabad, Faisalabad, 38000 Pakistan
| | - Andrew D. W. Geering
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 Australia
| | | | - Florian Maumus
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
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Boutanaev AM, Nemchinov LG. Genome-wide identification of endogenous viral sequences in alfalfa (Medicago sativa L.). Virol J 2021; 18:185. [PMID: 34503524 PMCID: PMC8428138 DOI: 10.1186/s12985-021-01650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/26/2021] [Indexed: 11/10/2022] Open
Abstract
Endogenous viral elements (EVEs) have been for the most part described in animals and to a less extent in plants. The endogenization was proposed to contribute toward evolution of living organisms via horizontal gene transfer of novel genetic material and resultant genetic diversity. During the last two decades, several full-length and fragmented EVEs of pararetroviral and non-retroviral nature have been identified in different plant genomes, both monocots and eudicots. Prior to this work, no EVEs have been reported in alfalfa (Medicago sativa L.), the most cultivated forage legume in the world. In this study, taking advantage of the most recent developments in the field of alfalfa research, we have assessed alfalfa genome on the presence of viral-related sequences. Our analysis revealed segmented EVEs resembling two dsDNA reverse-transcribing virus species: Soybean chlorotic mottle virus (family Caulimoviridae, genus Soymovirus) and Figwort mosaic virus (family Caulimoviridae, genus Caulimovirus). The EVEs appear to be stable constituents of the host genome and in that capacity could potentially acquire functional roles in alfalfa’s development and response to environmental stresses.
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Affiliation(s)
- Alexander M Boutanaev
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA.
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Parry R, de Malmanche H, Asgari S. Persistent Spodoptera frugiperda rhabdovirus infection in Sf9 cells is not restricted by Wolbachia wMelPop-CLA and wAlbB strains and is targeted by the RNAi machinery. Virology 2021; 563:82-87. [PMID: 34492433 DOI: 10.1016/j.virol.2021.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/09/2021] [Revised: 08/13/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
The endosymbiotic bacterium Wolbachia pipientis confers RNA virus refractoriness in Drosophila and Aedes mosquitoes. Questions remain about the Wolbachia-virus restriction phenotype and how extensive this phenomenon may be within other arthropods. Here, we generated two Spodoptera frugiperda cell lines stably transinfected with two strains of Wolbachia, wAlbB and wMelPop-CLA. Despite the high density of Wolbachia in stably infected Sf9 cells, RT-PCR indicated the presence of the negative-sense RNA virus Spodoptera frugiperda rhabdovirus (SfRV) in Wolbachia-infected and uninfected cell lines. No differences in the replication of SfRV between Sf9 and Wolbachia-infected cells was found. RNA-Seq analysis of the parental Sf9 cells supported SfRV's presence in these cells with abundant 20 nt virus-derived small RNAs indicating active replication of SfRV in these cells. Overall, this study supports a growing body of evidence that Wolbachia does not restrict negative-sense RNA viruses and generates an in vitro model to examine Lepidoptera-Wolbachia virus interactions.
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Affiliation(s)
- Rhys Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Henry de Malmanche
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia.
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Serfraz S, Sharma V, Maumus F, Aubriot X, Geering ADW, Teycheney PY. Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant ( Solanum melongena). Front Plant Sci 2021; 12:683681. [PMID: 34367211 PMCID: PMC8346255 DOI: 10.3389/fpls.2021.683681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/30/2021] [Indexed: 05/20/2023]
Abstract
Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.
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Affiliation(s)
- Saad Serfraz
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Vikas Sharma
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Florian Maumus
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Xavier Aubriot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Andrew D. W. Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- *Correspondence: Pierre-Yves Teycheney,
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7
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Flegel TW. Research progress on viral accommodation 2009 to 2019. Dev Comp Immunol 2020; 112:103771. [PMID: 32634522 DOI: 10.1016/j.dci.2020.103771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 04/21/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
The viral accommodation hypothesis for crustaceans and insects was first proposed in 1998/2001, stimulated by observations that shrimp and insects or insect cell lines can coexist with both DNA or RNA viruses without showing any signs of disease (i.e., they tolerate, single to multiple, persistent infections, sometimes for a lifetime). A review of tests of the hypothesis up to 2007 was previously published in DCI. This was followed by a major revision in 2009 when the elusive memory element required by the hypothesis was proposed to reside in non-retroviral fragments of extant viruses, now called endogenous viral elements (EVE) that are autonomously inserted into the host genome as cDNA copied from viral mRNA. Here, progress in research on viral accommodation in crustaceans and insects over the decade following 2009 is reviewed. It culminates with a discussion of exiting research results from insects in 2019 that prove the existence of specific, adaptive and heritable immunity, at least in mosquitoes. It remains to be determined whether the same mechanisms also govern EVE acquisition and its protective RNA production in shrimp. The wide-ranging consequences of the revealed mechanisms for viral disease control in economic crustaceans and insects is discussed.
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Affiliation(s)
- T W Flegel
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Phayathai, Bangkok, 10300, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National for Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd, Phayathai, Bangkok, 10400, Thailand.
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Zhang Y, Wang J, Han GZ. Chalcid wasp paleoviruses bridge the evolutionary gap between bracoviruses and nudiviruses. Virology 2020; 542:34-39. [PMID: 32056666 DOI: 10.1016/j.virol.2020.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 12/14/2022]
Abstract
Polydnaviruses are obligate mutualists of parasitoid wasps and are divided into two genera, Bracovirus and Ichnovirus. Bracoviruses are thought to originate from a single integration of an ancestral nudivirus into the ancestor of microgastroid complex ~100 million years ago. However, all the known nudiviruses are only distantly related to bracoviruses, and much remains obscure about the origin of bracoviruses. Here we employ a paleovirological method to screen endogenous nudivirus-like elements across arthropods. Interestingly, we identify many endogenous nudivirus-like elements within the genome of Eurytoma brunniventris, a species of the Chalcidoidea superfamily. Among them, we find 14 core gene sequences are likely to be derived from a betanudivirus (designated EbrENV-β), suggesting that betanudivirus has been circulating in parasitoid wasps. Phylogenomic analysis suggests that EbrENV-β is the known closest relative of bracoviruses. Synteny analyses show the order of core genes is not well conserved between EbrENV-β and nudiviruses, revealing the dynamic nature of the evolution of nudivirus genome structures. Our findings narrow down the evolutionary gap between bracoviruses and nudiviruses and provide novel insights into the origin and evolution of polydnaviruses.
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Affiliation(s)
- Yu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Jianhua Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.
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Kaján GL, Doszpoly A, Tarján ZL, Vidovszky MZ, Papp T. Virus-Host Coevolution with a Focus on Animal and Human DNA Viruses. J Mol Evol 2019; 88:41-56. [PMID: 31599342 PMCID: PMC6943099 DOI: 10.1007/s00239-019-09913-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/23/2019] [Indexed: 01/21/2023]
Abstract
Viruses have been infecting their host cells since the dawn of life, and this extremely long-term coevolution gave rise to some surprising consequences for the entire tree of life. It is hypothesised that viruses might have contributed to the formation of the first cellular life form, or that even the eukaryotic cell nucleus originates from an infection by a coated virus. The continuous struggle between viruses and their hosts to maintain at least a constant fitness level led to the development of an unceasing arms race, where weapons are often shuttled between the participants. In this literature review we try to give a short insight into some general consequences or traits of virus–host coevolution, and after this we zoom in to the viral clades of adenoviruses, herpesviruses, nucleo-cytoplasmic large DNA viruses, polyomaviruses and, finally, circoviruses.
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Affiliation(s)
- Győző L Kaján
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary.
| | - Andor Doszpoly
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Zoltán László Tarján
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Márton Z Vidovszky
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Tibor Papp
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
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Taengchaiyaphum S, Srisala J, Bunphimpapha P, Supungul P, Tassanakajon A, Chaiyapechara S, Bowornpinyo S, Sritunyalucksana K, Flegel TW. Mendelian inheritance of endogenous viral elements (EVE) of white spot syndrome virus (WSSV) in shrimp. Dev Comp Immunol 2019; 96:144-149. [PMID: 30876958 DOI: 10.1016/j.dci.2019.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 01/10/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Previous work has shown that non-retroviral endogenous viral elements (EVE) are common in crustaceans, including penaeid shrimp. So far, they have been reported for infectious hypodermal and hematopoietic necrosis virus (IHHNV) and white spot syndrome virus (WSSV). For the latter, it was shown that shrimp sperm were positive for an EVE of WSSV called EVE366, suggesting that it was heritable, since shrimp sperm (non-motile) do not contain mitochondria. However, to prove this hypothesis that EVE366 was heritable and located in chromosomal DNA, it was necessary to carry out mating tests to show that EVE366 could be detected in parental shrimp and distributed in their offspring in a Mendelian fashion. To do this, we analyzed two shrimp crosses using polyacrylamide gels with a multiple-allele, microsatellite marker Pmo11 as a quality control for single allele detection. In both crosses, all of the shrimp (parents and siblings) were positive for 2 Pmo11 alleles as expected. In Cross 1, the female was PCR-positive for EVE366 while the male was negative, and in Cross 2, both the female and male were PCR-positive for EVE366. Individual analysis of the offspring of Cross 1 revealed a distribution of 1:1 for EVE366, indicating that the EVE366-positive female parent was heterozygous for EVE366. In the second cross, the distribution of EVE366 in the offspring was 3:1, indicating that both PCR-positive parents were heterozygous for EVE366. These results supported the hypothesis that EVE366 was present in shrimp chromosomal DNA and was heritable in a Mendelian fashion. This work provides a model to screen for heritable EVE in shrimp and shows that selection of one parent heterozygous for an EVE and the other negative for it can result in approximately half of the siblings positive and half negative for that EVE as expected. Dividing the siblings of such a cross into an EVE positive group and an EVE negative group followed by challenge with the originating lethal virus should reveal whether or not possession of that specific EVE results in any significant protection against disease caused by the homologous virus.
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Affiliation(s)
- Suparat Taengchaiyaphum
- Aquatic Animal Health Research Team (AQHT), National Center for Genetic Engineering and Biotechnology (BIOTEC), National for Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd, Phayathai, Bangkok, 10400, Thailand
| | - Jiraporn Srisala
- Aquatic Animal Health Research Team (AQHT), National Center for Genetic Engineering and Biotechnology (BIOTEC), National for Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd, Phayathai, Bangkok, 10400, Thailand
| | - Phimsucha Bunphimpapha
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Rd, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Premruethai Supungul
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Rd, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sage Chaiyapechara
- Aquaculture Product Development and Service Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Rd, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Suparerk Bowornpinyo
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd, Phayathai, Bangkok, 10400, Thailand
| | - Kallaya Sritunyalucksana
- Aquatic Animal Health Research Team (AQHT), National Center for Genetic Engineering and Biotechnology (BIOTEC), National for Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd, Phayathai, Bangkok, 10400, Thailand.
| | - Timothy W Flegel
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Rd, Khlong Luang, Pathum Thani, 12120, Thailand; Center for Excellence in Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd, Phayathai, Bangkok, 10400, Thailand.
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11
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Horie M, Tomonaga K. Paleovirology of bornaviruses: What can be learned from molecular fossils of bornaviruses. Virus Res 2018; 262:2-9. [PMID: 29630909 DOI: 10.1016/j.virusres.2018.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 02/13/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 02/05/2023]
Abstract
Endogenous viral elements (EVEs) are virus-derived sequences embedded in eukaryotic genomes formed by germline integration of viral sequences. As many EVEs were integrated into eukaryotic genomes millions of years ago, EVEs are considered molecular fossils of viruses. EVEs can be valuable informational sources about ancient viruses, including their time scale, geographical distribution, genetic information, and hosts. Although integration of viral sequences is not required for replications of viruses other than retroviruses, many non-retroviral EVEs have been reported to exist in eukaryotes. Investigation of these EVEs has expanded our knowledge regarding virus-host interactions, as well as provided information on ancient viruses. Among them, EVEs derived from bornaviruses, non-retroviral RNA viruses, have been relatively well studied. Bornavirus-derived EVEs are widely distributed in animal genomes, including the human genome, and the history of bornaviruses can be dated back to more than 65 million years. Although there are several reports focusing on the biological significance of bornavirus-derived sequences in mammals, paleovirology of bornaviruses has not yet been well described and summarized. In this paper, we describe what can be learned about bornaviruses from endogenous bornavirus-like elements from the view of paleovirology using published results and our novel data.
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Affiliation(s)
- Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan; Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Keizo Tomonaga
- Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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12
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Carrasco JL, Sánchez-Navarro JA, Elena SF. Exploring the role of cellular homologous of the 30K-superfamily of plant virus movement proteins. Virus Res 2018; 262:54-61. [PMID: 29475053 DOI: 10.1016/j.virusres.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 09/28/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 12/22/2022]
Abstract
Genes orthologous to the 30K-superfamily of movement proteins (MP) from plant viruses have been recently discovered by bioinformatics analyses as integrated elements in the genome of most vascular plants. However, their functional relevance for plants is still unclear. Here, we undertake some preliminary steps into the functional characterization of one of these putative MP genes found in Arabidopsis thaliana. We found that the AtMP gene is expressed at different stages of the plant development, with accumulation being highest in flowers but lowest in mature siliques. We also found down-regulation of the gene may result in a small delay in plant development and in an exacerbation of the negative effect of salinity in germination efficiency. We have also explored whether changes in expression of the endogenous AtMP have any effect on susceptibility to infection with several viruses, and found that the infectivity of tobacco rattle tobravirus was strongly dependent on the expression of the endogenous AtMP. Finally, we have cloned the endogenous MP from four different plant species into an expression vector that allows for specifically assessing their activity as cell-to-cell movement proteins and have shown that though some may still retain the ancestral activity, they do so in a quite inefficient manner, thus suggesting they have acquired a novel function during adaptation to the host genome.
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Affiliation(s)
- José L Carrasco
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain
| | - Jesús A Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain; Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Parc Científic UV, Catedrático Agustín Escardino 9, 46980, Paterna, València, Spain; The Santa Fe Institute,1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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Inoue Y, Kumagai M, Zhang X, Saga T, Wang D, Koga A, Takeda H. Fusion of piggyBac-like transposons and herpesviruses occurs frequently in teleosts. Zoological Lett 2018; 4:6. [PMID: 29484202 PMCID: PMC5822658 DOI: 10.1186/s40851-018-0089-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 02/06/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Endogenous viral elements play important roles in eukaryotic evolution by giving rise to genetic novelties. Herpesviruses are a large family of DNA viruses, most of which do not have the ability to endogenize into host genomes. Recently, we identified a novel type of endogenous herpesvirus, which we named "Teratorn", from the medaka (Oryzias latipes) genome, in which the herpesvirus is fused with a piggyBac-like DNA transposon, forming a novel mobile element. Teratorn is a unique herpesvirus that retains its viral genes intact and has acquired the endogenized lifestyle by hijacking the transposon system. However, it is unclear how this novel element evolved in the teleost lineage and whether fusion of two mobile elements is a general phenomenon in vertebrates. RESULTS Here we performed a comprehensive genomic survey searching for Teratorn-like viruses in publicly available genome data and found that they are widely distributed in teleosts, forming a clade within Alloherpesviridae. Importantly, at least half of the identified Teratorn-like viruses contain piggyBac-like transposase genes, suggesting the generality of the transposon-herpesvirus fusion in teleosts. Phylogenetic tree topologies between the piggyBac-like transposase gene and herpesvirus-like genes are nearly identical, supporting the idea of a long-term evolutionary relationship between them. CONCLUSION We propose that piggyBac-like elements and Teratorn-like viruses have co-existed for a long time, and that fusion of the two mobile genetic elements occurred frequently in teleosts.
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Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Xianbo Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715 China
| | - Tomonori Saga
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715 China
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506 Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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Palatini U, Miesen P, Carballar-Lejarazu R, Ometto L, Rizzo E, Tu Z, van Rij RP, Bonizzoni M. Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus. BMC Genomics 2017; 18:512. [PMID: 28676109 PMCID: PMC5497376 DOI: 10.1186/s12864-017-3903-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/26/2017] [Indexed: 02/08/2023] Open
Abstract
Background Arthropod-borne viruses (arboviruses) transmitted by mosquito vectors cause many important emerging or resurging infectious diseases in humans including dengue, chikungunya and Zika. Understanding the co-evolutionary processes among viruses and vectors is essential for the development of novel transmission-blocking strategies. Episomal viral DNA fragments are produced from arboviral RNA upon infection of mosquito cells and adults. Additionally, sequences from insect-specific viruses and arboviruses have been found integrated into mosquito genomes. Results We used a bioinformatic approach to analyse the presence, abundance, distribution, and transcriptional activity of integrations from 425 non-retroviral viruses, including 133 arboviruses, across the presently available 22 mosquito genome sequences. Large differences in abundance and types of viral integrations were observed in mosquito species from the same region. Viral integrations are unexpectedly abundant in the arboviral vector species Aedes aegypti and Ae. albopictus, in which they are approximately ~10-fold more abundant than in other mosquito species analysed. Additionally, viral integrations are enriched in piRNA clusters of both the Ae. aegypti and Ae. albopictus genomes and, accordingly, they express piRNAs, but not siRNAs. Conclusions Differences in the number of viral integrations in the genomes of mosquito species from the same geographic area support the conclusion that integrations of viral sequences is not dependent on viral exposure, but that lineage-specific interactions exist. Viral integrations are abundant in Ae. aegypti and Ae. albopictus, and represent a thus far underappreciated component of their genomes. Additionally, the genome locations of viral integrations and their production of piRNAs indicate a functional link between viral integrations and the piRNA pathway. These results greatly expand the breadth and complexity of small RNA-mediated regulation and suggest a role for viral integrations in antiviral defense in these two mosquito species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3903-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Umberto Palatini
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, Nijmegen, The Netherlands
| | | | - Lino Ometto
- Indepenent Researcher, Mezzocorona, Trento, Italy
| | | | - Zhijian Tu
- Department of Biochemistry and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, Nijmegen, The Netherlands
| | - Mariangela Bonizzoni
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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Metegnier G, Becking T, Chebbi MA, Giraud I, Moumen B, Schaack S, Cordaux R, Gilbert C. Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups. Mob DNA 2015; 6:16. [PMID: 26388953 PMCID: PMC4573495 DOI: 10.1186/s13100-015-0047-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/10/2015] [Indexed: 01/08/2023] Open
Abstract
Background The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host (endogenous viral elements; EVEs) has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions. Here, we report the results of a comprehensive screen for EVEs in crustaceans. Following up on the recent discovery of EVEs in the terrestrial isopod, Armadillidium vulgare, we scanned the genomes of six crustacean species: a terrestrial isopod (Armadillidium nasatum), two water fleas (Daphnia pulex and D. pulicaria), two copepods (the salmon louse, Lepeophtheirus salmonis and Eurytemora affinis), and a freshwater amphipod (Hyalella azteca). Results In total, we found 210 EVEs representing 14 different lineages belonging to five different viral groups that are present in two to five species: Bunyaviridae (−ssRNA), Circoviridae (ssDNA), Mononegavirales (−ssRNA), Parvoviridae (ssDNA) and Totiviridae (dsRNA). The identification of shared orthologous insertions between A. nasatum and A. vulgare indicates that EVEs have been maintained over several millions of years, although we did not find any evidence supporting exaptation. Overall, the different degrees of EVE degradation (from none to >10 nonsense mutations) suggest that endogenization has been recurrent during the evolution of the various crustacean taxa. Our study is the first to report EVEs in D. pulicaria, E. affinis and H. azteca, many of which are likely to result from recent endogenization of currently circulating viruses. Conclusions In conclusion, we have unearthed a large diversity of EVEs from crustacean genomes, and shown that four of the five viral groups we uncovered (Bunyaviridae, Circoviridae, Mononegavirales, Parvoviridae) were and may still be present in three to four highly divergent crustacean taxa. In addition, the discovery of recent EVEs offers an interesting opportunity to characterize new exogenous viruses currently circulating in economically or ecologically important copepod species. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0047-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel Metegnier
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Thomas Becking
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Mohamed Amine Chebbi
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Isabelle Giraud
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Bouziane Moumen
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR USA
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
| | - Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, building B8-B35, 6 rue Michel Brunet, TSA 51106 F-86073 Poitiers, Cedex 9 France
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