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Mahar JE, Wille M, Harvey E, Moritz CC, Holmes EC. The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat. Virus Evol 2024; 10:veae044. [PMID: 38854849 PMCID: PMC11160328 DOI: 10.1093/ve/veae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024] Open
Abstract
Lizards have diverse ecologies and evolutionary histories, and represent a promising group to explore how hosts shape virome structure and virus evolution. Yet, little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than thirty novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as the Flaviviridae, Picornaviridae, Bornaviridae, Iridoviridae, and Rhabdoviridae. Members of the Flaviviridae were particularly abundant across species sampled here, largely belonging to the genus Hepacivirus: fourteen novel hepaciviruses were identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness in the animals sampled here was shaped by host taxonomy and habitat. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.
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Affiliation(s)
- Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Michelle Wille
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Craig C Moritz
- Research School of Biology & Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT 2600, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
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2
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Gagne RB, Crooks KR, Craft ME, Chiu ES, Fountain-Jones NM, Malmberg JL, Carver S, Funk WC, VandeWoude S. Parasites as conservation tools. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13719. [PMID: 33586245 DOI: 10.1111/cobi.13719] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Parasite success typically depends on a close relationship with one or more hosts; therefore, attributes of parasitic infection have the potential to provide indirect details of host natural history and are biologically relevant to animal conservation. Characterization of parasite infections has been useful in delineating host populations and has served as a proxy for assessment of environmental quality. In other cases, the utility of parasites is just being explored, for example, as indicators of host connectivity. Innovative studies of parasite biology can provide information to manage major conservation threats by using parasite assemblage, prevalence, or genetic data to provide insights into the host. Overexploitation, habitat loss and fragmentation, invasive species, and climate change are major threats to animal conservation, and all of these can be informed by parasites.
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Affiliation(s)
- Roderick B Gagne
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, Minnesota, USA
| | - Elliott S Chiu
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Jennifer L Malmberg
- Department of Veterinary Sciences, Wyoming State Veterinary Laboratory, University of Wyoming, Laramie, Wyoming, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - W Chris Funk
- Graduate Degree Program in Ecology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
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3
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Vertical transmission in Caenorhabditis nematodes of RNA molecules encoding a viral RNA-dependent RNA polymerase. Proc Natl Acad Sci U S A 2019; 116:24738-24747. [PMID: 31740606 PMCID: PMC6900638 DOI: 10.1073/pnas.1903903116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In organisms composed of a single cell, RNAs of viral origin may be transmitted to daughter cells at cell division without passing through an extracellular virion stage. These RNAs usually encode an RNA-dependent RNA polymerase that enables their replication. For some of these agents, such as Narnaviruses, no capsid protein is expressed, and thus, they are called capsidless viruses. Here, we identify putative capsidless viral RNAs in animals, in nematodes closely related to the model organism Caenorhabditis elegans. We show that these RNAs are transmitted vertically through the host germline. Our work provides evidence that animal cells harbor capsidless viruses. Here, we report on the discovery in Caenorhabditis nematodes of multiple vertically transmitted RNAs coding for putative RNA-dependent RNA polymerases. Their sequences share similarity to distinct RNA viruses, including bunyaviruses, narnaviruses, and sobemoviruses. The sequences are present exclusively as RNA and are not found in DNA form. The RNAs persist in progeny after bleach treatment of adult animals, indicating vertical transmission of the RNAs. We tested one of the infected strains for transmission to an uninfected strain and found that mating of infected animals with uninfected animals resulted in infected progeny. By in situ hybridization, we detected several of these RNAs in the cytoplasm of the male and female germline of the nematode host. The Caenorhabditis hosts were found defective in degrading exogenous double-stranded RNAs, which may explain retention of viral-like RNAs. Strikingly, one strain, QG551, harbored three distinct virus-like RNA elements. Specific patterns of small RNAs complementary to the different viral-like RNAs were observed, suggesting that the different RNAs are differentially recognized by the RNA interference (RNAi) machinery. While vertical transmission of viruses in the family Narnaviridae, which are known as capsidless viruses, has been described in fungi, these observations provide evidence that multicellular animal cells harbor similar viruses.
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4
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The behavioral repertoire of Drosophila melanogaster in the presence of two predator species that differ in hunting mode. PLoS One 2019; 14:e0216860. [PMID: 31150415 PMCID: PMC6544228 DOI: 10.1371/journal.pone.0216860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/30/2019] [Indexed: 12/02/2022] Open
Abstract
The fruit fly, Drosophila melanogaster, has proven to be an excellent model organism for genetic, genomic and neurobiological studies. However, relatively little is known about the natural history of D. melanogaster. In particular, neither the natural predators faced by wild populations of D. melanogaster, nor the anti-predatory behaviors they may employ to escape and avoid their enemies have been documented. Here we observe and describe the influence of two predators that differ in their mode of hunting: zebra jumping spiders, Salticus scenicus (active hunters) and Chinese praying mantids, Tenodera sinensis (ambush predators) on the behavioral repertoire of Drosophila melanogaster. We documented three particularly interesting behaviors: abdominal lifting, stopping, and retreat—which were performed at higher frequency by D. melanogaster in the presence of predators. While mantids had only a modest influence on the locomotory activity of D. melanogaster, we observed a significant increase in the overall activity of D. melanogaster in the presence of jumping spiders. Finally, we observed considerable among-individual behavioral variation in response to both predators.
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Duxbury EML, Day JP, Maria Vespasiani D, Thüringer Y, Tolosana I, Smith SCL, Tagliaferri L, Kamacioglu A, Lindsley I, Love L, Unckless RL, Jiggins FM, Longdon B. Host-pathogen coevolution increases genetic variation in susceptibility to infection. eLife 2019; 8:e46440. [PMID: 31038124 PMCID: PMC6491035 DOI: 10.7554/elife.46440] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/07/2019] [Indexed: 12/31/2022] Open
Abstract
It is common to find considerable genetic variation in susceptibility to infection in natural populations. We have investigated whether natural selection increases this variation by testing whether host populations show more genetic variation in susceptibility to pathogens that they naturally encounter than novel pathogens. In a large cross-infection experiment involving four species of Drosophila and four host-specific viruses, we always found greater genetic variation in susceptibility to viruses that had coevolved with their host. We went on to examine the genetic architecture of resistance in one host species, finding that there are more major-effect genetic variants in coevolved host-pathogen interactions. We conclude that selection by pathogens has increased genetic variation in host susceptibility, and much of this effect is caused by the occurrence of major-effect resistance polymorphisms within populations.
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Affiliation(s)
- Elizabeth ML Duxbury
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- School of Biological SciencesUniversity of East AngliaNorwichUnited Kingdom
| | - Jonathan P Day
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Yannik Thüringer
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Ignacio Tolosana
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Sophia CL Smith
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Lucia Tagliaferri
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Altug Kamacioglu
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Imogen Lindsley
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Luca Love
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Robert L Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceUnited States
| | - Francis M Jiggins
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Ben Longdon
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- Centre for Ecology and Conservation, BiosciencesUniversity of Exeter (Penryn Campus)CornwallUnited Kingdom
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6
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Longdon B, Day JP, Schulz N, Leftwich PT, de Jong MA, Breuker CJ, Gibbs M, Obbard DJ, Wilfert L, Smith SCL, McGonigle JE, Houslay TM, Wright LI, Livraghi L, Evans LC, Friend LA, Chapman T, Vontas J, Kambouraki N, Jiggins FM. Vertically transmitted rhabdoviruses are found across three insect families and have dynamic interactions with their hosts. Proc Biol Sci 2017; 284:20162381. [PMID: 28100819 PMCID: PMC5310039 DOI: 10.1098/rspb.2016.2381] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/20/2016] [Indexed: 11/17/2022] Open
Abstract
A small number of free-living viruses have been found to be obligately vertically transmitted, but it remains uncertain how widespread vertically transmitted viruses are and how quickly they can spread through host populations. Recent metagenomic studies have found several insects to be infected with sigma viruses (Rhabdoviridae). Here, we report that sigma viruses that infect Mediterranean fruit flies (Ceratitis capitata), Drosophila immigrans, and speckled wood butterflies (Pararge aegeria) are all vertically transmitted. We find patterns of vertical transmission that are consistent with those seen in Drosophila sigma viruses, with high rates of maternal transmission, and lower rates of paternal transmission. This mode of transmission allows them to spread rapidly in populations, and using viral sequence data we found the viruses in D. immigrans and C. capitata had both recently swept through host populations. The viruses were common in nature, with mean prevalences of 12% in C. capitata, 38% in D. immigrans and 74% in P. aegeria We conclude that vertically transmitted rhabdoviruses may be widespread in a broad range of insect taxa, and that these viruses can have dynamic interactions with their hosts.
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Affiliation(s)
- Ben Longdon
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Nora Schulz
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Maaike A de Jong
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Casper J Breuker
- Evolutionary Developmental Biology Research Group, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford OX3 0BP, UK
| | - Melanie Gibbs
- NERC Centre for Ecology and Hydrology, Crowmarsh Gifford, Maclean Building, Wallingford, Oxfordshire OX10 8BB, UK
| | - Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Lena Wilfert
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn Campus TR10 9FE, UK
| | - Sophia C L Smith
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - John E McGonigle
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Thomas M Houslay
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn Campus TR10 9FE, UK
| | - Lucy I Wright
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn Campus TR10 9FE, UK
- Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Luca Livraghi
- Evolutionary Developmental Biology Research Group, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford OX3 0BP, UK
| | - Luke C Evans
- Evolutionary Developmental Biology Research Group, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford OX3 0BP, UK
- Ecology and Evolutionary Biology Research Division, School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Lucy A Friend
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - John Vontas
- Lab Pesticide Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
- Molecular Entomology, Institute Molecular Biology and Biotechnology/Foundation for Research and Technology, Voutes, 70013, Heraklio, Crete, Greece
| | - Natasa Kambouraki
- Lab Pesticide Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
- Molecular Entomology, Institute Molecular Biology and Biotechnology/Foundation for Research and Technology, Voutes, 70013, Heraklio, Crete, Greece
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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8
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Piontkivska H, Matos LF, Paul S, Scharfenberg B, Farmerie WG, Miyamoto MM, Wayne ML. Role of Host-Driven Mutagenesis in Determining Genome Evolution of Sigma Virus (DMelSV; Rhabdoviridae) in Drosophila melanogaster. Genome Biol Evol 2016; 8:2952-2963. [PMID: 27614234 PMCID: PMC5630973 DOI: 10.1093/gbe/evw212] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sigma virus (DMelSV) is ubiquitous in natural populations of Drosophila melanogaster. Host-mediated, selective RNA editing of adenosines to inosines (ADAR) may contribute to control of viral infection by preventing transcripts from being transported into the cytoplasm or being translated accurately; or by increasing the viral genomic mutation rate. Previous PCR-based studies showed that ADAR mutations occur in DMelSV at low frequency. Here we use SOLiDTM deep sequencing of flies from a single host population from Athens, GA, USA to comprehensively evaluate patterns of sequence variation in DMelSV with respect to ADAR. GA dinucleotides, which are weak targets of ADAR, are strongly overrepresented in the positive strand of the virus, consistent with selection to generate ADAR resistance on this complement of the transient, double-stranded RNA intermediate in replication and transcription. Potential ADAR sites in a worldwide sample of viruses are more likely to be “resistant” if the sites do not vary among samples. Either variable sites are less constrained and hence are subject to weaker selection than conserved sites, or the variation is driven by ADAR. We also find evidence of mutations segregating within hosts, hereafter referred to as hypervariable sites. Some of these sites were variable only in one or two flies (i.e., rare); others were shared by four or even all five of the flies (i.e., common). Rare and common hypervariable sites were indistinguishable with respect to susceptibility to ADAR; however, polymorphism in rare sites were more likely to be consistent with the action of ADAR than in common ones, again suggesting that ADAR is deleterious to the virus. Thus, in DMelSV, host mutagenesis is constraining viral evolution both within and between hosts.
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Affiliation(s)
- Helen Piontkivska
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH
| | - Luis F Matos
- Department of Entomology & Nematology, University of Florida, Gainesville, FL Department of Biology, Eastern Washington University, Cheney, WA
| | - Sinu Paul
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Brian Scharfenberg
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH Ohio University Heritage College of Osteopathic Medicine, Athens, OH
| | - William G Farmerie
- Interdisciplinary Center for Biotechnology Research University of Florida, Gainesville, FL
| | | | - Marta L Wayne
- Department of Biology, University of Florida, Gainesville, FL Emerging Pathogens Institute University of Florida, Gainesville, FL
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9
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Kriesner P, Conner WR, Weeks AR, Turelli M, Hoffmann AA. Persistence of a Wolbachia infection frequency cline in Drosophila melanogaster and the possible role of reproductive dormancy. Evolution 2016; 70:979-97. [PMID: 27076356 PMCID: PMC4874875 DOI: 10.1111/evo.12923] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/30/2016] [Accepted: 04/04/2016] [Indexed: 12/17/2022]
Abstract
Field populations of arthropods are often polymorphic for Wolbachia but the factors maintaining intermediate Wolbachia frequencies are generally not understood. In Drosophila melanogaster, Wolbachia frequencies are highly variable across the globe. We document the persistence of a Wolbachia infection frequency cline in D. melanogaster populations from eastern Australia across at least 20 years, with frequencies generally high in the tropics but lower in cool temperate regions. The results are interpreted using a model of frequency dynamics incorporating cytoplasmic incompatibility (CI), imperfect maternal transmission and Wolbachia effects on fitness. Clinal variation is less pronounced in eastern North America which may reflect annual recolonization at higher latitudes. Limited samples from Africa from latitudes matching our tropical and subtropical samples from Australia and North America show comparably high infection frequencies, but some equatorial samples show lower frequencies. Adult dormancy across cold periods may contribute to the Australian Wolbachia cline. Infected flies exposed to cold conditions for an extended period had reduced fecundity and viability, an effect not evident in unexposed controls. These fitness costs may contribute to the relatively low Wolbachia frequencies in Australian temperate areas; whereas different processes, including CI induced by young males, may contribute to higher frequencies in tropical locations.
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Affiliation(s)
- Peter Kriesner
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, 3010, Australia
| | - William R. Conner
- Department of Evolution and Ecology, University of California, Davis, USA
| | - Andrew R. Weeks
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Michael Turelli
- Department of Evolution and Ecology, University of California, Davis, USA
| | - Ary A. Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, 3010, Australia
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10
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Hill T, Schlötterer C, Betancourt AJ. Hybrid Dysgenesis in Drosophila simulans Associated with a Rapid Invasion of the P-Element. PLoS Genet 2016; 12:e1005920. [PMID: 26982327 PMCID: PMC4794157 DOI: 10.1371/journal.pgen.1005920] [Citation(s) in RCA: 48] [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: 10/26/2015] [Accepted: 02/14/2016] [Indexed: 11/22/2022] Open
Abstract
In a classic example of the invasion of a species by a selfish genetic element, the P-element was horizontally transferred from a distantly related species into Drosophila melanogaster. Despite causing ‘hybrid dysgenesis’, a syndrome of abnormal phenotypes that include sterility, the P-element spread globally in the course of a few decades in D. melanogaster. Until recently, its sister species, including D. simulans, remained P-element free. Here, we find a hybrid dysgenesis-like phenotype in the offspring of crosses between D. simulans strains collected in different years; a survey of 181 strains shows that around 20% of strains induce hybrid dysgenesis. Using genomic and transcriptomic data, we show that this dysgenesis-inducing phenotype is associated with the invasion of the P-element. To characterize this invasion temporally and geographically, we survey 631 D. simulans strains collected on three continents and over 27 years for the presence of the P-element. We find that the D. simulans P-element invasion occurred rapidly and nearly simultaneously in the regions surveyed, with strains containing P-elements being rare in 2006 and common by 2014. Importantly, as evidenced by their resistance to the hybrid dysgenesis phenotype, strains collected from the latter phase of this invasion have adapted to suppress the worst effects of the P-element. Some genes perform necessary organismal functions, others hijack the cellular machinery to replicate themselves, potentially harming the host in the process. These ‘selfish genes’ can spread through genomes and species; as a result, eukaryotic genomes are typically saddled with large amounts of parasitic DNA. Here, we chronicle the surprisingly rapid global spread of a selfish transposable element through a close relative of the genetic model, Drosophila melanogaster. We see that, as it spreads, the transposable element is associated with damaging effects, including sterility, but that the flies quickly adapt to the negative consequences of the transposable element.
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Affiliation(s)
- Tom Hill
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
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11
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Ribeiro JMC, Kazimirova M, Takac P, Andersen JF, Francischetti IMB. An insight into the sialome of the horse fly, Tabanus bromius. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 65:83-90. [PMID: 26369729 PMCID: PMC4646416 DOI: 10.1016/j.ibmb.2015.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/03/2015] [Accepted: 09/06/2015] [Indexed: 05/17/2023]
Abstract
Blood feeding animals face their host's defenses against tissue injury and blood loss while attempting to feed. One adaptation to surmount these barriers involves the evolution of a salivary potion that disarms their host's inflammatory and anti-hemostatic processes. The composition of the peptide moiety of this potion, or sialome (from the Greek sialo = saliva), can be deducted in part by proper interpretation of the blood feeder' sialotranscriptome. In this work we disclose the sialome of the blood feeding adult female Tabanus bromius. Following assembly of over 75 million Illumina reads (101 nt long) 16,683 contigs were obtained from which 4078 coding sequences were extracted. From these, 320 were assigned as coding for putative secreted proteins. These 320 contigs mapped 85% of the reads. The antigen-5 proteins family was studied in detail, indicating three Tabanus specific clades with and without disintegrin domains, as well as with and without leukotriene binding domains. Defensins were also detailed; a clade of salivary tabanid peptides was found lacking the propeptide domain ending in the KR dipeptide signaling furin cleavage. Novel protein families were also disclosed. Viral transcripts were identified closely matching the Kotonkan virus capsid proteins. Full length Mariner transposases were also identified. A total of 3043 coding sequences and their protein products were deposited in Genbank. Hyperlinked excel spreadsheets containing the coding sequences and their annotation are available at http://exon.niaid.nih.gov/transcriptome/T_bromius/Tbromius-web.xlsx (hyperlinked excel spreadsheet, 11 MB) and http://exon.niaid.nih.gov/transcriptome/T_bromius/Tbromius-SA.zip (Standalone excel with all local links, 360 MB). These sequences provide for a platform from which further proteomic studies may be designed to identify salivary proteins from T. bromius that are of pharmacological interest or used as immunological markers of host exposure.
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Affiliation(s)
- José M C Ribeiro
- National Institute of Allergy and Infectious Diseases, Laboratory of Malaria and Vector Research, 12735 Twinbrook Parkway, Maryland 20852, USA.
| | - Maria Kazimirova
- Institute of Zoology, Slovak Academy of Sciences, Dubravska cesta 9, SK-84506 Bratislava, Slovakia
| | - Peter Takac
- Institute of Zoology, Slovak Academy of Sciences, Dubravska cesta 9, SK-84506 Bratislava, Slovakia
| | - John F Andersen
- National Institute of Allergy and Infectious Diseases, Laboratory of Malaria and Vector Research, 12735 Twinbrook Parkway, Maryland 20852, USA
| | - Ivo M B Francischetti
- National Institute of Allergy and Infectious Diseases, Laboratory of Malaria and Vector Research, 12735 Twinbrook Parkway, Maryland 20852, USA
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12
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Webster CL, Waldron FM, Robertson S, Crowson D, Ferrari G, Quintana JF, Brouqui JM, Bayne EH, Longdon B, Buck AH, Lazzaro BP, Akorli J, Haddrill PR, Obbard DJ. The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster. PLoS Biol 2015; 13:e1002210. [PMID: 26172158 PMCID: PMC4501690 DOI: 10.1371/journal.pbio.1002210] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 06/26/2015] [Indexed: 11/18/2022] Open
Abstract
Drosophila melanogaster is a valuable invertebrate model for viral infection and antiviral immunity, and is a focus for studies of insect-virus coevolution. Here we use a metagenomic approach to identify more than 20 previously undetected RNA viruses and a DNA virus associated with wild D. melanogaster. These viruses not only include distant relatives of known insect pathogens but also novel groups of insect-infecting viruses. By sequencing virus-derived small RNAs, we show that the viruses represent active infections of Drosophila. We find that the RNA viruses differ in the number and properties of their small RNAs, and we detect both siRNAs and a novel miRNA from the DNA virus. Analysis of small RNAs also allows us to identify putative viral sequences that lack detectable sequence similarity to known viruses. By surveying >2,000 individually collected wild adult Drosophila we show that more than 30% of D. melanogaster carry a detectable virus, and more than 6% carry multiple viruses. However, despite a high prevalence of the Wolbachia endosymbiont--which is known to be protective against virus infections in Drosophila--we were unable to detect any relationship between the presence of Wolbachia and the presence of any virus. Using publicly available RNA-seq datasets, we show that the community of viruses in Drosophila laboratories is very different from that seen in the wild, but that some of the newly discovered viruses are nevertheless widespread in laboratory lines and are ubiquitous in cell culture. By sequencing viruses from individual wild-collected flies we show that some viruses are shared between D. melanogaster and D. simulans. Our results provide an essential evolutionary and ecological context for host-virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research.
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Affiliation(s)
- Claire L. Webster
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Fergal M. Waldron
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Shaun Robertson
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Daisy Crowson
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Giada Ferrari
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Juan F. Quintana
- Institute of Immunity and Infection Research, and the Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Jean-Michel Brouqui
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Elizabeth H. Bayne
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Ben Longdon
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy H. Buck
- Institute of Immunity and Infection Research, and the Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Brian P. Lazzaro
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
| | - Jewelna Akorli
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Penelope R. Haddrill
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Darren J. Obbard
- Institute of Evolutionary Biology and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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Obbard DJ, Dudas G. The genetics of host-virus coevolution in invertebrates. Curr Opin Virol 2014; 8:73-8. [PMID: 25063907 PMCID: PMC4199324 DOI: 10.1016/j.coviro.2014.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 11/19/2022]
Abstract
Although viral infection and antiviral defence are ubiquitous, genetic data are currently unavailable from the vast majority of animal phyla-potentially biasing our overall perspective of the coevolutionary process. Rapid adaptive evolution is seen in some insect antiviral genes, consistent with invertebrate-virus 'arms-race' coevolution, but equivalent signatures of selection are hard to detect in viruses. We find that, despite the large differences in vertebrate, invertebrate, and plant immune responses, comparison of viral evolution fails to identify any difference among these hosts in the impact of positive selection. The best evidence for invertebrate-virus coevolution is currently provided by large-effect polymorphisms for host resistance and/or viral evasion, as these often appear to have arisen and spread recently, and can be favoured by virus-mediated selection.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh, UK; Centre for Infection Immunity and Evolution, University of Edinburgh, Kings Buildings, Edinburgh, UK.
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh, UK
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