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Betancourt AJ, Wei KHC, Huang Y, Lee YCG. Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective. Annu Rev Genomics Hum Genet 2024; 25:1-25. [PMID: 38603565 DOI: 10.1146/annurev-genom-120822-105708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes, including humans. This evolutionary success of TEs is due to their replicative activity, involving insertion into new genomic locations. TE activity varies at multiple levels, from between taxa to within individuals. The rapidly accumulating evidence of the influence of TE activity on human health, as well as the rapid growth of new tools to study it, motivated an evaluation of what we know about TE activity thus far. Here, we discuss why TE activity varies, and the consequences of this variation, from an evolutionary perspective. By studying TE activity in nonhuman organisms in the context of evolutionary theories, we can shed light on the factors that affect TE activity. While the consequences of TE activity are usually deleterious, some have lasting evolutionary impacts by conferring benefits on the host or affecting other evolutionary processes.
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Affiliation(s)
- Andrea J Betancourt
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kevin H-C Wei
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Yuh Chwen G Lee
- Center for Complex Biological Systems, University of California, Irvine, California, USA;
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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2
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Wallace MA, Obbard DJ. Naturally occurring viruses of Drosophila reduce offspring number and lifespan. Proc Biol Sci 2024; 291:20240518. [PMID: 38747703 DOI: 10.1098/rspb.2024.0518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/23/2024] [Indexed: 07/31/2024] Open
Abstract
Drosophila remains a pre-eminent insect model system for host-virus interaction, but the host range and fitness consequences of the drosophilid virome are poorly understood. Metagenomic studies have reported approximately 200 viruses associated with Drosophilidae, but few isolates are available to characterize the Drosophila immune response, and most characterization has relied on injection and systemic infection. Here, we use a more natural infection route to characterize the fitness effects of infection and to study a wider range of viruses. We exposed laboratory Drosophila melanogaster to 23 naturally occurring viruses from wild-collected drosophilids. We recorded transmission rates along with two components of female fitness: survival and the lifetime number of adult offspring produced. Nine different viruses transmitted during contact with laboratory D. melanogaster, although for the majority, rates of transmission were less than 20%. Five virus infections led to a significant decrease in lifespan (D. melanogaster Nora virus, D. immigrans Nora virus, Muthill virus, galbut virus and Prestney Burn virus), and three led to a reduction in the total number of offspring. Our findings demonstrate the utility of the Drosophila model for community-level studies of host-virus interactions, and suggest that viral infection could be a substantial fitness burden on wild flies.
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Affiliation(s)
- Megan A Wallace
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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Tembrock LR, Zink FA, Gilligan TM. Viral Prevalence and Genomic Xenology in the Coevolution of HzNV-2 (Nudiviridae) with Host Helicoverpa zea (Lepidoptera: Noctuidae). INSECTS 2023; 14:797. [PMID: 37887809 PMCID: PMC10607169 DOI: 10.3390/insects14100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/16/2023] [Accepted: 09/24/2023] [Indexed: 10/28/2023]
Abstract
Insect viruses have been described from numerous lineages, yet patterns of genetic exchange and viral prevalence, which are essential to understanding host-virus coevolution, are rarely studied. In Helicoverpa zea, the virus HzNV-2 can cause deformity of male and female genitalia, resulting in sterility. Using ddPCR, we found that male H. zea with malformed genitalia (agonadal) contained high levels of HzNV-2 DNA, confirming previous work. HzNV-2 was found to be prevalent throughout the United States, at more than twice the rate of the baculovirus HaSNPV, and that it contained several host-acquired DNA sequences. HzNV-2 possesses four recently endogenized lepidopteran genes and several more distantly related genes, including one gene with a bacteria-like sequence found in both host and virus. Among the recently acquired genes is cytosolic serine hydroxymethyltransferase (cSHMT). In nearly all tested H. zea, cSHMT contained a 200 bp transposable element (TE) that was not found in cSHMT of the sister species H. armigera. No other virus has been found with host cSHMT, and the study of this shared copy, including possible interactions, may yield new insights into the function of this gene with possible applications to insect biological control, and gene editing.
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Affiliation(s)
- Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Frida A. Zink
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Todd M. Gilligan
- USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, Fort Collins, CO 80526, USA
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Arunkumar R, Zhou SO, Day JP, Bakare S, Pitton S, Zhang Y, Hsing CY, O’Boyle S, Pascual-Gil J, Clark B, Chandler RJ, Leitão AB, Jiggins FM. Natural selection has driven the recurrent loss of an immunity gene that protects Drosophila against a major natural parasite. Proc Natl Acad Sci U S A 2023; 120:e2211019120. [PMID: 37552757 PMCID: PMC10438844 DOI: 10.1073/pnas.2211019120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 06/26/2023] [Indexed: 08/10/2023] Open
Abstract
Polymorphisms in immunity genes can have large effects on susceptibility to infection. To understand the origins of this variation, we have investigated the genetic basis of resistance to the parasitoid wasp Leptopilina boulardi in Drosophila melanogaster. We found that increased expression of the gene lectin-24A after infection by parasitic wasps was associated with a faster cellular immune response and greatly increased rates of killing the parasite. lectin-24A encodes a protein that is strongly up-regulated in the fat body after infection and localizes to the surface of the parasite egg. In certain susceptible lines, a deletion upstream of the lectin-24A has largely abolished expression. Other mutations predicted to abolish the function of this gene have arisen recurrently in this gene, with multiple loss-of-expression alleles and premature stop codons segregating in natural populations. The frequency of these alleles varies greatly geographically, and in some southern African populations, natural selection has driven them near to fixation. We conclude that natural selection has favored the repeated loss of an important component of the immune system, suggesting that in some populations, a pleiotropic cost to lectin-24A expression outweighs the benefits of resistance.
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Affiliation(s)
- Ramesh Arunkumar
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Shuyu Olivia Zhou
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Jonathan P. Day
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Sherifat Bakare
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Department of Biochemical Sciences, School of Biosciences, University of Surrey, 388 Stag Hill, Guildford,GU2 7XH, United Kingdom
| | - Simone Pitton
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Biosciences Department, Università degli Studi di Milano, Via Celoria 26, Milano, MI20133, Italy
| | - Yexin Zhang
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Chi-Yun Hsing
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Sinead O’Boyle
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- School of Biomolecular and Biomedical Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Juan Pascual-Gil
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Facultad de Ciencias, Universidad Autónoma de Madrid, C. Francisco Tomás y Valiente 7, 28049Madrid, Spain
| | - Belinda Clark
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Rachael J. Chandler
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Department of Biochemical Sciences, School of Biosciences, University of Surrey, 388 Stag Hill, Guildford,GU2 7XH, United Kingdom
| | - Alexandre B. Leitão
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
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5
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Zhao M, Plough LV, Behringer DC, Bojko J, Kough AS, Alper NW, Xu L, Schott EJ. Cross-Hemispheric Genetic Diversity and Spatial Genetic Structure of Callinectes sapidus Reovirus 1 (CsRV1). Viruses 2023; 15:v15020563. [PMID: 36851777 PMCID: PMC9962310 DOI: 10.3390/v15020563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The movement of viruses in aquatic systems is rarely studied over large geographic scales. Oceanic currents, host migration, latitude-based variation in climate, and resulting changes in host life history are all potential drivers of virus connectivity, adaptation, and genetic structure. To expand our understanding of the genetic diversity of Callinectes sapidus reovirus 1 (CsRV1) across a broad spatial and host life history range of its blue crab host (Callinectes sapidus), we obtained 22 complete and 96 partial genomic sequences for CsRV1 strains from the US Atlantic coast, Gulf of Mexico, Caribbean Sea, and the Atlantic coast of South America. Phylogenetic analyses of CsRV1 genomes revealed that virus genotypes were divided into four major genogroups consistent with their host geographic origins. However, some CsRV1 sequences from the US mid-Atlantic shared high genetic similarity with the Gulf of Mexico genotypes, suggesting potential human-mediated movement of CsRV1 between the US mid-Atlantic and Gulf coasts. This study advances our understanding of how climate, coastal geography, host life history, and human activity drive patterns of genetic structure and diversity of viruses in marine animals and contributes to the capacity to infer broadscale host population connectivity in marine ecosystems from virus population genetic data.
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Affiliation(s)
- Mingli Zhao
- Institute of Marine and Environmental Technology, University of Maryland Baltimore County, Baltimore, MD 21202, USA
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London AL9 7TA, UK
| | - Louis V. Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
| | - Donald C. Behringer
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL 32653, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, USA
| | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
| | - Andrew S. Kough
- John G. Shedd Aquarium, Haerther Center for Conservation Research, Chicago, IL 60605, USA
| | - Nathaniel W. Alper
- Baltimore Polytechnic Institute, Columbia University, New York, NY 20027, USA
| | - Lan Xu
- Department of Marine Biotechnology and Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD 21202, USA
| | - Eric J. Schott
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
- Correspondence:
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Gao J, Zhao BR, Zhang H, You YL, Li F, Wang XW. Interferon functional analog activates antiviral Jak/Stat signaling through integrin in an arthropod. Cell Rep 2021; 36:109761. [PMID: 34592151 DOI: 10.1016/j.celrep.2021.109761] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 07/19/2021] [Accepted: 09/03/2021] [Indexed: 12/15/2022] Open
Abstract
Drosophila Vago is a small antiviral peptide. Its ortholog in Culex mosquito was found to be an interferon-like cytokine that limits virus replication through activating Jak/Stat signaling. However, this activation is independent of Domeless, the sole homolog of vertebrate type I cytokine receptor. How Vago activates the Jak/Stat pathway remains unknown. Herein, we report this process is dependent on integrin in kuruma shrimp (Marsupenaeus japonicus). Shrimp Vago-like (MjVago-L) plays an antiviral role by activating the Jak/Stat pathway and inducing Stat-regulated Ficolin. Blocking integrin abrogates the role of MjVago-L. The interaction between MjVago-L and integrin β3 is confirmed. An Asp residue in MjVago-L is found critical for the interaction and MjVago-L's antiviral role. Moreover, Fak, a key adaptor of integrin signaling, mediates MjVago-L-induced Jak/Stat activation. Therefore, this study reveals that integrin, as the receptor of MjVago-L, mediates Jak/Stat activation. The establishment of the MjVago-L/integrin/Fak/Jak/Stat/Ficolin axis provides insights into antiviral cytokine signaling in invertebrates.
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Affiliation(s)
- Jie Gao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Bao-Rui Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Hui Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yan-Lin You
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Fang Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xian-Wei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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7
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Agnati LF, Anderlini D, Guidolin D, Marcoli M, Maura G. Man is a "Rope" Stretched Between Virosphere and Humanoid Robots: On the Urgent Need of an Ethical Code for Ecosystem Survival. FOUNDATIONS OF SCIENCE 2021; 27:311-325. [PMID: 34177285 PMCID: PMC8210962 DOI: 10.1007/s10699-021-09796-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 06/13/2023]
Abstract
In this paper we compare the strategies applied by two successful biological components of the ecosystem, the viruses and the human beings, to interact with the environment. Viruses have had and still exert deep and vast actions on the ecosystem especially at the genome level of most of its biotic components. We discuss on the importance of the human being as contraptions maker in particular of robots, hence of machines capable of automatically carrying out complex series of actions. Beside the relevance of designing and assembling these contraptions, it is of basic importance the goal for which they are assembled and future scenarios of their possible impact on the ecosystem. We can't procrastinate the development and implementation of a highly inspired and stringent "ethical code" for human beings and humanoid robots because it will be a crucial aspect for the wellbeing of the mankind and of the entire ecosystem.
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Affiliation(s)
- Luigi F. Agnati
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Deanna Anderlini
- Centre for Sensorimotor Performance, The University of Queensland, Brisbane, Australia
| | - Diego Guidolin
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, GENOVA, Italy
| | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, GENOVA, Italy
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Barrantes FJ. Structural biology of coronavirus ion channels. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:391-402. [PMID: 33825700 DOI: 10.1107/s2059798321001431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/08/2021] [Indexed: 01/08/2023]
Abstract
Viral infection compromises specific organelles of the cell and readdresses its functional resources to satisfy the needs of the invading body. Around 70% of the coronavirus positive-sense single-stranded RNA encodes proteins involved in replication, and these viruses essentially take over the biosynthetic and transport mechanisms to ensure the efficient replication of their genome and trafficking of their virions. Some coronaviruses encode genes for ion-channel proteins - the envelope protein E (orf4a), orf3a and orf8 - which they successfully employ to take control of the endoplasmic reticulum-Golgi complex intermediate compartment or ERGIC. The E protein, which is one of the four structural proteins of SARS-CoV-2 and other coronaviruses, assembles its transmembrane protomers into homopentameric channels with mild cationic selectivity. Orf3a forms homodimers and homotetramers. Both carry a PDZ-binding domain, lending them the versatility to interact with more than 400 target proteins in infected host cells. Orf8 is a very short 29-amino-acid single-passage transmembrane peptide that forms cation-selective channels when assembled in lipid bilayers. This review addresses the contribution of biophysical and structural biology approaches that unravel different facets of coronavirus ion channels, their effects on the cellular machinery of infected cells and some structure-functional correlations with ion channels of higher organisms.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA) - National Scientific and Technical Research Council (CONICET), C1107AFF Buenos Aires, Argentina
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9
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Genomic diversity in a population of Spodoptera frugiperda nucleopolyhedrovirus. INFECTION GENETICS AND EVOLUTION 2021; 90:104749. [PMID: 33540087 DOI: 10.1016/j.meegid.2021.104749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/10/2021] [Accepted: 01/29/2021] [Indexed: 01/05/2023]
Abstract
Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) represents a strong candidate to develop environmental-friendly pesticides against the fall armyworm (Spodoptera frugiperda), a widespread pest that poses a severe threat to different crops around the world. To date, SfMNPV genomic diversity of different isolates has been mainly studied by means of restriction pattern analyses and by sequencing of the egt region. Here, the genomic diversity present inside an isolate of SfMNPV was explored using high-throughput sequencing for the first time. We identified 704 intrahost single nucleotide variants, from which 184 are nonsynonymous mutations distributed among 82 different coding sequences. We detected several structural variants affecting SfMNPV genome, including two previously reported deletions inside the egt region. A comparative analysis between polymorphisms present in different SfMNPV isolates and our intraisolate diversity data suggests that coding regions with higher genetic diversity are associated with oral infectivity or unknown functions. In this context, through molecular evolution studies we provide evidence of diversifying selection acting on sf29, a putative collagenase which could contribute to the oral infectivity of SfMNPV. Overall, our results contribute to deepen our understanding of the coevolution between SfMNPV and the fall armyworm and will be useful to improve the applicability of this virus as a biological control agent.
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10
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Amiri E, Herman JJ, Strand MK, Tarpy DR, Rueppell O. Egg transcriptome profile responds to maternal virus infection in honey bees, Apis mellifera. INFECTION GENETICS AND EVOLUTION 2020; 85:104558. [PMID: 32947033 DOI: 10.1016/j.meegid.2020.104558] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Trans-generational disease effects include vertical pathogen transmission but also immune priming to enhance offspring immunity. Accordingly, the survival consequences of maternal virus infection can vary and its molecular consequences during early development are poorly understood. The honey bee queen is long-lived and represents the central hub for vertical virus transmission as the sole reproductive individual in her colony. Even though virus symptoms in queens are mild, viral infection may have severe consequences for the offspring. Thus, transcriptome patterns during early developmental are predicted to respond to maternal virus infection. To test this hypothesis, gene expression patterns were compared among pooled honey bee eggs laid by queens that were either infected with Deformed wing virus (DWV1), Sacbrood virus (SBV2), both viruses (DWV and SBV), or no virus. Whole transcriptome analyses revealed significant expression differences of a few genes, some of which have hitherto no known function. Despite the paucity of single gene effects, functional enrichment analyses revealed numerous biological processes in the embryos to be affected by virus infection. Effects on several regulatory pathways were consistent with maternal responses to virus infection and correlated with responses to DWV and SBV in honey bee larvae and pupae. Overall, effects on egg transcriptome patterns were specific to each virus and the results of dual-infection samples suggested synergistic effects of DWV and SBV. We interpret our results as consequences of maternal infections. Thus, this first study to document and characterize virus-associated changes in the transcriptome of honey bee eggs represents an important contribution to understanding trans-generational virus effects, although more in-depth studies are needed to understand the detailed mechanisms of how viruses affect honey bee embryos.
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Affiliation(s)
- Esmaeil Amiri
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402, USA; Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
| | - Jacob J Herman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Micheline K Strand
- Life Sciences Division, U.S. Army Research Office, CCDC-ARL, Research Triangle Park, Durham, NC 27709, USA
| | - David R Tarpy
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402, USA; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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11
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Abundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary Implications. mSystems 2020; 5:5/4/e00039-20. [PMID: 32636338 PMCID: PMC7343303 DOI: 10.1128/msystems.00039-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Increasing data indicate that insects serve as major reservoirs and vectors of viruses, which account for the continuously increasing ecological burden and infectious disease outbreaks. Uncovering the hidden diversity of viruses in insects will further the understanding of the ecological and evolutionary perspectives in the emergence of insect-associated virus diseases. In this study, we queried transcriptome sequencing (RNA-Seq) data from more than 600 species across 32 insect orders dwelling in different ecological habitats and recovered more than 1,213 RNA viruses that were recapitulated in 40 families, 2 unclassified genera, and many unspecified viral groups. These novel viruses included the well-known insect-associated viruses within Flaviviridae, Picornavirales, Bunyavirales, Mononegavirales, Nidovirales, Reoviridae, and Negevirus More appeared to form novel clusters within previously described taxa or could be resolved as paraphyletic, including the first astrovirus identified in insects, in which many were sufficiently divergent to warrant the establishment of new virus genera or families. Additionally, some viruses were closely related to the recognized plant-, fungus-, and vertebrate-specific species, implying the importance of relationships between insect behavior and virus spread. Comparative genome analyses also revealed high genomic variability with respect to the flexible gene pool and genome architecture of these newly described viruses, including the evidence for genome reshuffling first discovered in Dicistroviridae The data reflecting the genetically and ecologically diverse viral populations in insects greatly expand our understanding of RNA viruses in nature and highlight that the biodiversity of RNA viruses remains largely unexplored.IMPORTANCE Insects comprise the largest proportion of animals on earth and are frequently implicated in the transmission of vector-borne diseases. However, considerable attention has been paid to the phytophagous and hematophagous insects, with results that provide insufficient and biased information about the viruses in insects. Here, we have delivered compelling evidence for the exceptional abundance and genetic diversity of RNA viruses in a wide range of insects. Novel viruses were found to cover major categories of RNA viruses, and many formed novel clusters divergent from the previously described taxa, dramatically broadening the range of known RNA viruses in insects. These newly characterized RNA viruses exhibited high levels of genomic plasticity in genome size, open reading frame (ORF) number, intergenic structure, and gene rearrangement and segmentation. This work provides comprehensive insight into the origin, spread, and evolution of RNA viruses. Of course, a large-scale virome project involving more organisms would provide more-detailed information about the virus infections in insects.
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13
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Niu J, Li XL, Wu YL, Sun QZ, Zhang W, Cao M, Wang JJ. RNA virome screening in diverse but ecologically related citrus pests reveals potential virus-host interactions. J Invertebr Pathol 2020; 170:107329. [PMID: 31962124 DOI: 10.1016/j.jip.2020.107329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 12/13/2022]
Abstract
As an evergreen ecosystem, citrus orchards have specialized pest species and stable ecological homeostasis; thus, they provide an ideal model for investigating RNA viromes in diverse but ecologically related species. For this purpose, we collected specialized citrus pests from three classes of invertebrates, Insecta, Arachnida, and Gastropoda and we constructed two kinds of libraries (RNA and small RNA) for the pests by deep sequencing. In total, six virus-derived sequences were identified, including four Picornavirales, one Jingchuvirales and one Nidovirales. The picornavirus-derived small RNAs showed significant small RNA peaks and symmetric distribution patterns along the genome, which suggests these viruses infected the hosts and triggered host antiviral immunity RNA interference. Screening of virus-derived sequences in multiple species of citrus pests (n = 10 per species) showed that Eotetranychus kankitus picorna-like virus and Tetranychus urticae mivirus may be present in multiple pests. Our investigation in citrus pests confirmed that RNA viruses revealed by metagenomics could impact host immunity (e.g. RNAi). An approach with parallel deep sequencing of RNAs and small RNAs is useful not only for viral discoveries but also for understanding virus-host interactions of ecologically related but divergent pest species.
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Affiliation(s)
- Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiao-Lin Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yue-Ling Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Qin-Zhe Sun
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Mengji Cao
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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14
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Rosani U, Bai CM, Maso L, Shapiro M, Abbadi M, Domeneghetti S, Wang CM, Cendron L, MacCarthy T, Venier P. A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks. BMC Evol Biol 2019; 19:149. [PMID: 31337330 PMCID: PMC6651903 DOI: 10.1186/s12862-019-1472-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
Background Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. Results We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets. Conclusions We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1472-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 32121, Padova, Italy. .,Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute (AWI), Wadden Sea Station, 25992, List auf Sylt, Germany.
| | - Chang-Ming Bai
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Lorenzo Maso
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Miriam Abbadi
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, Italy
| | | | - Chong-Ming Wang
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Laura Cendron
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Paola Venier
- Department of Biology, University of Padova, 32121, Padova, Italy.
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15
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Kolliopoulou A, Santos D, Taning CNT, Wynant N, Vanden Broeck J, Smagghe G, Swevers L. PIWI pathway against viruses in insects. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1555. [PMID: 31183996 DOI: 10.1002/wrna.1555] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/26/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are an animal-specific class of small non-coding RNAs that are generated via a biogenesis pathway distinct from small interfering RNAs (siRNAs) and microRNAs (miRNAs). There are variations in piRNA biogenesis that depend on several factors, such as the cell type (germline or soma), the organism, and the purpose for which they are being produced, such as transposon-targeting, viral-targeting, or gene-derived piRNAs. Interestingly, the genes involved in the PIWI/piRNA pathway are more rapidly evolving compared with other RNA interference (RNAi) genes. In this review, the role of the piRNA pathway in the antiviral response is reviewed based on recent findings in insect models such as Drosophila, mosquitoes, midges and the silkworm, Bombyx mori. We extensively discuss the special features that characterize host-virus piRNA responses with respect to the proteins and the genes involved, the viral piRNAs' sequence characteristics, the target strand orientation biases as well as the viral piRNA target hotspots across the viral genomes. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Dulce Santos
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Clauvis Nji Tizi Taning
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Niels Wynant
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
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16
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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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17
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Chisholm PJ, Busch JW, Crowder DW. Effects of life history and ecology on virus evolutionary potential. Virus Res 2019; 265:1-9. [PMID: 30831177 DOI: 10.1016/j.virusres.2019.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 11/28/2022]
Abstract
The life history traits of viruses pose many consequences for viral population structure. In turn, population structure may influence the evolutionary trajectory of a virus. Here we review factors that affect the evolutionary potential of viruses, including rates of mutation and recombination, bottlenecks, selection pressure, and ecological factors such as the requirement for hosts and vectors. Mutation, while supplying a pool of raw genetic material, also results in the generation of numerous unfit mutants. The infection of multiple host species may expand a virus' ecological niche, although it may come at a cost to genetic diversity. Vector-borne viruses often experience a diminished frequency of positive selection and exhibit little diversity, and resistance against vector-borne viruses may thus be more durable than against non-vectored viruses. Evidence indicates that adaptation to a vector is more evolutionarily difficult than adaptation to a host. Overall, a better understanding of how various factors influence viral dynamics in both plant and animal pathosystems will lead to more effective anti-viral treatments and countermeasures.
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Affiliation(s)
- Paul J Chisholm
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA.
| | - David W Crowder
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
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18
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Rosani U, Shapiro M, Venier P, Allam B. A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data. Viruses 2019; 11:v11030205. [PMID: 30832203 PMCID: PMC6466128 DOI: 10.3390/v11030205] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 02/08/2023] Open
Abstract
Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4% of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated with bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. Single Nucleotide Polymorphism (SNP) analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padua, 35121 Padua, Italy.
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794-5000, USA.
| | - Paola Venier
- Department of Biology, University of Padua, 35121 Padua, Italy.
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
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19
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Kariithi HM, Boucias DG, Murungi EK, Meki IK, Demirbaş-Uzel G, van Oers MM, Vreysen MJB, Abd-Alla AMM, Vlak JM. Coevolution of hytrosaviruses and host immune responses. BMC Microbiol 2018; 18:183. [PMID: 30470186 PMCID: PMC6251100 DOI: 10.1186/s12866-018-1296-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Hytrosaviruses (SGHVs; Hytrosaviridae family) are double-stranded DNA (dsDNA) viruses that cause salivary gland hypertrophy (SGH) syndrome in flies. Two structurally and functionally distinct SGHVs are recognized; Glossina pallidipes SGHV (GpSGHV) and Musca domestica SGHV (MdSGHV), that infect the hematophagous tsetse fly and the filth-feeding housefly, respectively. Genome sizes and gene contents of GpSGHV (~ 190 kb; 160-174 genes) and MdSGHV (~ 124 kb; 108 genes) may reflect an evolution with the SGHV-hosts resulting in differences in pathobiology. Whereas GpSGHV can switch from asymptomatic to symptomatic infections in response to certain unknown cues, MdSGHV solely infects symptomatically. Overt SGH characterizes the symptomatic infections of SGHVs, but whereas MdSGHV induces both nuclear and cellular hypertrophy (enlarged non-replicative cells), GpSGHV induces cellular hyperplasia (enlarged replicative cells). Compared to GpSGHV's specificity to Glossina species, MdSGHV infects other sympatric muscids. The MdSGHV-induced total shutdown of oogenesis inhibits its vertical transmission, while the GpSGHV's asymptomatic and symptomatic infections promote vertical and horizontal transmission, respectively. This paper reviews the coevolution of the SGHVs and their hosts (housefly and tsetse fly) based on phylogenetic relatedness of immune gene orthologs/paralogs and compares this with other virus-insect models. RESULTS Whereas MdSGHV is not vertically transmitted, GpSGHV is both vertically and horizontally transmitted, and the balance between the two transmission modes may significantly influence the pathogenesis of tsetse virus. The presence and absence of bacterial symbionts (Wigglesworthia and Sodalis) in tsetse and Wolbachia in the housefly, respectively, potentially contributes to the development of SGH symptoms. Unlike MdSGHV, GpSGHV contains not only host-derived proteins, but also appears to have evolutionarily recruited cellular genes from ancestral host(s) into its genome, which, although may be nonessential for viral replication, potentially contribute to the evasion of host's immune responses. Whereas MdSGHV has evolved strategies to counteract both the housefly's RNAi and apoptotic responses, the housefly has expanded its repertoire of immune effector, modulator and melanization genes compared to the tsetse fly. CONCLUSIONS The ecologies and life-histories of the housefly and tsetse fly may significantly influence coevolution of MdSGHV and GpSGHV with their hosts. Although there are still many unanswered questions regarding the pathogenesis of SGHVs, and the extent to which microbiota influence expression of overt SGH symptoms, SGHVs are attractive 'explorers' to elucidate the immune responses of their hosts, and the transmission modes of other large DNA viruses.
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Affiliation(s)
- Henry M Kariithi
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O Box 57811, Kaptagat Rd, Loresho, Nairobi, 00200, Kenya. .,Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria. .,Present Address: US National Poultry Research Centre, Southeast Poultry Research Laboratory, USDA-ARS, 934 College Station Road, Athens, GA, 30605, USA.
| | - Drion G Boucias
- Entomology and Nematology Department, University of Florida, 970 Natural Area Drive, Gainesville, FL, 32611, USA
| | - Edwin K Murungi
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, 20115, Kenya
| | - Irene K Meki
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria.,Laboratory of Virology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Güler Demirbaş-Uzel
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Marc J B Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria
| | - Just M Vlak
- Laboratory of Virology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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20
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Mondotte JA, Gausson V, Frangeul L, Blanc H, Lambrechts L, Saleh MC. Immune priming and clearance of orally acquired RNA viruses in Drosophila. Nat Microbiol 2018; 3:1394-1403. [PMID: 30374170 DOI: 10.1038/s41564-018-0265-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/06/2018] [Indexed: 12/17/2022]
Abstract
Immune responses in insects are differentially triggered depending on the infection route used by the pathogen. In most studies involving Drosophila melanogaster and viruses, infection is done by injection, while oral infection, which is probably the most common route of viral entry in nature, remains unexplored. Here, we orally infected adults and larvae from wild-type and RNA interference (RNAi) mutant flies with different RNA viruses. We found that, in contrast with what is observed following virus injection, oral infections initiated at larval or adult stages are cleared in adult flies. Virus elimination occurred despite a larger infectious dose than for injected flies and evidence of viral replication. RNAi mutant flies suffered greater mortality relative to wild-type flies following oral infection, but they also eliminated the virus, implying that RNAi is not essential for viral clearance and that other immune mechanisms act during oral infections. We further showed that information of infection by RNA viruses acquired orally leaves a trace under a DNA form, which confers protection against future reinfection by the same virus. Together, this work presents evidence of clearance and immune priming for RNA viruses in insects and challenges the current view of antiviral immunity in insects.
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Affiliation(s)
- Juan A Mondotte
- Institut Pasteur, Viruses and RNA Interference Unit, Department of Virology, CNRS Unité Mixte de Recherche 3569, Paris, France
| | - Valérie Gausson
- Institut Pasteur, Viruses and RNA Interference Unit, Department of Virology, CNRS Unité Mixte de Recherche 3569, Paris, France
| | - Lionel Frangeul
- Institut Pasteur, Viruses and RNA Interference Unit, Department of Virology, CNRS Unité Mixte de Recherche 3569, Paris, France
| | - Hervé Blanc
- Institut Pasteur, Viruses and RNA Interference Unit, Department of Virology, CNRS Unité Mixte de Recherche 3569, Paris, France
| | - Louis Lambrechts
- Institut Pasteur, Insect-Virus Interactions Group, Department of Genomes and Genetics, CNRS Unité Mixte de Recherche 2000, Paris, France
| | - Maria-Carla Saleh
- Institut Pasteur, Viruses and RNA Interference Unit, Department of Virology, CNRS Unité Mixte de Recherche 3569, Paris, France.
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21
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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22
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Abstract
The power and ease of Drosophila genetics and the medical relevance of mosquito-transmitted viruses have made dipterans important model organisms in antiviral immunology. Studies of virus-host interactions at the molecular and population levels have illuminated determinants of resistance to virus infection. Here, we review the sources and nature of variation in antiviral immunity and virus susceptibility in model dipteran insects, specifically the fruit fly Drosophila melanogaster and vector mosquitoes of the genera Aedes and Culex. We first discuss antiviral immune mechanisms and describe the virus-specificity of these responses. In the following sections, we review genetic and microbiota-dependent variation in antiviral immunity. In the final sections, we explore less well-studied sources of variation, including abiotic factors, sexual dimorphism, infection history, and endogenous viral elements. We borrow from work on other pathogen types and non-dipteran species when it parallels or complements studies in dipterans. Understanding natural variation in virus-host interactions may lead to the identification of novel restriction factors and immune mechanisms and shed light on the molecular determinants of vector competence.
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Affiliation(s)
- William H Palmer
- Institute of Evolutionary Biology and Centre for Infection, Evolution and Immunity, University of Edinburgh, Edinburgh EH9 3FL UK.
| | - Finny S Varghese
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands.
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands.
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.
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23
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Complex Coding and Regulatory Polymorphisms in a Restriction Factor Determine the Susceptibility of Drosophila to Viral Infection. Genetics 2017. [PMID: 28630113 PMCID: PMC5560813 DOI: 10.1534/genetics.117.201970] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
It is common to find that major-effect genes are an important cause of variation in susceptibility to infection. Here we have characterized natural variation in a gene called pastrel that explains over half of the genetic variance in susceptibility to the Drosophila C virus (DCV) in populations of Drosophila melanogaster We found extensive allelic heterogeneity, with a sample of seven alleles of pastrel from around the world conferring four phenotypically distinct levels of resistance. By modifying candidate SNPs in transgenic flies, we show that the largest effect is caused by an amino acid polymorphism that arose when an ancestral threonine was mutated to alanine, greatly increasing resistance to DCV. Overexpression of the ancestral, susceptible allele provides strong protection against DCV; indicating that this mutation acted to improve an existing restriction factor. The pastrel locus also contains complex structural variation and cis-regulatory polymorphisms altering gene expression. We find that higher expression of pastrel is associated with increased survival after DCV infection. To understand why this variation is maintained in populations, we investigated genetic variation surrounding the amino acid variant that is causing flies to be resistant. We found no evidence of natural selection causing either recent changes in allele frequency or geographical variation in frequency, suggesting that this is an old polymorphism that has been maintained at a stable frequency. Overall, our data demonstrate how complex genetic variation at a single locus can control susceptibility to a virulent natural pathogen.
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24
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Early AM, Clark AG. Genomic signatures of local adaptation in the Drosophila immune response. Fly (Austin) 2017; 11:277-283. [PMID: 28586288 DOI: 10.1080/19336934.2017.1337612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
As environments and pathogen landscapes shift, host defenses must evolve to remain effective. Due to this selection pressure, among-species comparisons of genetic sequence data often find immune genes to be among the fastest evolving genes across the genome. The full extent and nature of these immune adaptations, however, remain largely unexplored. In a recent study, we analyzed patterns of selection within distinct components of the Drosophila melanogaster immune pathway. While we found evidence of positive selection within some immune processes, immune genes were not universally characterized by signatures of strong selection. On the contrary, we even found that some immune functions show greater than expected constraint. Overall these results highlight 2 major factors that appear to play an outsize role in determining a gene's evolutionary rate: the type of pathogen the gene targets and the gene's position within the immune network. These results join a growing body of literature that highlight the complexity of immune adaptation. Rather than there being uniformly strong selection across all immune genes, a combination of pathogen-specificity and host genetic constraints appear to play key roles in determining each immune gene's individual evolutionary trajectory.
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Affiliation(s)
- Angela M Early
- a Department of Molecular Biology and Genetics , Cornell University , Ithaca , NY.,b Infectious Disease and Microbiome Program , Broad Institute of MIT and Harvard , Cambridge , MA
| | - Andrew G Clark
- a Department of Molecular Biology and Genetics , Cornell University , Ithaca , NY
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25
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Yang P, Habekuß A, Hofinger BJ, Kanyuka K, Kilian B, Graner A, Ordon F, Stein N. Sequence diversification in recessive alleles of two host factor genes suggests adaptive selection for bymovirus resistance in cultivated barley from East Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:331-344. [PMID: 27830284 PMCID: PMC5263206 DOI: 10.1007/s00122-016-2814-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/14/2016] [Indexed: 05/04/2023]
Abstract
Two distinct patterns of sequence diversity for the recessive alleles of two host factors HvPDIL5 - 1 and HvEIF4E indicated the adaptive selection for bymovirus resistance in cultivated barley from East Asia. Plant pathogens are constantly challenging plant fitness and driving resistance gene evolution in host species. Little is known about the evolution of sequence diversity in host recessive resistance genes that interact with plant viruses. Here, by combining previously published and newly generated targeted re-sequencing information, we systematically analyzed natural variation in a broad collection of wild (Hordeum spontaneum; Hs) and domesticated barleys (Hordeum vulgare; Hv) using the full-length coding sequence of the two host factor genes, HvPDIL5-1 and HvEIF4E, conferring recessive resistance to the agriculturally important Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV). Interestingly, two types of gene evolution conferred by sequence variation in domesticated barley, but not in wild barley were observed. Whereas resistance-conferring alleles of HvEIF4E exclusively contained non-synonymous amino acid substitutions (including in-frame sequence deletions and insertions), loss-of-function alleles were predominantly responsible for the HvPDIL5-1 conferred bymovirus resistance. A strong correlation between the geographic origin and the frequency of barley accessions carrying resistance-conferring alleles was evident for each of the two host factor genes, indicating adaptive selection for bymovirus resistance in cultivated barley from East Asia.
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Affiliation(s)
- Ping Yang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, 06484, Quedlinburg, Germany
| | - Bernhard J Hofinger
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Kostya Kanyuka
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, 06484, Quedlinburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany.
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Severson DW, Behura SK. Genome Investigations of Vector Competence in Aedes aegypti to Inform Novel Arbovirus Disease Control Approaches. INSECTS 2016; 7:insects7040058. [PMID: 27809220 PMCID: PMC5198206 DOI: 10.3390/insects7040058] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 11/16/2022]
Abstract
Dengue (DENV), yellow fever, chikungunya, and Zika virus transmission to humans by a mosquito host is confounded by both intrinsic and extrinsic variables. Besides virulence factors of the individual arboviruses, likelihood of virus transmission is subject to variability in the genome of the primary mosquito vector, Aedes aegypti. The “vectorial capacity” of A. aegypti varies depending upon its density, biting rate, and survival rate, as well as its intrinsic ability to acquire, host and transmit a given arbovirus. This intrinsic ability is known as “vector competence”. Based on whole transcriptome analysis, several genes and pathways have been predicated to have an association with a susceptible or refractory response in A. aegypti to DENV infection. However, the functional genomics of vector competence of A. aegypti is not well understood, primarily due to lack of integrative approaches in genomic or transcriptomic studies. In this review, we focus on the present status of genomics studies of DENV vector competence in A. aegypti as limited information is available relative to the other arboviruses. We propose future areas of research needed to facilitate the integration of vector and virus genomics and environmental factors to work towards better understanding of vector competence and vectorial capacity in natural conditions.
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Affiliation(s)
- David W Severson
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
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Campillo-Balderas JA, Lazcano A, Becerra A. Viral Genome Size Distribution Does not Correlate with the Antiquity of the Host Lineages. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00143] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gibbs AJ, Nguyen HD, Ohshima K. The 'emergence' of turnip mosaic virus was probably a 'gene-for-quasi-gene' event. Curr Opin Virol 2015; 10:20-6. [PMID: 25559881 DOI: 10.1016/j.coviro.2014.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 12/04/2014] [Accepted: 12/10/2014] [Indexed: 11/18/2022]
Abstract
Turnip mosaic potyvirus is a virus of brassicas that emerged from a lineage of monocotyledon-infecting potyviruses about 1000 years ago. In vivo and in silico studies all indicate that sites, primarily in its protein 3 (P3) and cylindrical inclusion protein (CI) genes, but also its small 6 kDa 2 protein (6K2) and genome-linked viral protein (VPg) genes, control host specificity in a dynamic way. It is most likely that non-unique combinations of transient viral genomic single nucleotide polymorphisms (SNPs), not all of them non-synonymous, allowed the host switch to occur. These SNPs were probably ephemeral and replaced over time by other combinations as the population subsequently diverged within, and adapted to, the brassica host population.
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Affiliation(s)
- Adrian J Gibbs
- Australian National University Emeritus Faculty, Canberra, ACT 2601, Australia.
| | - Huy Duc Nguyen
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan; Department of Plant Pathology, Faculty of Agronomy, Vietnam National University of Agriculture, Trauquy, Gialam, Hanoi, Viet Nam
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
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