1
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Coffman KA, Kauwe AN, Gillette NE, Burke GR, Geib SM. Host range of a parasitoid wasp is linked to host susceptibility to its mutualistic viral symbiont. Mol Ecol 2024; 33:e17485. [PMID: 39080979 DOI: 10.1111/mec.17485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/28/2024]
Abstract
Parasitoid wasps are one of the most species-rich groups of animals on Earth, due to their ability to successfully develop as parasites of nearly all types of insects. Unlike most known parasitoid wasps that specialize towards one or a few host species, Diachasmimorpha longicaudata is a generalist that can survive within multiple genera of tephritid fruit fly hosts, including many globally important pest species. Diachasmimorpha longicaudata has therefore been widely released to suppress pest populations as part of biological control efforts in tropical and subtropical agricultural ecosystems. In this study, we investigated the role of a mutualistic poxvirus in shaping the host range of D. longicaudata across three genera of agricultural pest species: two of which are permissive hosts for D. longicaudata parasitism and one that is a nonpermissive host. We found that permissive hosts Ceratitis capitata and Bactrocera dorsalis were highly susceptible to manual virus injection, displaying rapid virus replication and abundant fly mortality. However, the nonpermissive host Zeugodacus cucurbitae largely overcame virus infection, exhibiting substantially lower mortality and no virus replication. Investigation of transcriptional dynamics during virus infection demonstrated hindered viral gene expression and limited changes in fly gene expression within the nonpermissive host compared with the permissive species, indicating that the host range of the viral symbiont may influence the host range of D. longicaudata wasps. These findings also reveal that viral symbiont activity may be a major contributor to the success of D. longicaudata as a generalist parasitoid species and a globally successful biological control agent.
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Affiliation(s)
- K A Coffman
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - A N Kauwe
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA
| | - N E Gillette
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA
- College of Agriculture, Forestry and Natural Resource Management, University of Hawai'i at Hilo, Hilo, Hawaii, USA
| | - G R Burke
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - S M Geib
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA
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2
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Lorenzi A, Legeai F, Jouan V, Girard PA, Strand MR, Ravallec M, Eychenne M, Bretaudeau A, Robin S, Rochefort J, Villegas M, Burke GR, Rebollo R, Nègre N, Volkoff AN. Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps. PLoS Pathog 2024; 20:e1011980. [PMID: 38662774 DOI: 10.1371/journal.ppat.1011980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/07/2024] [Accepted: 03/22/2024] [Indexed: 05/08/2024] Open
Abstract
Thousands of endoparasitoid wasp species in the families Braconidae and Ichneumonidae harbor "domesticated endogenous viruses" (DEVs) in their genomes. This study focuses on ichneumonid DEVs, named ichnoviruses (IVs). Large quantities of DNA-containing IV virions are produced in ovary calyx cells during the pupal and adult stages of female wasps. Females parasitize host insects by injecting eggs and virions into the body cavity. After injection, virions rapidly infect host cells which is followed by expression of IV genes that promote the successful development of wasp offspring. IV genomes consist of two components: proviral segment loci that serve as templates for circular dsDNAs that are packaged into capsids, and genes from an ancestral virus that produce virions. In this study, we generated a chromosome-scale genome assembly for Hyposoter didymator that harbors H. didymator ichnovirus (HdIV). We identified a total of 67 HdIV loci that are amplified in calyx cells during the wasp pupal stage. We then focused on an HdIV gene, U16, which is transcribed in calyx cells during the initial stages of replication. Sequence analysis indicated that U16 contains a conserved domain in primases from select other viruses. Knockdown of U16 by RNA interference inhibited virion morphogenesis in calyx cells. Genome-wide analysis indicated U16 knockdown also inhibited amplification of HdIV loci in calyx cells. Altogether, our results identified several previously unknown HdIV loci, demonstrated that all HdIV loci are amplified in calyx cells during the pupal stage, and showed that U16 is required for amplification and virion morphogenesis.
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Affiliation(s)
- Ange Lorenzi
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Fabrice Legeai
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | | | | | - Michael R Strand
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | | | | | - Anthony Bretaudeau
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | - Stéphanie Robin
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | | | | | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Rita Rebollo
- INRAE, INSA Lyon, BF2I, UMR203, Villeurbanne, France
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3
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Guinet B, Leobold M, Herniou EA, Bloin P, Burlet N, Bredlau J, Navratil V, Ravallec M, Uzbekov R, Kester K, Gundersen Rindal D, Drezen JM, Varaldi J, Bézier A. A novel and diverse family of filamentous DNA viruses associated with parasitic wasps. Virus Evol 2024; 10:veae022. [PMID: 38617843 PMCID: PMC11013392 DOI: 10.1093/ve/veae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/20/2023] [Accepted: 02/23/2024] [Indexed: 04/16/2024] Open
Abstract
Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.
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Affiliation(s)
- Benjamin Guinet
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Matthieu Leobold
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Pierrick Bloin
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Nelly Burlet
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Justin Bredlau
- Department of Biology, Virginia Commonwealth University, 1000 W. Cary Street, Room 126, Richmond, VA 23284-9067, USA
| | - Vincent Navratil
- PRABI, Rhône-Alpes Bioinformatics Center, Université Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX 69622, France
- UMS 3601, Institut Français de Bioinformatique, IFB-Core, 2 rue Gaston Crémieu, Évry CEDEX 91057, France
- European Virus Bioinformatics Center, Leutragraben 1, Jena 07743, Germany
| | - Marc Ravallec
- Diversité, génomes et interactions microorganismes insectes (DGIMI), UMR 1333 INRA, Université de Montpellier 2, 2 Place Eugène Bataillon cc101, Montpellier CEDEX 5 34095, France
| | - Rustem Uzbekov
- Laboratory of Cell Biology and Electron Microscopy, Faculty of Medicine, Université de Tours, 10 bd Tonnelle, BP 3223, Tours CEDEX 37032, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskye Gory 73, Moscow 119992, Russia
| | - Karen Kester
- Department of Biology, Virginia Commonwealth University, 1000 W. Cary Street, Room 126, Richmond, VA 23284-9067, USA
| | - Dawn Gundersen Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD 20705, USA
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Julien Varaldi
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
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4
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Caldas-Garcia GB, Santos VC, Fonseca PLC, de Almeida JPP, Costa MA, Aguiar ERGR. The Viromes of Six Ecosystem Service Provider Parasitoid Wasps. Viruses 2023; 15:2448. [PMID: 38140687 PMCID: PMC10747428 DOI: 10.3390/v15122448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 12/24/2023] Open
Abstract
Parasitoid wasps are fundamental insects for the biological control of agricultural pests. Despite the importance of wasps as natural enemies for more sustainable and healthy agriculture, the factors that could impact their species richness, abundance, and fitness, such as viral diseases, remain almost unexplored. Parasitoid wasps have been studied with regard to the endogenization of viral elements and the transmission of endogenous viral proteins that facilitate parasitism. However, circulating viruses are poorly characterized. Here, RNA viromes of six parasitoid wasp species are studied using public libraries of next-generation sequencing through an integrative bioinformatics pipeline. Our analyses led to the identification of 18 viruses classified into 10 families (Iflaviridae, Endornaviridae, Mitoviridae, Partitiviridae, Virgaviridae, Rhabdoviridae, Chuviridae, Orthomyxoviridae, Xinmoviridae, and Narnaviridae) and into the Bunyavirales order. Of these, 16 elements were described for the first time. We also found a known virus previously identified on a wasp prey which suggests viral transmission between the insects. Altogether, our results highlight the importance of virus surveillance in wasps as its service disruption can affect ecology, agriculture and pest management, impacting the economy and threatening human food security.
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Affiliation(s)
- Gabriela B. Caldas-Garcia
- Virus Bioinformatics Laboratory, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil; (G.B.C.-G.); (P.L.C.F.)
| | - Vinícius Castro Santos
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil; (V.C.S.); (J.P.P.d.A.)
| | - Paula Luize Camargos Fonseca
- Virus Bioinformatics Laboratory, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil; (G.B.C.-G.); (P.L.C.F.)
- Department of Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil
| | - João Paulo Pereira de Almeida
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil; (V.C.S.); (J.P.P.d.A.)
| | - Marco Antônio Costa
- Departament of Biological Sciences, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil;
| | - Eric Roberto Guimarães Rocha Aguiar
- Virus Bioinformatics Laboratory, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil; (G.B.C.-G.); (P.L.C.F.)
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5
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Lorenzi A, Arvin MJ, Burke GR, Strand MR. Functional characterization of Microplitis demolitor bracovirus genes that encode nucleocapsid components. J Virol 2023; 97:e0081723. [PMID: 37877717 PMCID: PMC10688341 DOI: 10.1128/jvi.00817-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/19/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE Understanding how bracoviruses (BVs) function in wasps is of broad interest in the study of virus evolution. This study characterizes most of the Microplitis demolitor bracovirus (MdBV) genes whose products are nucleocapsid components. Results indicate several genes unknown outside of nudiviruses and BVs are essential for normal capsid assembly. Results also indicate most MdBV tyrosine recombinase family members and the DNA binding protein p6.9-1 are required for DNA processing and packaging into nucleocapsids.
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Affiliation(s)
- Ange Lorenzi
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Michael J. Arvin
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Gaelen R. Burke
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Michael R. Strand
- Department of Entomology, University of Georgia, Athens, Georgia, USA
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6
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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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7
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Mao M, Simmonds TJ, Stouthamer CM, Kehoe TM, Geib SM, Burke GR. A chromosome scale assembly of the parasitoid wasp Venturia canescens provides insight into the process of virus domestication. G3 (BETHESDA, MD.) 2023; 13:jkad137. [PMID: 37345948 PMCID: PMC10542567 DOI: 10.1093/g3journal/jkad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/16/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023]
Abstract
The parasitoid wasp Venturia canescens is an important biological control agent of stored products moth pests and serves as a model to study the function and evolution of domesticated endogenous viruses (DEVs). The DEVs discovered in V. canescens are known as virus-like particles (VcVLPs), which are produced using nudivirus-derived components and incorporate wasp-derived virulence proteins instead of packaged nucleic acids. Previous studies of virus-derived components in the V. canescens genome identified 53 nudivirus-like genes organized in six gene clusters and several viral pseudogenes, but how VcVLP genes are organized among wasp chromosomes following their integration in the ancestral wasp genome is largely unknown. Here, we present a chromosomal scale genome of V. canescens consisting of 11 chromosomes and 56 unplaced small scaffolds. The genome size is 290.8 Mbp with a N50 scaffold size of 24.99 Mbp. A high-quality gene set including 11,831 protein-coding genes were produced using RNA-Seq data as well as publicly available peptide sequences from related Hymenoptera. A manual annotation of genes of viral origin produced 61 intact and 19 pseudogenized nudivirus-derived genes. The genome assembly revealed that two previously identified clusters were joined into a single cluster and a total of 5 gene clusters comprising of 60 intact nudivirus-derived genes were located in three chromosomes. In contrast, pseudogenes are dispersed among 8 chromosomes with only 4 pseudogenes associated with nudivirus gene clusters. The architecture of genes encoding VcVLP components suggests it originates from a recent virus acquisition and there is a link between the processes of dispersal and pseudogenization. This high-quality genome assembly and annotation represents the first chromosome-scale assembly for parasitoid wasps associated with VLPs, and is publicly available in the National Center for Biotechnology Information Genome and RefSeq databases, providing a valuable resource for future studies of DEVs in parasitoid wasps.
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Affiliation(s)
- Meng Mao
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Tyler J Simmonds
- Tropical Pest Genetics and Molecular Biology Research Unit, USDA-ARS Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, USDA-ARS, Hilo, HI 96720, USA
- Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37830, USA
| | | | - Tara M Kehoe
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Scott M Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, USDA-ARS Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, USDA-ARS, Hilo, HI 96720, USA
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
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van Oers MM, Herniou EA, Jehle JA, Krell PJ, Abd-Alla AMM, Ribeiro BM, Theilmann DA, Hu Z, Harrison RL. Developments in the classification and nomenclature of arthropod-infecting large DNA viruses that contain pif genes. Arch Virol 2023; 168:182. [PMID: 37322175 PMCID: PMC10271883 DOI: 10.1007/s00705-023-05793-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Viruses of four families of arthropod-specific, large dsDNA viruses (the nuclear arthropod large DNA viruses, or NALDVs) possess homologs of genes encoding conserved components involved in the baculovirus primary infection mechanism. The presence of such homologs encoding per os infectivity factors (pif genes), along with their absence from other viruses and the occurrence of other shared characteristics, suggests a common origin for the viruses of these families. Therefore, the class Naldaviricetes was recently established, accommodating these four families. In addition, within this class, the ICTV approved the creation of the order Lefavirales for three of these families, whose members carry homologs of the baculovirus genes that code for components of the viral RNA polymerase, which is responsible for late gene expression. We further established a system for the binomial naming of all virus species in the order Lefavirales, in accordance with a decision by the ICTV in 2019 to move towards a standardized nomenclature for all virus species. The binomial species names for members of the order Lefavirales consist of the name of the genus to which the species belongs (e.g., Alphabaculovirus), followed by a single epithet that refers to the host species from which the virus was originally isolated. The common names of viruses and the abbreviations thereof will not change, as the format of virus names lies outside the remit of the ICTV.
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Affiliation(s)
- Monique M van Oers
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands.
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - University of Tours, 37200, Tours, France
| | - Johannes A Jehle
- Institute for Biological Control, Julius Kühn-Institut, 69221, Dossenheim, Germany
| | - Peter J Krell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Adly M M Abd-Alla
- Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna International Centre, Vienna, Austria
| | - Bergmann M Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, Brasília, Brazil
| | - David A Theilmann
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Box 5000, Summerland, BC, V0H1Z0, Canada
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 Barc‑West, Beltsville, MD, 20705, USA
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9
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Guinet B, Lepetit D, Charlat S, Buhl PN, Notton DG, Cruaud A, Rasplus JY, Stigenberg J, de Vienne DM, Boussau B, Varaldi J. Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses. eLife 2023; 12:85993. [PMID: 37278068 DOI: 10.7554/elife.85993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/12/2023] [Indexed: 06/07/2023] Open
Abstract
The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses have been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto, and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparison with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Second, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn, increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.
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Affiliation(s)
- Benjamin Guinet
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - David Lepetit
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Sylvain Charlat
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Peter N Buhl
- Zoological Museum, Department of Entomology, University of Copenhagen, Universitetsparken, Copenhagen, Denmark
| | - David G Notton
- Natural Sciences Department, National Museums Collection Centre, Edinburgh, United Kingdom
| | - Astrid Cruaud
- INRAE, UMR 1062 CBGP, 755 avenue 11 du campus Agropolis CS 30016, 34988, Montferrier-sur-Lez, France
| | - Jean-Yves Rasplus
- INRAE, UMR 1062 CBGP, 755 avenue 11 du campus Agropolis CS 30016, 34988, Montferrier-sur-Lez, France
| | - Julia Stigenberg
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Damien M de Vienne
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Bastien Boussau
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Julien Varaldi
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
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10
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Du Q, Peng F, Xiong Q, Xu K, Yang KY, Wang M, Wu Z, Li S, Cheng X, Rao X, Wang Y, Tsui SKW, Zeng X. Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences. Viruses 2023; 15:v15040909. [PMID: 37112889 PMCID: PMC10145014 DOI: 10.3390/v15040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/11/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of B. belcheri beihai, of which most were observed on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, particularly in their CDS regions and promoters. A range of amphioxus genes with a high frequency of HFs is proposed, including histone-related genes that are homologous to the Histone H4 or Histone H2B domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus.
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Affiliation(s)
- Qiao Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Peng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Kejin Xu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhitian Wu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shanying Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaorui Cheng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinjie Rao
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyouye Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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11
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Picciotti U, Araujo Dalbon V, Ciancio A, Colagiero M, Cozzi G, De Bellis L, Finetti-Sialer MM, Greco D, Ippolito A, Lahbib N, Logrieco AF, López-Llorca LV, Lopez-Moya F, Luvisi A, Mincuzzi A, Molina-Acevedo JP, Pazzani C, Scortichini M, Scrascia M, Valenzano D, Garganese F, Porcelli F. "Ectomosphere": Insects and Microorganism Interactions. Microorganisms 2023; 11:440. [PMID: 36838405 PMCID: PMC9967823 DOI: 10.3390/microorganisms11020440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
This study focuses on interacting with insects and their ectosymbiont (lato sensu) microorganisms for environmentally safe plant production and protection. Some cases help compare ectosymbiont microorganisms that are insect-borne, -driven, or -spread relevant to endosymbionts' behaviour. Ectosymbiotic bacteria can interact with insects by allowing them to improve the value of their pabula. In addition, some bacteria are essential for creating ecological niches that can host the development of pests. Insect-borne plant pathogens include bacteria, viruses, and fungi. These pathogens interact with their vectors to enhance reciprocal fitness. Knowing vector-phoront interaction could considerably increase chances for outbreak management, notably when sustained by quarantine vector ectosymbiont pathogens, such as the actual Xylella fastidiosa Mediterranean invasion episode. Insect pathogenic viruses have a close evolutionary relationship with their hosts, also being highly specific and obligate parasites. Sixteen virus families have been reported to infect insects and may be involved in the biological control of specific pests, including some economic weevils. Insects and fungi are among the most widespread organisms in nature and interact with each other, establishing symbiotic relationships ranging from mutualism to antagonism. The associations can influence the extent to which interacting organisms can exert their effects on plants and the proper management practices. Sustainable pest management also relies on entomopathogenic fungi; research on these species starts from their isolation from insect carcasses, followed by identification using conventional light or electron microscopy techniques. Thanks to the development of omics sciences, it is possible to identify entomopathogenic fungi with evolutionary histories that are less-shared with the target insect and can be proposed as pest antagonists. Many interesting omics can help detect the presence of entomopathogens in different natural matrices, such as soil or plants. The same techniques will help localize ectosymbionts, localization of recesses, or specialized morphological adaptation, greatly supporting the robust interpretation of the symbiont role. The manipulation and modulation of ectosymbionts could be a more promising way to counteract pests and borne pathogens, mitigating the impact of formulates and reducing food insecurity due to the lesser impact of direct damage and diseases. The promise has a preventive intent for more manageable and broader implications for pests, comparing what we can obtain using simpler, less-specific techniques and a less comprehensive approach to Integrated Pest Management (IPM).
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Affiliation(s)
- Ugo Picciotti
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
- Department of Marine Science and Applied Biology, University of Alicante, 03690 Alicante, Spain
| | | | - Aurelio Ciancio
- Institute for Sustainable Plant Protection, National Research Council (CNR), Via G. Amendola 122/D, 70126 Bari, Italy
| | - Mariantonietta Colagiero
- Institute for Sustainable Plant Protection, National Research Council (CNR), Via G. Amendola 122/D, 70126 Bari, Italy
| | - Giuseppe Cozzi
- Institute of Food Production Sciences, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | | | - Davide Greco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Antonio Ippolito
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Nada Lahbib
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
- Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis 1002, Tunisia
| | - Antonio Francesco Logrieco
- Institute of Food Production Sciences, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | | | - Federico Lopez-Moya
- Department of Marine Science and Applied Biology, University of Alicante, 03690 Alicante, Spain
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Annamaria Mincuzzi
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Juan Pablo Molina-Acevedo
- Colombian Corporation for Agricultural Research Agrosavia C. I. Turipana-AGROSAVIA, Km. 13, Vía Montería-Cereté 230558, Colombia
| | - Carlo Pazzani
- Dipartimento di Bioscienze, Biotecnologie e Ambiente (DBBA), University of Bari Aldo Moro, 70126 Bari, Italy
| | - Marco Scortichini
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), 00134 Roma, Italy
| | - Maria Scrascia
- Dipartimento di Bioscienze, Biotecnologie e Ambiente (DBBA), University of Bari Aldo Moro, 70126 Bari, Italy
| | - Domenico Valenzano
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Francesca Garganese
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Francesco Porcelli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
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12
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Gao HS, Hu RM, Wang ZH, Ye XQ, Wu XT, Huang JH, Wang ZZ, Chen XX. A Polydnavirus Protein Tyrosine Phosphatase Negatively Regulates the Host Phenoloxidase Pathway. Viruses 2022; 15:56. [PMID: 36680096 PMCID: PMC9866809 DOI: 10.3390/v15010056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
Polydnavirus (PDV) is a parasitic factor of endoparasitic wasps and contributes greatly to overcoming the immune response of parasitized hosts. Protein tyrosine phosphatases (PTPs) regulate a wide variety of biological processes at the post-transcriptional level in mammals, but knowledge of PDV PTP action during a parasitoid−host interaction is limited. In this study, we characterized a PTP gene, CvBV_12-6, derived from Cotesia vestalis bracovirus (CvBV), and explored its possible regulatory role in the immune response of the host Plutella xylostella. Our results from qPCR show that CvBV_12-6 was highly expressed in hemocytes at an early stage of parasitization. To explore CvBV_12-6 function, we specifically expressed CvBV_12-6 in Drosophila melanogaster hemocytes. The results show that Hml-Gal4 > CvBV_12-6 suppressed the phenoloxidase activity of hemolymph in D. melanogaster, but exerted no effect on the total count or the viability of the hemocytes. In addition, the Hml-Gal4 > CvBV_12-6 flies exhibited decreased antibacterial abilities against Staphylococcus aureus. Similarly, we found that CvBV_12-6 significantly suppressed the melanization of the host P. xylostella 24 h post parasitization and reduced the viability, but not the number, of hemocytes. In conclusion, CvBV_12-6 negatively regulated both cellular and humoral immunity in P. xylostella, and the related molecular mechanism may be universal to insects.
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Affiliation(s)
- Hong-Shuai Gao
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Rong-Min Hu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Ze-Hua Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Xi-Qian Ye
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Tong Wu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Jian-Hua Huang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Zhi-Zhi Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
- The Rural Development Academy, Zhejiang University, Hangzhou 310058, China
| | - Xue-Xin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
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13
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Abstract
White spot syndrome virus (WSSV) is a major cause of disease in shrimp cultures worldwide. The infection process of this large circular double-stranded DNA virus has been well studied, but its entry mechanism remains controversial. The major virion envelope protein VP28 has been implicated in oral and systemic viral infection in shrimp. However, genetic analysis of viral DNA has shown the presence of a few genes related to proteins of per os infectivity factor (PIF) complex in baculoviruses. This complex is essential for the entry of baculoviruses, large terrestrial circular DNA viruses, into the midgut epithelial cells of insect larvae. In this study, we aimed to determine whether a PIF complex exists in WSSV, the components of this complex, whether it functions as an oral infectivity complex in shrimp, and the biochemical properties that contribute to its function in a marine environment. The results revealed a WSSV PIF complex (~720 kDa) comprising at least eight proteins, four of which were not identified as PIF homologs: WSV134, VP124 (WSV216), WSSV021, and WSV136. WSV134 is suggested to be a PIF4 homolog due to predicted structural similarity and amino acid sequence identity. The WSSV PIF complex is resistant to alkali, proteolysis, and high salt, properties that are important for maintaining infectivity in aquatic environments. Oral infection can be neutralized by PIF-specific antibodies but not by VP28-specific antibodies. These results indicate that the WSSV PIF complex is critical for WSSV entry into shrimp; the complex's evolutionary significance is also discussed. IMPORTANCE White spot disease, caused by the white spot syndrome virus (WSSV), is a major scourge in cultured shrimp production facilities worldwide. This disease is only effectively controlled by sanitation. Intervention strategies are urgently needed but are limited by a lack of appropriate targets. Our identification of a per os infectivity factor (PIF) complex, which is pivotal for the entry of WSSV into shrimp, could provide new targets for antibody- or dsRNA-based intervention strategies. In addition, the presence of a PIF complex with at least eight components in WSSV, which is ancestrally related to the PIF complex of invertebrate baculoviruses, suggests that this complex is structurally and functionally conserved in disparate virus taxa.
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14
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Heisserer C, Selosse MA, Drezen JM. [Plants and animals biological functions obtained from viruses]. Med Sci (Paris) 2022; 38:1016-1027. [PMID: 36692281 DOI: 10.1051/medsci/2022171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Viruses can provide new biological functions to plants and animals. Some viruses persisting at low levels in plants might confer resistance to stress and parasites. In animals, more numerous examples of genes originating from viruses and used by different organisms have been described. For examples these genes might contribute to protect from new infections, or to ensure communication between neurons or to enable placenta development. In parasitic wasps, a complex viral machinery has been conserved as an endogenous virus dispersed in the wasp genome, which produces virions. These virions infect the parasitized host resulting in the production of virulence factors that inhibit defense mechanisms against the parasite. Different organisms have used the same viral functions repeatedly during animal evolution.
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Affiliation(s)
- Camille Heisserer
- Institut de recherche sur la biologie de l'insecte, UMR 7261 CNRS-Université de Tours, Parc de Grandmont 37200 Tours, France
| | - Marc-André Selosse
- Institut de systématique, évolution, biodiversité, UMR 7205 MNHN-CNRS-SU-EPHE-UA, 12 rue Buffon 75005 Paris, France
| | - Jean-Michel Drezen
- Institut de recherche sur la biologie de l'insecte, UMR 7261 CNRS-Université de Tours, Parc de Grandmont 37200 Tours, France
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15
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Liang Y, Xu W, Zhou Y, Gao Y, Tian H, Wu X, Xu Y, Wang H. Midgut membrane protein BmSUH facilitates Bombyx mori nucleopolyhedrovirus oral infection. PLoS Pathog 2022; 18:e1010938. [PMID: 36383572 PMCID: PMC9668127 DOI: 10.1371/journal.ppat.1010938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Baculoviruses are virulent pathogens that infect a wide range of insects. They initiate infections via specific interactions between the structural proteins on the envelopes of occlusion-derived virions (ODVs) and the midgut cell surface receptors in hosts. However, host factors that are hijacked by baculoviruses for efficient infection remain largely unknown. In this study, we identified a membrane-associated protein sucrose hydrolase (BmSUH) as an ODV binding factor during Bombyx mori nucleopolyhedrovirus (BmNPV) primary infection. BmSUH was specifically expressed in the midgut microvilli where the ODV-midgut fusion happened. Knockout of BmSUH by CRISPR/Cas9 resulted in a significantly higher survival rate after BmNPV orally infection. Liquid chromatography-tandem mass spectrometry analysis and co-immunoprecipitation analysis demonstrated that PIF protein complex required for ODV binding could interact with BmSUH. Furthermore, fluorescence dequenching assay showed that the amount of ODV binding and fusion to the midgut decreased in BmSUH mutants compared to wild-type silkworm, suggesting the role of BmSUH as an ODV binding factor that mediates the ODV entry process. Based on a multilevel survey, the data showed that BmSUH acted as a host factor that facilitates BmNPV oral infection. More generally, this study indicated that disrupting essential protein-protein interactions required for baculovirus efficient entry may be broadly applicable to against viral infection. Baculoviridae is a large family of pathogens that infect insects and frequently cause fatal diseases. Bombyx mori nucleopolyhedrovirus (BmNPV) is a major threat to the sericulture industry. Although we have learned a lot about baculoviruses over the past several decades, the detailed interaction patterns between host proteins and viral proteins that lead to infection remain underexplored. Here, we determined that BmSUH, a midgut microvilli protein, was required for the efficient oral infection of BmNPV. Our research suggests that BmSUH mediates the entry of occlusion-derived virions into the midgut epithelia by interacting with per os infectivity factors. According to the findings, inhibition of viral binding to host cells is an attractive strategy to prevent infection. This study provides an approach for preventing BmNPV infection through developing genetic resistance to viruses by using CRISPR/Cas9 system to abolish the host factors that are essential for viral entry.
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Affiliation(s)
- Yanting Liang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Weifan Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yanyan Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yun Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huan Tian
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
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16
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Cerqueira de Araujo A, Josse T, Sibut V, Urabe M, Asadullah A, Barbe V, Nakai M, Huguet E, Periquet G, Drezen JM. Chelonus inanitus bracovirus encodes lineage-specific proteins and truncated immune IκB-like factors. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bracoviruses and ichnoviruses are endogenous viruses of parasitic wasps that produce particles containing virulence genes expressed in host tissues and necessary for parasitism success. In the case of bracoviruses the particles are produced by conserved genes of nudiviral origin integrated permanently in the wasp genome, whereas the virulence genes can strikingly differ depending on the wasp lineage. To date most data obtained on bracoviruses concerned species from the braconid subfamily of Microgastrinae. To gain a broader view on the diversity of virulence genes we sequenced the genome packaged in the particles of Chelonus inanitus bracovirus (CiBV) produced by a wasp belonging to a different subfamily: the Cheloninae. These are egg-larval parasitoids, which means that they oviposit into the host egg and the wasp larvae then develop within the larval stages of the host. We found that most of CiBV virulence genes belong to families that are specific to Cheloninae. As other bracoviruses and ichnoviruses however, CiBV encode v-ank genes encoding truncated versions of the immune cactus/IκB factor, which suggests these proteins might play a key role in host–parasite interactions involving domesticated endogenous viruses. We found that the structures of CiBV V-ANKs are different from those previously reported. Phylogenetic analysis supports the hypothesis that they may originate from a cactus/IκB immune gene from the wasp genome acquired by the bracovirus. However, their evolutionary history is different from that shared by other V-ANKs, whose common origin probably reflects horizontal gene transfer events of virus sequences between braconid and ichneumonid wasps.
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Affiliation(s)
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Vonick Sibut
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Mariko Urabe
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Azam Asadullah
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Madoka Nakai
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Georges Periquet
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
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17
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Cerqueira de Araujo A, Leobold M, Bézier A, Musset K, Uzbekov R, Volkoff AN, Drezen JM, Huguet E, Josse T. Conserved Viral Transcription Plays a Key Role in Virus-Like Particle Production of the Parasitoid Wasp Venturia canescens. J Virol 2022; 96:e0052422. [PMID: 35678601 PMCID: PMC9278141 DOI: 10.1128/jvi.00524-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Nudiviruses are large double-stranded DNA viruses related to baculoviruses known to be endogenized in the genomes of certain parasitic wasp species. These wasp-virus associations allow the production of viral particles or virus-like particles that ensure wasp parasitism success within lepidopteran hosts. Venturia canescens is an ichneumonid wasp belonging to the Campopleginae subfamily that has endogenized nudivirus genes belonging to the Alphanudivirus genus to produce "virus-like particles" (Venturia canescens virus-like particles [VcVLPs]), which package proteic virulence factors. The main aim of this study was to determine whether alphanudivirus gene functions have been conserved following endogenization. The expression dynamics of alphanudivirus genes was monitored by a high throughput transcriptional approach, and the functional role of lef-4 and lef-8 genes predicted to encode viral RNA polymerase components was investigated by RNA interference. As described for baculovirus infections and for endogenized nudivirus genes in braconid wasp species producing bracoviruses, a transcriptional cascade involving early and late expressed alphanudivirus genes could be observed. The expression of lef-4 and lef-8 was also shown to be required for the expression of alphanudivirus late genes allowing correct particle formation. Together with previous literature, the results show that endogenization of nudiviruses in parasitoid wasps has repeatedly led to the conservation of the viral RNA polymerase function, allowing the production of viruses or viral-like particles that differ in composition but enable wasp parasitic success. IMPORTANCE This study shows that endogenization of a nudivirus genome in a Campopleginae parasitoid wasp has led to the conservation, as for endogenized nudiviruses in braconid parasitoid wasps, of the viral RNA polymerase function, required for the transcription of genes encoding viral particles involved in wasp parasitism success. We also showed for the first time that RNA interference (RNAi) can be successfully used to downregulate gene expression in this species, a model in behavioral ecology. This opens the opportunity to investigate the function of genes involved in other traits important for parasitism success, such as reproductive strategies and host choice. Fundamental data acquired on gene function in Venturia canescens are likely to be transferable to other parasitoid wasp species used in biological control programs. This study also renders possible the investigation of other nudivirus gene functions, for which little data are available.
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Affiliation(s)
| | - Matthieu Leobold
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Rustem Uzbekov
- Université de Tours, Département des Microscopies, Tours, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Anne-Nathalie Volkoff
- Diversité, Génomes & Interactions Microorganismes - Insectes (DGIMI), UMR 1333, Université de Montpellier - INRAE, Montpellier, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, Tours, France
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18
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Zhou GF, Chen CX, Cai QC, Yan X, Peng NN, Li XC, Cui JH, Han YF, Zhang Q, Meng JH, Tang HM, Cai CH, Long J, Luo KJ. Bracovirus Sneaks Into Apoptotic Bodies Transmitting Immunosuppressive Signaling Driven by Integration-Mediated eIF5A Hypusination. Front Immunol 2022; 13:901593. [PMID: 35664011 PMCID: PMC9156803 DOI: 10.3389/fimmu.2022.901593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022] Open
Abstract
A typical characteristics of polydnavirus (PDV) infection is a persistent immunosuppression, governed by the viral integration and expression of virulence genes. Recently, activation of caspase-3 by Microplitis bicoloratus bracovirus (MbBV) to cleave Innexins, gap junction proteins, has been highlighted, further promoting apoptotic cell disassembly and apoptotic body (AB) formation. However, whether ABs play a role in immune suppression remains to be determined. Herein, we show that ABs transmitted immunosuppressive signaling, causing recipient cells to undergo apoptosis and dismigration. Furthermore, the insertion of viral–host integrated motif sites damaged the host genome, stimulating eIF5A nucleocytoplasmic transport and activating the eIF5A-hypusination translation pathway. This pathway specifically translates apoptosis-related host proteins, such as P53, CypA, CypD, and CypJ, to drive cellular apoptosis owing to broken dsDNA. Furthermore, translated viral proteins, such Vank86, 92, and 101, known to complex with transcription factor Dip3, positively regulated DHYS and DOHH transcription maintaining the activation of the eIF5A-hypusination. Mechanistically, MbBV-mediated extracellular vesicles contained inserted viral fragments that re-integrated into recipients, potentially via the homologous recombinant repair system. Meanwhile, this stimulation regulated activated caspase-3 levels via PI3K/AKT 308 and 473 dephosphorylation to promote apoptosis of granulocyte-like recipients Sf9 cell; maintaining PI3K/AKT 473 phosphorylation and 308 dephosphorylation inhibited caspase-3 activation leading to dismigration of plasmatocyte-like recipient High Five cells. Together, our results suggest that integration-mediated eIF5A hypusination drives extracellular vesicles for continuous immunosuppression.
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Affiliation(s)
- Gui-Fang Zhou
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Chang-Xu Chen
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Qiu-Chen Cai
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Xiang Yan
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Nan-Nan Peng
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Xing-Cheng Li
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Ji-Hui Cui
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Yun-Feng Han
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Qi Zhang
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Jiang-Hui Meng
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Hong-Mei Tang
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Chen-Hui Cai
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Jin Long
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Kai-Jun Luo
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
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19
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Talbert PB, Armache KJ, Henikoff S. Viral histones: pickpocket's prize or primordial progenitor? Epigenetics Chromatin 2022; 15:21. [PMID: 35624484 PMCID: PMC9145170 DOI: 10.1186/s13072-022-00454-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
The common histones H2A, H2B, H3, and H4 are the characteristic components of eukaryotic nucleosomes, which function to wrap DNA and compact the genome as well as to regulate access to DNA for transcription and replication in all eukaryotes. In the past two decades, histones have also been found to be encoded in some DNA viruses, where their functions and properties are largely unknown, though recently histones from two related viruses have been shown to form nucleosome-like structures in vitro. Viral histones can be highly similar to eukaryotic histones in primary sequence, suggesting they have been recently picked up from eukaryotic hosts, or they can be radically divergent in primary sequence and may occur as conjoined histone doublets, triplets, or quadruplets, suggesting ancient origins prior to the divergence of modern eukaryotes. Here, we review what is known of viral histones and discuss their possible origins and functions. We consider how the viral life cycle may affect their properties and histories, and reflect on the possible roles of viruses in the origin of the nucleus of modern eukaryotic cells.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute and Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute and Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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20
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Santos BF, Klopfstein S, Whitfield JB, Sharanowski BJ. Many evolutionary roads led to virus domestication in ichneumonoid parasitoid wasps. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100861. [PMID: 34896617 DOI: 10.1016/j.cois.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/13/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
The investigation of endogenous viral elements (EVEs) has historically focused on only a few lineages of parasitoid wasps, with negative results consistently underreported. Recent studies show that multiple viral lineages were integrated in at least seven instances in Ichneumonoidea and may be much more widespread than previously thought. Increasingly affordable genomic and bioinformatic approaches have made it feasible to search for viral sequences within wasp genomes, opening an extremely promising research avenue. Advances in wasp phylogenetics have shed light on the evolutionary history of EVE integration, although many questions remain. Phylogenetic proximity can be used as a guide to facilitate targeted screening, to estimate the number and age of integration events and to identify taxa involved in major host switches.
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Affiliation(s)
- Bernardo F Santos
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, 57 rue Cuvier CP50, Paris Cedex 05, 75231, France
| | - Seraina Klopfstein
- Naturhistorisches Museum Basel, Augustinergasse 2, Basel, 4501, Switzerland
| | - James B Whitfield
- Department of Entomology, 505 S. Goodwin Ave., University of Illinois, Urbana, IL 61801, USA
| | - Barbara J Sharanowski
- University of Central Florida, Department of Biology, 4110 Libra Drive, Biological Sciences Bldg Rm 301, Orlando, FL 32816, USA.
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21
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The Complete Genome of Chelonus insularis Reveals Dynamic Arrangement of Genome Components in Parasitoid Wasps That Produce Bracoviruses. J Virol 2022; 96:e0157321. [PMID: 34985997 DOI: 10.1128/jvi.01573-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bracoviruses (BVs) are endogenized nudiviruses in parasitoid wasps of the microgastroid complex (family Braconidae). Microgastroid wasps have coopted nudivirus genes to produce replication-defective virions that females use to transfer virulence genes to parasitized hosts. The microgastroid complex further consists of six subfamilies and ∼50,000 species but current understanding of BV gene inventories and organization primarily derives from analysis of two wasp species in the subfamily Microgastrinae (Microplitis demolitor and Cotesia congregata) that produce M. demolitor BV (MdBV) and C. congregata BV (CcBV). Notably, several genomic features of MdBV and CcBV remain conserved since divergence of M. demolitor and C. congregata ∼53 million years ago (MYA). However, it is unknown whether these conserved traits more broadly reflect BV evolution, because no complete genomes exist for any microgastroid wasps outside the Microgastrinae. In this regard, the subfamily Cheloninae is of greatest interest because it diverged earliest from the Microgastrinae (∼85 MYA) after endogenization of the nudivirus ancestor. Here, we present the complete genome of Chelonus insularis, which is an egg-larval parasitoid in the Cheloninae that produces C. insularis BV (CinsBV). We report that the inventory of nudivirus genes in C. insularis is conserved but are dissimilarly organized compared to M. demolitor and C. congregata. Reciprocally, CinsBV proviral segments share organizational features with MdBV and CcBV but virulence gene inventories exhibit almost no overlap. Altogether, our results point to the functional importance of a conserved inventory of nudivirus genes and a dynamic set of virulence genes for the successful parasitism of hosts. Our results also suggest organizational features previously identified in MdBV and CcBV are likely not essential for BV virion formation. IMPORTANCE Bracoviruses are a remarkable example of virus endogenization, because large sets of genes from a nudivirus ancestor continue to produce virions that thousands of wasp species rely upon to parasitize hosts. Understanding how these genes interact and have been coopted by wasps for novel functions is of broad interest in the study of virus evolution. This work characterizes bracovirus genome components in the parasitoid wasp Chelonus insularis, which together with existing wasp genomes captures a large portion of the diversity among wasp species that produce bracoviruses. Results provide new information about how bracovirus genome components are organized in different wasps while also providing additional insights on key features required for function.
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22
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Liu S, Sappington TW, Coates BS, Bonning BC. Sequences Encoding a Novel Toursvirus Identified from Southern and Northern Corn Rootworms (Coleoptera: Chrysomelidae). Viruses 2022; 14:v14020397. [PMID: 35215990 PMCID: PMC8879594 DOI: 10.3390/v14020397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 02/05/2023] Open
Abstract
Sequences derived from a novel toursvirus were identified from pooled genomic short read data from U.S. populations of southern corn rootworm (SCR, Diabrotica undecimpunctata howardi Barber) and northern corn rootworm (NCR, Diabrotica barberi Smith & Lawrence). Most viral sequences were identified from the SCR genomic dataset. As proteins encoded by toursvirus sequences from SCR and NCR were almost identical, the contig sets from SCR and NCR were combined to generate 26 contigs. A total of 108,176 bp were assembled from these contigs, with 120 putative toursviral ORFs identified indicating that most of the viral genome had been recovered. These ORFs included all 40 genes that are common to members of the Ascoviridae. Two genes typically present in Ascoviridae (ATP binding cassette transport system permeases and Baculovirus repeated open reading frame), were not detected. There was evidence for transposon insertion in viral sequences at different sites in the two host species. Phylogenetic analyses based on a concatenated set of 45 translated protein sequences clustered toursviruses into a distinct clade. Based on the combined evidence, we propose taxonomic separation of toursviruses from Ascoviridae.
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Affiliation(s)
- Sijun Liu
- Department of Entomology, Iowa State University, Ames, IA 50011, USA;
| | - Thomas W. Sappington
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA; (T.W.S.); (B.S.C.)
| | - Brad S. Coates
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA; (T.W.S.); (B.S.C.)
| | - Bryony C. Bonning
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
- Correspondence:
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23
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Lorenzi A, Strand MR, Burke GR, Volkoff AN. Identifying bracovirus and ichnovirus genes involved in virion morphogenesis. CURRENT OPINION IN INSECT SCIENCE 2022; 49:63-70. [PMID: 34839031 DOI: 10.1016/j.cois.2021.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/03/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
Bracoviruses (BVs) and ichnoviruses (IVs) evolved from different endogenized viruses but through convergence have been coopted by parasitoids in the families Braconidae and Ichneumonidae for similar functions in parasitizing hosts. Experimentally studying the role of endogenized viral genes in virion morphogenesis remains a key challenge in the study of BVs and IVs. Here we summarize how multiomics, electron microscopy, and RNA interference (RNAi) methods have provided new insights about BV and IV gene function.
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Affiliation(s)
- Ange Lorenzi
- Department of Entomology, University of Georgia, Athens 30602, GA, USA.
| | - Michael R Strand
- Department of Entomology, University of Georgia, Athens 30602, GA, USA
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens 30602, GA, USA
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24
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Drezen JM, Bézier A, Burke GR, Strand MR. Bracoviruses, ichnoviruses, and virus-like particles from parasitoid wasps retain many features of their virus ancestors. CURRENT OPINION IN INSECT SCIENCE 2022; 49:93-100. [PMID: 34954138 DOI: 10.1016/j.cois.2021.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Animal genomes commonly contain genes or sequences that have been acquired from different types of viruses. The vast majority of these endogenous virus elements (EVEs) are inactive or consist of only a small number of components that show no evidence of cooption for new functions or interaction. Unlike most EVEs, bracoviruses (BVs), ichnoviruses (IVs) and virus-like particles (VLPs) in parasitoid wasps have evolved through retention and interaction of many genes from virus ancestors. Here, we discuss current understanding of BV, IV and VLP evolution along with associated implications for what constitutes a virus. We suggest that BVs and IVs are domesticated endogenous viruses (DEVs) that differ in several important ways from other known EVEs.
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Affiliation(s)
- Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS - Université de Tours, Tours, France.
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS - Université de Tours, Tours, France
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Michael R Strand
- Department of Entomology, University of Georgia, Athens, GA 30602, USA.
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25
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Magaña AJ, Dáder B, Sancho G, Adán Á, Morales I, Viñuela E. Comparison of the Parasitization of Chelonus inanitus L. (Hymenoptera: Braconidae) in Two Spodoptera Pests and Evaluation of the Procedure for Its Production. INSECTS 2022; 13:99. [PMID: 35055942 PMCID: PMC8779801 DOI: 10.3390/insects13010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/10/2022]
Abstract
Chelonus inanitus (L.) is an egg-larval parasitoid of noctuids Spodoptera exigua (Hübner) and S. littoralis (Boisduval), whose mass rearing or real potential has not been targeted yet. To improve the rearing in the factitious host Ephestia kuehniella Zeller, we investigated the influence of host age and number of females parasitizing simultaneously on the overall rearing success, the influence of host age on the life cycle, and the influence of host species on the parasitoid body size. The proportion of emerging C. inanitus was higher from young host eggs, but more females emerged from mature eggs. Under high parasitoid competition, we observed a reduction in non-parasitized hosts without reducing parasitoid emergence. The parasitoid life cycle was longer in females, but the mismatch between sexes was smaller in mature eggs. The parasitoid size was smaller in the factitious host than in the natural hosts. Under semi-field conditions, we investigated the competition among parasitoid females on the overall parasitism success. The reproductive parasitism was more successful in S. exigua than in S. littoralis, and the maximum emergence was reached with three and four females, respectively. The control of S. littoralis may be attributed to the high developmental mortality, a non-reproductive parasitism that is often underestimated.
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Affiliation(s)
| | - Beatriz Dáder
- Unidad de Protección de Cultivos, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Avda. Puerta de Hierro 2, 28040 Madrid, Spain; (A.J.M.); (G.S.); (Á.A.); (I.M.); (E.V.)
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26
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Petersen JM, Bézier A, Drezen JM, van Oers MM. The naked truth: An updated review on nudiviruses and their relationship to bracoviruses and baculoviruses. J Invertebr Pathol 2022; 189:107718. [DOI: 10.1016/j.jip.2022.107718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
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27
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Wang ZH, Zhou YN, Ye XQ, Wu XT, Yang P, Shi M, Huang JH, Chen XX. CLP gene family, a new gene family of Cotesia vestalis bracovirus inhibits melanization of Plutella xylostella hemolymph. INSECT SCIENCE 2021; 28:1567-1581. [PMID: 33155403 DOI: 10.1111/1744-7917.12883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/19/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
Polydnaviruses (PDVs) are obligatory symbionts of parasitoid wasps and play an important role in suppressing host immune defenses. Although PDV genes that inhibit host melanization are known in Microplitis bracovirus, the functional homologs in Cotesia bracoviruses remain unknown. Here, we find that Cotesia vestalis bracovirus (CvBV) can inhibit hemolymph melanization of its host, Plutella xylostella larvae, during the early stages of parasitization, and that overexpression of highly expressed CvBV genes reduced host phenoloxidase activity. Furthermore, CvBV-7-1 in particular reduced host phenoloxidase activity within 12 h, and the injection of anti-CvBV-7-1 antibody increased the melanization of parasitized host larvae. Further analyses showed that CvBV-7-1 and three homologs from other Cotesia bracoviruses possessed a C-terminal leucine/isoleucine-rich region and had a similar function in inhibiting melanization. Therefore, a new family of bracovirus genes was proposed and named as C-terminal Leucine/isoleucine-rich Protein (CLP). Ectopic expression of CvBV-7-1 in Drosophila hemocytes increased susceptibility to bacterial repression of melanization and reduced the melanotic encapsulation of parasitized D. melanogaster by the parasitoid Leptopilina boulardi. The formation rate of wasp pupae and the eclosion rate of C. vestalis were affected when the function of CvBV-7-1 was blocked. Our findings suggest that CLP genes from Cotesia bracoviruses encoded proteins that contain a C-terminal leucine/isoleucine-rich region and function as melanization inhibitors during the early stage of parasitization, which is important for successful parasitization.
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Affiliation(s)
- Ze-Hua Wang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yue-Nan Zhou
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xi-Qian Ye
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xiao-Tong Wu
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Pei Yang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Min Shi
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Jian-Hua Huang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xue-Xin Chen
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, China
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28
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Muller H, Chebbi MA, Bouzar C, Périquet G, Fortuna T, Calatayud PA, Le Ru B, Obonyo J, Kaiser L, Drezen JM, Huguet E, Gilbert C. Genome-Wide Patterns of Bracovirus Chromosomal Integration into Multiple Host Tissues during Parasitism. J Virol 2021; 95:e0068421. [PMID: 34319152 PMCID: PMC8549517 DOI: 10.1128/jvi.00684-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/07/2021] [Indexed: 12/23/2022] Open
Abstract
Bracoviruses are domesticated viruses found in parasitic wasp genomes. They are composed of genes of nudiviral origin that are involved in particle production and proviral segments containing virulence genes that are necessary for parasitism success. During particle production, proviral segments are amplified and individually packaged as DNA circles in nucleocapsids. These particles are injected by parasitic wasps into host larvae together with their eggs. Bracovirus circles of two wasp species were reported to undergo chromosomal integration in parasitized host hemocytes, through a conserved sequence named the host integration motif (HIM). Here, we used bulk Illumina sequencing to survey integrations of Cotesia typhae bracovirus circles in the DNA of its host, the maize corn borer (Sesamia nonagrioides), 7 days after parasitism. First, assembly and annotation of a high-quality genome for C. typhae enabled us to characterize 27 proviral segments clustered in proviral loci. Using these data, we characterized large numbers of chromosomal integrations (from 12 to 85 events per host haploid genome) for all 16 bracovirus circles containing a HIM. Integrations were found in four S. nonagrioides tissues and in the body of a caterpillar in which parasitism had failed. The 12 remaining circles do not integrate but are maintained at high levels in host tissues. Surprisingly, we found that HIM-mediated chromosomal integration in the wasp germ line has occurred accidentally at least six times during evolution. Overall, our study furthers our understanding of wasp-host genome interactions and supports HIM-mediated chromosomal integration as a possible mechanism of horizontal transfer from wasps to their hosts. IMPORTANCE Bracoviruses are endogenous domesticated viruses of parasitoid wasps that are injected together with wasp eggs into wasp host larvae during parasitism. Several studies have shown that some DNA circles packaged into bracovirus particles become integrated into host somatic genomes during parasitism, but the phenomenon has never been studied using nontargeted approaches. Here, we use bulk Illumina sequencing to systematically characterize and quantify bracovirus circle integrations that occur in four tissues of the Mediterranean corn borer (Sesamia nonagrioides) during parasitism by the Cotesia typhae wasp. Our analysis reveals that all circles containing a HIM integrate at substantial levels (from 12 to 85 integrations per host cell, in total) in all tissues, while other circles do not integrate. In addition to shedding new light on wasp-bracovirus-host interactions, our study supports HIM-mediated chromosomal integration of bracovirus as a possible source of wasp-to-host horizontal transfer, with long-term evolutionary consequences.
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Affiliation(s)
- Héloïse Muller
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement, et Écologie, Gif-sur-Yvette, France
| | - Mohamed Amine Chebbi
- UMR 7261 CNRS, Institut de Recherche sur la Biologie de l'Insecte, Faculté des Sciences et Techniques, Université de Tours, Tours, France
- ViroScan3D SAS, Lyon, France
| | - Clémence Bouzar
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement, et Écologie, Gif-sur-Yvette, France
| | - George Périquet
- UMR 7261 CNRS, Institut de Recherche sur la Biologie de l'Insecte, Faculté des Sciences et Techniques, Université de Tours, Tours, France
| | - Taiadjana Fortuna
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement, et Écologie, Gif-sur-Yvette, France
| | - Paul-André Calatayud
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement, et Écologie, Gif-sur-Yvette, France
- International Centre of Insect Physiology and Ecology, Institut de Recherche pour le Développement Team, Nairobi, Kenya
| | - Bruno Le Ru
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement, et Écologie, Gif-sur-Yvette, France
- International Centre of Insect Physiology and Ecology, Institut de Recherche pour le Développement Team, Nairobi, Kenya
| | - Julius Obonyo
- International Centre of Insect Physiology and Ecology, Institut de Recherche pour le Développement Team, Nairobi, Kenya
| | - Laure Kaiser
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement, et Écologie, Gif-sur-Yvette, France
| | - Jean-Michel Drezen
- UMR 7261 CNRS, Institut de Recherche sur la Biologie de l'Insecte, Faculté des Sciences et Techniques, Université de Tours, Tours, France
| | - Elisabeth Huguet
- UMR 7261 CNRS, Institut de Recherche sur la Biologie de l'Insecte, Faculté des Sciences et Techniques, Université de Tours, Tours, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement, et Écologie, Gif-sur-Yvette, France
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29
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Heve WK, Adjadeh TA, Billah MK. Overview and future research needs for development of effective biocontrol strategies for management of Bactrocera dorsalis Hendel (Diptera: Tephritidae) in sub-Saharan Africa. PEST MANAGEMENT SCIENCE 2021; 77:4224-4237. [PMID: 34031975 DOI: 10.1002/ps.6485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Infestation of fruits by native and invasive fruit flies causes significant economic losses. In most cases, incidence of 'regulated' dangerous fruit flies in orchards results in restrictions on export of fruits from such places to international markets. Unfortunately, use of insecticides applied on foliage and fruits does not kill the fruit-to-soil stages of fruit flies. However, diverse biological control agents (BCAs) do so. Thus, prevalence of native and invasive fruit flies in orchards will require that a combination of BCAs is included in integrated pest management (IPM) programmes. In the case of Bactrocera dorsalis Hendel and other economically important fruit flies found in sub-Saharan Africa (SSA), use of classical biocontrol approach involves concomitant releases of two exotic parasitoids (Fopius arisanus Sonan and Diachasmimorpha longicaudata Ashmead). These non-native wasps may have complemented the indigenous parasitoids in combination with application of entomopathogenic fungi (EPFs) and conservation of predatory ants (Oecophylla longinoda Latreille, with O. smaragdina) in fruit fly IPM plans. Consequently, some levels of decline in fruit infestation have been observed. Although interspecific interactions between BCAs against several insect pests have produced varying results, including threatening the survival of other BCAs, the prevalence of B. dorsalis in orchards across SSA requires further research to investigate effects of coalescing biocontrol approaches in IPM strategies. Therefore, future research into combining parasitoids, EPFs and entomopathogenic nematodes, in addition to conservation of predatory ants (O. longinoda, O. smaragdina and others) in IPM plans may improve the effectiveness of currently used strategies for the management of fruit-infesting tephritids. © 2021 Society of Chemical Industry.
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Affiliation(s)
- William K Heve
- Department of Biological, Physical and Mathematical Sciences, School of Natural and Environmental Sciences, University of Environment and Sustainable Development, Somanya, Ghana
| | | | - Maxwell K Billah
- Department of Animal Biology and Conservation Science, University of Ghana, Accra, Ghana
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30
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Wang Z, Ye X, Zhou Y, Wu X, Hu R, Zhu J, Chen T, Huguet E, Shi M, Drezen JM, Huang J, Chen X. Bracoviruses recruit host integrases for their integration into caterpillar's genome. PLoS Genet 2021; 17:e1009751. [PMID: 34492000 PMCID: PMC8460044 DOI: 10.1371/journal.pgen.1009751] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 09/23/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
Some DNA viruses infect host animals usually by integrating their DNAs into the host genome. However, the mechanisms for integration remain largely unknown. Here, we find that Cotesia vestalis bracovirus (CvBV), a polydnavirus of the parasitic wasp C. vestalis (Haliday), integrates its DNA circles into host Plutella xylostella (L.) genome by two distinct strategies, conservatively and randomly, through high-throughput sequencing analysis. We confirmed that the conservatively integrating circles contain an essential "8+5" nucleotides motif which is required for integration. Then we find CvBV circles are integrated into the caterpillar's genome in three temporal patterns, the early, mid and late stage-integration. We further identify that three CvBV-encoded integrases are responsible for some, but not all of the virus circle integrations, indeed they mainly participate in the processes of early stage-integration. Strikingly, we find two P. xylostella retroviral integrases (PxIN1 and PxIN2) are highly induced upon wasp parasitism, and PxIN1 is crucial for integration of some other early-integrated CvBV circles, such as CvBV_04, CvBV_12 and CvBV_24, while PxIN2 is important for integration of a late-integrated CvBV circle, CvBV_21. Our data uncover a novel mechanism in which CvBV integrates into the infected host genome, not only by utilizing its own integrases, but also by recruiting host enzymes. These findings will strongly deepen our understanding of how bracoviruses regulate and integrate into their hosts.
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Affiliation(s)
- Zehua Wang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xiqian Ye
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yuenan Zhou
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xiaotong Wu
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Rongmin Hu
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Jiachen Zhu
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Ting Chen
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Elisabeth Huguet
- UMR CNRS/ Université de Tours 7261 -IRBI: Institut de Recherche sur la Biologie de l’Insecte, Tours, France
| | - Min Shi
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Jean-Michel Drezen
- UMR CNRS/ Université de Tours 7261 -IRBI: Institut de Recherche sur la Biologie de l’Insecte, Tours, France
| | - Jianhua Huang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xuexin Chen
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, China
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31
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Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies. Viruses 2021; 13:v13091694. [PMID: 34578276 PMCID: PMC8472649 DOI: 10.3390/v13091694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
Multiple enveloped viruses with rod-shaped nucleocapsids have been described, infecting the epithelial cell nuclei within the hepatopancreas tubules of crustaceans. These bacilliform viruses share the ultrastructural characteristics of nudiviruses, a specific clade of viruses infecting arthropods. Using histology, electron microscopy and high throughput sequencing, we characterise two further bacilliform viruses from aquatic hosts, the brown shrimp (Crangon crangon) and the European shore crab (Carcinus maenas). We assembled the full double stranded, circular DNA genome sequences of these viruses (~113 and 132 kbp, respectively). Comparative genomics and phylogenetic analyses confirm that both belong within the family Nudiviridae but in separate clades representing nudiviruses found in freshwater and marine environments. We show that the three thymidine kinase (tk) genes present in all sequenced nudivirus genomes, thus far, were absent in the Crangon crangon nudivirus, suggesting there are twenty-eight core genes shared by all nudiviruses. Furthermore, the phylogenetic data no longer support the subdivision of the family Nudiviridae into four genera (Alphanudivirus to Deltanudivirus), as recently adopted by the International Committee on Taxonomy of Viruses (ICTV), but rather shows two main branches of the family that are further subdivided. Our data support a recent proposal to create two subfamilies within the family Nudiviridae, each subdivided into several genera.
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32
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Cheng RL, Li XF, Zhang CX. Nudivirus Remnants in the Genomes of Arthropods. Genome Biol Evol 2021; 12:578-588. [PMID: 32282886 PMCID: PMC7250505 DOI: 10.1093/gbe/evaa074] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
Endogenous viral elements (EVEs), derived from all major types of viruses, have been discovered in many eukaryotic genomes, representing "fossil records" of past viral infections. The endogenization of nudiviruses has been reported in several insects, leading to the question of whether genomic integration is a common phenomenon for these viruses. In this study, genomic assemblies of insects and other arthropods were analyzed to identify endogenous sequences related to Nudiviridae. A total of 359 nudivirus-like genes were identified in 43 species belonging to different groups; however, none of these genes were detected in the known hosts of nudiviruses. A large proportion of the putative EVEs identified in this study encode intact open reading frames or are transcribed as mRNAs, suggesting that they result from recent endogenization of nudiviruses. Phylogenetic analyses of the identified EVEs and inspections of their flanking regions indicated that integration of nudiviruses has occurred recurrently during the evolution of arthropods. This is the first report of a comprehensive screening for nudivirus-derived EVEs in arthropod genomes. The results of this study demonstrated that a large variety of arthropods, especially hemipteran and hymenopteran insects, have previously been or are still infected by nudiviruses. These findings have greatly extended the host range of Nudiviridae and provide new insights into viral diversity, evolution, and host-virus interactions.
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Affiliation(s)
- Ruo-Lin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Xiao-Feng Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Chuan-Xi Zhang
- Institute of Plant Virology, Ningbo University, China.,Institute of Insect Science, Zhejiang University, Hangzhou, China
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33
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Burke GR, Hines HM, Sharanowski BJ. The Presence of Ancient Core Genes Reveals Endogenization from Diverse Viral Ancestors in Parasitoid Wasps. Genome Biol Evol 2021; 13:evab105. [PMID: 33988720 PMCID: PMC8325570 DOI: 10.1093/gbe/evab105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
The Ichneumonoidea (Ichneumonidae and Braconidae) is an incredibly diverse superfamily of parasitoid wasps that includes species that produce virus-like entities in their reproductive tracts to promote successful parasitism of host insects. Research on these entities has traditionally focused upon two viral genera Bracovirus (in Braconidae) and Ichnovirus (in Ichneumonidae). These viruses are produced using genes known collectively as endogenous viral elements (EVEs) that represent historical, now heritable viral integration events in wasp genomes. Here, new genome sequence assemblies for 11 species and 6 publicly available genomes from the Ichneumonoidea were screened with the goal of identifying novel EVEs and characterizing the breadth of species in lineages with known EVEs. Exhaustive similarity searches combined with the identification of ancient core genes revealed sequences from both known and novel EVEs. One species harbored a novel, independently derived EVE related to a divergent large double-stranded DNA (dsDNA) virus that manipulates behavior in other hymenopteran species. Although bracovirus or ichnovirus EVEs were identified as expected in three species, the absence of ichnoviruses in several species suggests that they are independently derived and present in two younger, less widespread lineages than previously thought. Overall, this study presents a novel bioinformatic approach for EVE discovery in genomes and shows that three divergent virus families (nudiviruses, the ancestors of ichnoviruses, and Leptopilina boulardi Filamentous Virus-like viruses) are recurrently acquired as EVEs in parasitoid wasps. Virus acquisition in the parasitoid wasps is a common process that has occurred in many more than two lineages from a diverse range of arthropod-infecting dsDNA viruses.
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Affiliation(s)
- Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Heather M Hines
- Department of Biology and Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
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34
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Di Giovanni D, Lepetit D, Guinet B, Bennetot B, Boulesteix M, Couté Y, Bouchez O, Ravallec M, Varaldi J. A Behavior-Manipulating Virus Relative as a Source of Adaptive Genes for Drosophila Parasitoids. Mol Biol Evol 2021; 37:2791-2807. [PMID: 32080746 DOI: 10.1093/molbev/msaa030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Some species of parasitic wasps have domesticated viral machineries to deliver immunosuppressive factors to their hosts. Up to now, all described cases fall into the Ichneumonoidea superfamily, which only represents around 10% of hymenoptera diversity, raising the question of whether such domestication occurred outside this clade. Furthermore, the biology of the ancestral donor viruses is completely unknown. Since the 1980s, we know that Drosophila parasitoids belonging to the Leptopilina genus, which diverged from the Ichneumonoidea superfamily 225 Ma, do produce immunosuppressive virus-like structure in their reproductive apparatus. However, the viral origin of these structures has been the subject of debate. In this article, we provide genomic and experimental evidence that those structures do derive from an ancestral virus endogenization event. Interestingly, its close relatives induce a behavior manipulation in present-day wasps. Thus, we conclude that virus domestication is more prevalent than previously thought and that behavior manipulation may have been instrumental in the birth of such associations.
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Affiliation(s)
- Deborah Di Giovanni
- Université de Lyon Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - David Lepetit
- Université de Lyon Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Benjamin Guinet
- Université de Lyon Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Bastien Bennetot
- Université de Lyon Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France.,Ecologie Systématique & Evolution (UMR 8079), Université Paris Sud, Orsay, France
| | - Matthieu Boulesteix
- Université de Lyon Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Yohann Couté
- Université de Grenoble Alpes, CEA, Inserm, IRIG-BGE, Grenoble, France
| | - Olivier Bouchez
- Institut National de la Recherche Agronomique (INRA), US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Marc Ravallec
- UMR 1333 INRAE - Université Montpellier "Diversité, Génomes et Interactions Microorganismes-Insectes" (DGIMI), Montpellier, France
| | - Julien Varaldi
- Université de Lyon Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
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35
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Arvin MJ, Lorenzi A, Burke GR, Strand MR. MdBVe46 is an envelope protein that is required for virion formation by Microplitis demolitor bracovirus. J Gen Virol 2021; 102:001565. [PMID: 33591247 PMCID: PMC8515855 DOI: 10.1099/jgv.0.001565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/18/2021] [Indexed: 11/18/2022] Open
Abstract
Bracoviruses (BVs) are endogenized nudiviruses that braconid parasitoid wasps have coopted for functions in parasitizing hosts. Microplitis demolitor is a braconid wasp that produces Microplitis demolitor bracovirus (MdBV) and parasitizes the larval stage of the moth Chrysodeixis includens. Some BV core genes are homologs of genes also present in baculoviruses while others are only known from nudiviruses or other BVs. In this study, we had two main goals. The first was to separate MdBV virions into envelope and nucleocapsid fractions before proteomic analysis to identify core gene products that were preferentially associated with one fraction or the other. Results indicated that nearly all MdBV baculovirus-like gene products that were detected by our proteomic analysis had similar distributions to homologs in the occlusion-derived form of baculoviruses. Several core gene products unknown from baculoviruses were also identified as envelope or nucleocapsid components. Our second goal was to functionally characterize a core gene unknown from baculoviruses that was originally named HzNVorf64-like. Immunoblotting assays supported our proteomic data that identified HzNVorf64-like as an envelope protein. We thus renamed HzNVorf64-like as MdBVe46, which we further hypothesized was important for infection of C. includens. Knockdown of MdBVe46 by RNA interference (RNAi) greatly reduced transcript and protein abundance. Knockdown of MdBVe46 also altered virion morphogenesis, near-fully inhibited infection of C. includens, and significantly reduced the proportion of hosts that were successfully parasitized by M. demolitor.
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Affiliation(s)
- Michael J. Arvin
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Ange Lorenzi
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Gaelen R. Burke
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Michael R. Strand
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
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36
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Liu S, Sappington TW, Coates BS, Bonning BC. Nudivirus Sequences Identified from the Southern and Western Corn Rootworms (Coleoptera: Chrysomelidae). Viruses 2021; 13:v13020269. [PMID: 33572446 PMCID: PMC7916170 DOI: 10.3390/v13020269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 01/08/2023] Open
Abstract
Analysis of pooled genomic short read sequence data revealed the presence of nudivirus-derived sequences from U.S. populations of both southern corn rootworm (SCR, Diabrotica undecimpunctata howardi Barber) and western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte). A near complete nudivirus genome sequence was assembled from sequence data for an SCR population with relatively high viral titers. A total of 147,179 bp was assembled from five contigs that collectively encode 109 putative open reading frames (ORFs) including 20 nudivirus core genes. In contrast, genome sequence recovery was incomplete for a second nudivirus from WCR, although sequences derived from this virus were present in three geographically dispersed populations. Only 48,989 bp were assembled with 48 putative ORFs including 13 core genes, representing about 20% of a typical nudivirus genome. Phylogenetic analysis indicated that both corn rootworm nudiviruses grouped with the third known nudivirus of beetles, Oryctes rhinoceros nudivirus in the genus Alphanudivirus. On the basis of phylogenetic and additional analyses, we propose further taxonomic separation of nudiviruses within Alphanudivirus and Betanudivirus into two subfamilies and five genera. Identification of nudivirus-derived sequences from two species of corn rootworm highlights the diversity of viruses associated with these agricultural insect pests.
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Affiliation(s)
- Sijun Liu
- Department of Entomology, Iowa State University, Ames, IA 50011, USA;
| | - Thomas W. Sappington
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA; (T.W.S.); (B.S.C.)
| | - Brad S. Coates
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA; (T.W.S.); (B.S.C.)
| | - Bryony C. Bonning
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
- Correspondence:
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37
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Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol 2021; 4:104. [PMID: 33483589 PMCID: PMC7822920 DOI: 10.1038/s42003-020-01623-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.
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Affiliation(s)
- Jérémy Gauthier
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France ,grid.466902.f0000 0001 2248 6951Geneva Natural History Museum, 1208 Geneva, Switzerland
| | - Hélène Boulain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France ,grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Joke J. F. A. van Vugt
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Emma Persyn
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Jean-Marc Aury
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Benjamin Noel
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Anthony Bretaudeau
- grid.410368.80000 0001 2191 9284IGEPP, INRAE, Institut Agro, Univ Rennes, 35000 Rennes, France ,grid.420225.30000 0001 2298 7270Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Fabrice Legeai
- grid.410368.80000 0001 2191 9284IGEPP, INRAE, Institut Agro, Univ Rennes, 35000 Rennes, France ,grid.420225.30000 0001 2298 7270Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Sven Warris
- grid.4818.50000 0001 0791 5666Applied Bioinformatics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamed A. Chebbi
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Géraldine Dubreuil
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Bernard Duvic
- grid.503158.aUniversité Montpellier, INRAE, DGIMI, 34095 Montpellier, France
| | - Natacha Kremer
- grid.462854.90000 0004 0386 3493Laboratoire de Biométrie et Biologie Evolutive Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, 43 bd du 11 novembre 1918, bat. G. Mendel, 69622 Villeurbanne Cedex, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Christophe Bressac
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Sébastien Moreau
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Georges Periquet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Myriam Harry
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Nicolas Montagné
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Isabelle Boulogne
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Mahnaz Sabeti-Azad
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Martine Maïbèche
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Thomas Chertemps
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Frédérique Hilliou
- grid.435437.20000 0004 0385 8766Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia-Antipolis, France
| | - David Siaussat
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Joëlle Amselem
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Isabelle Luyten
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Claire Capdevielle-Dulac
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Karine Labadie
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Bruna Laís Merlin
- grid.11899.380000 0004 1937 0722Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Valérie Barbe
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Jetske G. de Boer
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands ,grid.4830.f0000 0004 0407 1981Evolutionary Genetics, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France
| | - Fernando Luis Cônsoli
- grid.11899.380000 0004 1937 0722Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Stéphane Dupas
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Gaelle Le Goff
- grid.435437.20000 0004 0385 8766Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia-Antipolis, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Emmanuelle Jacquin-Joly
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - James B. Whitfield
- Department of Entomology, 320 Morrill Hall, 505 South Goodwin Avenue, University of Illinois, Urbana, IL 61801 USA
| | - Louise E. M. Vet
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Hans M. Smid
- grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Laure Kaiser
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
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Kimenyi KM, Abry MF, Okeyo W, Matovu E, Masiga D, Kulohoma BW. Detecting bracoviral orthologs distribution in five tsetse fly species and the housefly genomes. BMC Res Notes 2020; 13:318. [PMID: 32616010 PMCID: PMC7331153 DOI: 10.1186/s13104-020-05161-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/27/2020] [Indexed: 01/22/2023] Open
Abstract
Objective Mutualism between endogenous viruses and eukaryotes is still poorly understood. Several endogenous double-stranded polydnaviruses, bracoviruses, homologous to those present in parasitic braconid wasp genomes were detected in the tsetse fly (Glossina morsitans morsitans). This is peculiar since tsetse flies do not share a reproductive lifestyle similar to wasps, but deliver fully developed larvae that pupate within minutes of exiting their mothers. The objective of this study is to investigate genomic distribution of bracoviral sequences in five tsetse fly species and the housefly, and examine its value as a potential vector control strategy target point. We use comparative genomics to determine the presence, distribution across Glossina species genomes, and evolutionary relationships of bracoviruses of five tsetse fly species and the housefly. Results We report on homologous bracoviruses in multiple Dipteran genomes. Phylogenetic reconstruction using within-species concatenated bracoviral orthologs shows great congruence with previously reconstructed insect species phylogenies. Our findings suggest that bracoviruses present in Diptera originate from a single integration event of the viral genome that occurred in an ancestor insect before the evolutionary radiation of different insect orders.
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Sharanowski BJ, Ridenbaugh RD, Piekarski PK, Broad GR, Burke GR, Deans AR, Lemmon AR, Moriarty Lemmon EC, Diehl GJ, Whitfield JB, Hines HM. Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization. Mol Phylogenet Evol 2020; 156:107023. [PMID: 33253830 DOI: 10.1016/j.ympev.2020.107023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/28/2020] [Accepted: 11/23/2020] [Indexed: 12/26/2022]
Abstract
Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.
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Affiliation(s)
| | - Ryan D Ridenbaugh
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Patrick K Piekarski
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA; Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Gavin R Broad
- Department of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30606, USA
| | - Andrew R Deans
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Gloria J Diehl
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - James B Whitfield
- Department of Entomology, University of Illinois, Urbana, IL 61801, USA
| | - Heather M Hines
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802; Department of Biology, Pennsylvania State University, University Park, PA, 16802
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40
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Coffman KA, Burke GR. Genomic analysis reveals an exogenous viral symbiont with dual functionality in parasitoid wasps and their hosts. PLoS Pathog 2020; 16:e1009069. [PMID: 33253317 PMCID: PMC7728225 DOI: 10.1371/journal.ppat.1009069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/10/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
Insects are known to host a wide variety of beneficial microbes that are fundamental to many aspects of their biology and have substantially shaped their evolution. Notably, parasitoid wasps have repeatedly evolved beneficial associations with viruses that enable developing wasps to survive as parasites that feed from other insects. Ongoing genomic sequencing efforts have revealed that most of these virus-derived entities are fully integrated into the genomes of parasitoid wasp lineages, representing endogenous viral elements (EVEs) that retain the ability to produce virus or virus-like particles within wasp reproductive tissues. All documented parasitoid EVEs have undergone similar genomic rearrangements compared to their viral ancestors characterized by viral genes scattered across wasp genomes and specific viral gene losses. The recurrent presence of viral endogenization and genomic reorganization in beneficial virus systems identified to date suggest that these features are crucial to forming heritable alliances between parasitoid wasps and viruses. Here, our genomic characterization of a mutualistic poxvirus associated with the wasp Diachasmimorpha longicaudata, known as Diachasmimorpha longicaudata entomopoxvirus (DlEPV), has uncovered the first instance of beneficial virus evolution that does not conform to the genomic architecture shared by parasitoid EVEs with which it displays evolutionary convergence. Rather, DlEPV retains the exogenous viral genome of its poxvirus ancestor and the majority of conserved poxvirus core genes. Additional comparative analyses indicate that DlEPV is related to a fly pathogen and contains a novel gene expansion that may be adaptive to its symbiotic role. Finally, differential expression analysis during virus replication in wasps and fly hosts demonstrates a unique mechanism of functional partitioning that allows DlEPV to persist within and provide benefit to its parasitoid wasp host.
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Affiliation(s)
- Kelsey A. Coffman
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Gaelen R. Burke
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
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41
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The Unconventional Viruses of Ichneumonid Parasitoid Wasps. Viruses 2020; 12:v12101170. [PMID: 33076395 PMCID: PMC7602663 DOI: 10.3390/v12101170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/18/2022] Open
Abstract
To ensure their own immature development as parasites, ichneumonid parasitoid wasps use endogenous viruses that they acquired through ancient events of viral genome integration. Thousands of species from the campoplegine and banchine wasp subfamilies rely, for their survival, on their association with these viruses, hijacked from a yet undetermined viral taxon. Here, we give an update of recent findings on the nature of the viral genes retained from the progenitor viruses and how they are organized in the wasp genome.
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42
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Hasegawa DK, Zhang P, Turnbull MW. Intracellular dynamics of polydnavirus innexin homologues. INSECT MOLECULAR BIOLOGY 2020; 29:477-489. [PMID: 32683761 DOI: 10.1111/imb.12657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Polydnaviruses associated with ichneumonid parasitoid wasps (Ichnoviruses) encode large numbers of genes, often in multigene families. The Ichnovirus Vinnexin gene family, which is expressed in parasitized lepidopteran larvae, encodes homologues of Innexins, the structural components of insect gap junctions. Here, we have examined intracellular behaviours of the Campoletis sonorensis Ichnovirus (CsIV) Vinnexins, alone and in combination with a host Innexin orthologue, Innexin2 (Inx2). QRT-PCR verified that transcription of CsIV vinnexins occurs contemporaneously with inx2, implying co-occurrence of Vinnexin and Inx2 proteins. Confocal microscopy demonstrated that epitope-tagged VinnexinG (VnxG) and VinnexinQ2 (VnxQ2) exhibit similar subcellular localization as Spodoptera frugiperda Inx2 (Sf-Inx2). Surface biotinylation assays verified that all three proteins localize to the cell surface, and cytochalasin B and nocodazole that they rely on actin and microtubule cytoskeletal networks for localization. Immunomicroscopy following co-transfection of constructs indicates extensive co-localization of Vinnexins with each other and Sf-Inx2, and live-cell imaging of mCherry-labelled Inx2 supports that Vinnexins may affect Sf-Inx2 distribution in a Vinnexin-specific fashion. Our findings support that the Vinnexins may disrupt host cell physiology in a protein-specific manner through altering gap junctional intercellular channel communication, as well as indirectly by affecting multicellular junction characteristics.
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Affiliation(s)
- D K Hasegawa
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA, USA
| | - P Zhang
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - M W Turnbull
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
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Benoist R, Capdevielle-Dulac C, Chantre C, Jeannette R, Calatayud PA, Drezen JM, Dupas S, Le Rouzic A, Le Ru B, Moreau L, Van Dijk E, Kaiser L, Mougel F. Quantitative trait loci involved in the reproductive success of a parasitoid wasp. Mol Ecol 2020; 29:3476-3493. [PMID: 32731311 DOI: 10.1111/mec.15567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022]
Abstract
Dissecting the genetic basis of intraspecific variations in life history traits is essential to understand their evolution, notably for potential biocontrol agents. Such variations are observed in the endoparasitoid Cotesia typhae (Hymenoptera: Braconidae), specialized on the pest Sesamia nonagrioides (Lepidoptera: Noctuidae). Previously, we identified two strains of C. typhae that differed significantly for life history traits on an allopatric host population. To investigate the genetic basis underlying these phenotypic differences, we used a quantitative trait locus (QTL) approach based on restriction site-associated DNA markers. The characteristic of C. typhae reproduction allowed us generating sisters sharing almost the same genetic content, named clonal sibship. Crosses between individuals from the two strains were performed to generate F2 and F8 recombinant CSS. The genotypes of 181 clonal sibships were determined as well as the phenotypes of the corresponding 4,000 females. Informative markers were then used to build a high-quality genetic map. These 465 markers spanned a total length of 1,300 cM and were organized in 10 linkage groups which corresponded to the number of C. typhae chromosomes. Three QTLs were detected for parasitism success and two for offspring number, while none were identified for sex ratio. The QTLs explained, respectively, 27.7% and 24.5% of the phenotypic variation observed. The gene content of the genomic intervals was investigated based on the genome of C. congregata and revealed 67 interesting candidates, as potentially involved in the studied traits, including components of the venom and of the symbiotic virus (bracovirus) shown to be necessary for parasitism success in related wasps.
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Affiliation(s)
- Romain Benoist
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Claire Capdevielle-Dulac
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Célina Chantre
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Rémi Jeannette
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Paul-André Calatayud
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France.,icipe, International Center of Insect Physiology and Ecology, Nairobi, Kenya
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, Université Tours, Tours, France
| | - Stéphane Dupas
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Bruno Le Ru
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE - Le Moulon, Gif-sur-Yvette, France
| | - Erwin Van Dijk
- Université Paris-Saclay, CNRS, CEA, UMR Institut de Biologie Intégrative de la Cellule, Gif-sur-Yvette, France
| | - Laure Kaiser
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Florence Mougel
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
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Liu S, Coates BS, Bonning BC. Endogenous viral elements integrated into the genome of the soybean aphid, Aphis glycines. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 123:103405. [PMID: 32534986 DOI: 10.1016/j.ibmb.2020.103405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Sequence analysis of the genomic DNA isolated from four biotypes of the soybean aphid, Aphis glycines (AG), revealed that in addition to the commonly observed retrovirus-related retrotransposons, viral sequences derived from multiple RNA and DNA viruses have integrated into the genome. Notably, sequences of more than 60 nudiviral genes were identified from de novo assembled DNA contigs, and mapped to assembled genomic scaffolds of AG, indicating that an ancient nudivirus, named Aphis glycines endogenous nudivirus (AgENV), had integrated into the AG genome. Furthermore, sequences derived from a similar endogenous nudivirus, Melanaphis sacchari endogenous nudivirus (MsENV), were identified from the genomic scaffolds of the sugarcane aphid, Melanaphis sacchari. Analysis of transcriptome and small RNA sequence data derived from AG did not provide evidence for transcription of the integrated AgENV genes. Hence, the genes of AgENV may be present as pseudogenes. Phylogenetic analysis based on nudivirus core genes indicated that these aphid ENVs belong to the genus Alphanudivirus.
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Affiliation(s)
- Sijun Liu
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Bryony C Bonning
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, 32611, USA.
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Legeai F, Santos BF, Robin S, Bretaudeau A, Dikow RB, Lemaitre C, Jouan V, Ravallec M, Drezen JM, Tagu D, Baudat F, Gyapay G, Zhou X, Liu S, Webb BA, Brady SG, Volkoff AN. Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. BMC Biol 2020; 18:89. [PMID: 32703219 PMCID: PMC7379367 DOI: 10.1186/s12915-020-00822-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/29/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Polydnaviruses (PDVs) are mutualistic endogenous viruses inoculated by some lineages of parasitoid wasps into their hosts, where they facilitate successful wasp development. PDVs include the ichnoviruses and bracoviruses that originate from independent viral acquisitions in ichneumonid and braconid wasps respectively. PDV genomes are fully incorporated into the wasp genomes and consist of (1) genes involved in viral particle production, which derive from the viral ancestor and are not encapsidated, and (2) proviral segments harboring virulence genes, which are packaged into the viral particle. To help elucidating the mechanisms that have facilitated viral domestication in ichneumonid wasps, we analyzed the structure of the viral insertions by sequencing the whole genome of two ichnovirus-carrying wasp species, Hyposoter didymator and Campoletis sonorensis. RESULTS Assemblies with long scaffold sizes allowed us to unravel the organization of the endogenous ichnovirus and revealed considerable dispersion of the viral loci within the wasp genomes. Proviral segments contained species-specific sets of genes and occupied distinct genomic locations in the two ichneumonid wasps. In contrast, viral machinery genes were organized in clusters showing highly conserved gene content and order, with some loci located in collinear wasp genomic regions. This genomic architecture clearly differs from the organization of PDVs in braconid wasps, in which proviral segments are clustered and viral machinery elements are more dispersed. CONCLUSIONS The contrasting structures of the two types of ichnovirus genomic elements are consistent with their different functions: proviral segments are vehicles for virulence proteins expected to adapt according to different host defense systems, whereas the genes involved in virus particle production in the wasp are likely more stable and may reflect ancestral viral architecture. The distinct genomic architectures seen in ichnoviruses versus bracoviruses reveal different evolutionary trajectories that have led to virus domestication in the two wasp lineages.
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Affiliation(s)
- Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Bernardo F Santos
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Rebecca B Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
| | - Claire Lemaitre
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Véronique Jouan
- DGIMI, INRAE, University of Montpellier, 34095, Montpellier, France
| | - Marc Ravallec
- DGIMI, INRAE, University of Montpellier, 34095, Montpellier, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, UFR des Sciences et Techniques, Parc de Grandmont, Tours, France
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | - Frédéric Baudat
- Institut de Génétique Humaine, CNRS, University of Montpellier, 34396, Montpellier, France
| | - Gabor Gyapay
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, People's Republic of China
| | - Bruce A Webb
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
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A Mutualistic Poxvirus Exhibits Convergent Evolution with Other Heritable Viruses in Parasitoid Wasps. J Virol 2020; 94:JVI.02059-19. [PMID: 32024779 DOI: 10.1128/jvi.02059-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/28/2020] [Indexed: 12/20/2022] Open
Abstract
For insects known as parasitoid wasps, successful development as a parasite results in the death of the host insect. As a result of this lethal interaction, wasps and their hosts have coevolved strategies to gain an advantage in this evolutionary arms race. Although normally considered to be strict pathogens, some viruses have established persistent infections within parasitoid wasp lineages and are beneficial to wasps during parasitism. Heritable associations between viruses and parasitoid wasps have evolved independently multiple times, but most of these systems remain largely understudied with respect to viral origin, transmission and replication strategies of the virus, and interactions between the virus and host insects. Here, we report a detailed characterization of Diachasmimorpha longicaudata entomopoxvirus (DlEPV), a poxvirus found within the venom gland of Diachasmimorpha longicaudata wasps. Our results show that DlEPV exhibits similar but distinct transmission and replication dynamics compared to those of other parasitoid viral elements, including vertical transmission of the virus within wasps, as well as virus replication in both female wasps and fruit fly hosts. Functional assays demonstrate that DlEPV is highly virulent within fly hosts, and wasps without DlEPV have severely reduced parasitism success compared to those with a typical viral load. Taken together, the data presented in this study illustrate a novel case of beneficial virus evolution, in which a virus of unique origin has undergone convergent evolution with other viral elements associated with parasitoid wasps to provide an analogous function throughout parasitism.IMPORTANCE Viruses are generally considered to be disease-causing agents, but several instances of beneficial viral elements have been identified in insects called parasitoid wasps. These virus-derived entities are passed on through wasp generations and enhance the success of the wasps' parasitic life cycle. Many parasitoid-virus partnerships studied to date exhibit common features among independent cases of this phenomenon, including a mother-to-offspring route of virus transmission, a restricted time and location for virus replication, and a positive effect of virus activity on wasp survival. Our characterization of Diachasmimorpha longicaudata entomopoxvirus (DlEPV), a poxvirus found in Diachasmimorpha longicaudata parasitoid wasps, represents a novel example of beneficial virus evolution. Here, we show that DlEPV exhibits functional similarities to known parasitoid viral elements that support its comparable role during parasitism. Our results also demonstrate unique differences that suggest DlEPV is more autonomous than other long-term viral associations described in parasitoid wasps.
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Zhang Y, Wang J, Han GZ. Chalcid wasp paleoviruses bridge the evolutionary gap between bracoviruses and nudiviruses. Virology 2020; 542:34-39. [PMID: 32056666 DOI: 10.1016/j.virol.2020.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 12/14/2022]
Abstract
Polydnaviruses are obligate mutualists of parasitoid wasps and are divided into two genera, Bracovirus and Ichnovirus. Bracoviruses are thought to originate from a single integration of an ancestral nudivirus into the ancestor of microgastroid complex ~100 million years ago. However, all the known nudiviruses are only distantly related to bracoviruses, and much remains obscure about the origin of bracoviruses. Here we employ a paleovirological method to screen endogenous nudivirus-like elements across arthropods. Interestingly, we identify many endogenous nudivirus-like elements within the genome of Eurytoma brunniventris, a species of the Chalcidoidea superfamily. Among them, we find 14 core gene sequences are likely to be derived from a betanudivirus (designated EbrENV-β), suggesting that betanudivirus has been circulating in parasitoid wasps. Phylogenomic analysis suggests that EbrENV-β is the known closest relative of bracoviruses. Synteny analyses show the order of core genes is not well conserved between EbrENV-β and nudiviruses, revealing the dynamic nature of the evolution of nudivirus genome structures. Our findings narrow down the evolutionary gap between bracoviruses and nudiviruses and provide novel insights into the origin and evolution of polydnaviruses.
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Affiliation(s)
- Yu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Jianhua Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.
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Michaud C, Hervé V, Dupont S, Dubreuil G, Bézier AM, Meunier J, Brune A, Dedeine F. Efficient but occasionally imperfect vertical transmission of gut mutualistic protists in a wood‐feeding termite. Mol Ecol 2019; 29:308-324. [DOI: 10.1111/mec.15322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Caroline Michaud
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS – Université de Tours Tours France
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis Max Planck Institute for Terrestrial Microbiology Marburg Germany
| | - Simon Dupont
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS – Université de Tours Tours France
| | - Géraldine Dubreuil
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS – Université de Tours Tours France
| | - Annie M. Bézier
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS – Université de Tours Tours France
| | - Joël Meunier
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS – Université de Tours Tours France
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis Max Planck Institute for Terrestrial Microbiology Marburg Germany
| | - Franck Dedeine
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS – Université de Tours Tours France
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49
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Lorenzi A, Ravallec M, Eychenne M, Jouan V, Robin S, Darboux I, Legeai F, Gosselin-Grenet AS, Sicard M, Stoltz D, Volkoff AN. RNA interference identifies domesticated viral genes involved in assembly and trafficking of virus-derived particles in ichneumonid wasps. PLoS Pathog 2019; 15:e1008210. [PMID: 31834912 PMCID: PMC6957214 DOI: 10.1371/journal.ppat.1008210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/13/2020] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
There are many documented examples of viral genes retained in the genomes of multicellular organisms that may in some cases bring new beneficial functions to the receivers. The ability of certain ichneumonid parasitic wasps to produce virus-derived particles, the so-called ichnoviruses (IVs), not only results from the capture and domestication of single viral genes but of almost entire ancestral virus genome(s). Indeed, following integration into wasp chromosomal DNA, the putative and still undetermined IV ancestor(s) evolved into encoding a ‘virulence gene delivery vehicle’ that is now required for successful infestation of wasp hosts. Several putative viral genes, which are clustered in distinct regions of wasp genomes referred to as IVSPERs (Ichnovirus Structural Protein Encoding Regions), have been assumed to be involved in virus-derived particles morphogenesis, but this question has not been previously functionally addressed. In the present study, we have successfully combined RNA interference and transmission electron microscopy to specifically identify IVSPER genes that are responsible for the morphogenesis and trafficking of the virus-derived particles in ovarian cells of the ichneumonid wasp Hyposoter didymator. We suggest that ancestral viral genes retained within the genomes of certain ichneumonid parasitoids possess conserved functions which were domesticated for the purpose of assembling viral vectors for the delivery of virulence genes to parasitized host animals. Thousands of parasitic wasp from the ichneumonid family rely on virus-derived particles, named Ichnoviruses (Polydnavirus family), to ensure their successful development. The particles are produced in a specialized ovarian tissue of the female wasp named calyx. Virions are assembled in the calyx cell nuclei and stored in the oviduct before being transferred to the parasitoid host upon female wasp oviposition. Genes encoding proteins associated with the particles had been previously identified. These genes are localized in clusters of genes in the wasp genome (named IVSPER for “Ichnovirus structural proteins encoding regions”), they are specifically transcribed in the calyx but not encapsidated. IVSPER genes were thus hypothesized to derive from the integration of a virus, however still undetermined. Indeed, none of the identified genes had similarity to known sequence, making in addition unclear their function in particle production. In this work, we use the RNA interference technology to decipher the function of six IVSPER genes from the ichneumonid wasp Hyposoter didymator. Thanks to this approach, combined with transmission electron microscopy, we show that the studied IVSPER genes are required in different steps of particle morphogenesis and trafficking, and that their functions are those expected of a typical virus.
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Affiliation(s)
- Ange Lorenzi
- DGIMI, INRA, University of Montpellier, Montpellier, France
| | - Marc Ravallec
- DGIMI, INRA, University of Montpellier, Montpellier, France
| | | | | | - Stéphanie Robin
- UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, Rennes, France
| | | | - Fabrice Legeai
- UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, Rennes, France
| | | | - Mathieu Sicard
- ISEM, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Don Stoltz
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
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50
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Shi M, Wang Z, Ye X, Xie H, Li F, Hu X, Wang Z, Yin C, Zhou Y, Gu Q, Zou J, Zhan L, Yao Y, Yang J, Wei S, Hu R, Guo D, Zhu J, Wang Y, Huang J, Pennacchio F, Strand MR, Chen X. The genomes of two parasitic wasps that parasitize the diamondback moth. BMC Genomics 2019; 20:893. [PMID: 31752718 PMCID: PMC6873472 DOI: 10.1186/s12864-019-6266-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 11/05/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Parasitic insects are well-known biological control agents for arthropod pests worldwide. They are capable of regulating their host's physiology, development and behaviour. However, many of the molecular mechanisms involved in host-parasitoid interaction remain unknown. RESULTS We sequenced the genomes of two parasitic wasps (Cotesia vestalis, and Diadromus collaris) that parasitize the diamondback moth Plutella xylostella using Illumina and Pacbio sequencing platforms. Genome assembly using SOAPdenovo produced a 178 Mb draft genome for C. vestalis and a 399 Mb draft genome for D. collaris. A total set that contained 11,278 and 15,328 protein-coding genes for C. vestalis and D. collaris, respectively, were predicted using evidence (homology-based and transcriptome-based) and de novo prediction methodology. Phylogenetic analysis showed that the braconid C. vestalis and the ichneumonid D. collaris diverged approximately 124 million years ago. These two wasps exhibit gene gains and losses that in some cases reflect their shared life history as parasitic wasps and in other cases are unique to particular species. Gene families with functions in development, nutrient acquisition from hosts, and metabolism have expanded in each wasp species, while genes required for biosynthesis of some amino acids and steroids have been lost, since these nutrients can be directly obtained from the host. Both wasp species encode a relative higher number of neprilysins (NEPs) thus far reported in arthropod genomes while several genes encoding immune-related proteins and detoxification enzymes were lost in both wasp genomes. CONCLUSIONS We present the annotated genome sequence of two parasitic wasps C. vestalis and D. collaris, which parasitize a common host, the diamondback moth, P. xylostella. These data will provide a fundamental source for studying the mechanism of host control and will be used in parasitoid comparative genomics to study the origin and diversification of the parasitic lifestyle.
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Affiliation(s)
- Min Shi
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Zhizhi Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Xiqian Ye
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
| | | | - Fei Li
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoxiao Hu
- BGI-Tech, BGI-Shenzhen, Shenzhen, 518083, China
- Xingzhi College, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Zehua Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Chuanlin Yin
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Yuenan Zhou
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Qijuan Gu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Jiani Zou
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Leqing Zhan
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Yuan Yao
- School of Physical Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Jian Yang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Shujun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Rongmin Hu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Dianhao Guo
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Jiangyan Zhu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
| | - Yanping Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
| | - Jianhua Huang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China.
| | - Francesco Pennacchio
- Dipartimento di Agraria, Laboratorio di Entomologia "E. Tremblay", Università di Napoli "Federico II", Via Università 100, 80055, Portici, NA, Italy
| | - Michael R Strand
- Department of Entomology, University of Georgia, Athens, GA, 30602, USA
| | - Xuexin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China.
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China.
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