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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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2
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Identification and analysis of putative tRNA genes in baculovirus genomes. Virus Res 2022; 322:198949. [PMID: 36181979 DOI: 10.1016/j.virusres.2022.198949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022]
Abstract
Transfer RNAs (tRNAs) genes are both coded for and arranged along some viral genomes representing the entire virosphere and seem to play different biological functions during infection, other than transferring the correct amino acid to a growing peptide chain. Baculovirus genome description and annotation has focused mostly on protein-coding genes, microRNA, and homologous regions. Here we carried out a large-scale in silico search for putative tRNA genes in baculovirus genomes. Ninety-six of 257 baculovirus genomes analyzed was found to contain at least one putative tRNA gene. We found great diversity in primary and secondary structure, in location within the genome, in intron presence and size, and in anti-codon identity. In some cases, genes of tRNA-containing genomes were found to have a bias for the codons specified by the tRNAs present in such genomes. Moreover, analysis revealed that most of the putative tRNA genes possessed conserved motifs for tRNA type 2 promoters, including the A-box and B-box motifs with few mismatches from the eukaryotic canonical motifs. From publicly available small RNA deep sequencing datasets of baculovirus-infected insect cells, we found evidence that a putative Autographa californica multiple nucleopolyhedrovirus Gln-tRNA gene was transcribed and modified with the addition of the non-templated 3'-CCA tail found at the end of all tRNAs. Further research is needed to determine the expression and functionality of these viral tRNAs.
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3
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Genome analysis of Psilogramma increta granulovirus and its intrapopulation diversity. Virus Res 2022; 322:198946. [PMID: 36179968 DOI: 10.1016/j.virusres.2022.198946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022]
Abstract
The complete genome of Psilogramma increta granulovirus (PsinGV), isolated from P. increta (Lepidoptera: Sphingidae), was ultra-deep sequenced with a Novaseq PE150 platform and de novo assembled and annotated. The PsinGV genome is a circular double-stranded DNA, 103,721 bp in length, with a G+C content of 33.0%, the third lowest G+C content in present sequenced baculoviruses. It encodes 123 putative open reading frames, including 38 baculovirus core genes, 42 lepidopteran baculovirus conserved genes, 38 betabaculovirus conserved genes, and 5 genes unique to PsinGV. Meanwhile, 3 homologous repeated regions with the core sequence TTGCAA and 3 direct repeated sequences were identified within the PsinGV genome. Kimura two-parameters distance analysis confirmed that Psilogramma increta granulovirus is a representative of a prospective new species of the genus Betabaculovirus. Phylogenetic analysis based on the baculovirus core genes showed that PsinGV is closely related to Choristoneura fumiferana granulovirus, Clostera anastomosis granulovirus-B, and Erinnyis ello granulovirus. These four species therefore share a common ancestor residing in the Betabaculovirus genus. The genome of the PsinGV isolate contained two p10 copies: p10 and p10-2. Phylogenetic reconstruction of P10 suggests a transfer event of the p10-2 gene from an alphabaculovirus to the aforementioned common ancestor. Analysis of genomic diversity showed that 203 intrahost variants, including 182 single nucleotide variants and 21 short insertions/deletions, are present within the PsinGV isolate. Meanwhile, allele frequency indicated that the isolate contains three major genotypes, implying the archived isolate consists of several P. increta carcasses killed by PsinGV with different genotypes.
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Muller H, Heisserer C, Fortuna T, Mougel F, Huguet E, Kaiser L, Gilbert C. Investigating bracovirus chromosomal integration and inheritance in lepidopteran host and nontarget species. Mol Ecol 2022; 31:5538-5551. [PMID: 36070218 DOI: 10.1111/mec.16685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 12/24/2022]
Abstract
Bracoviruses (BVs) are domesticated viruses found in braconid parasitoid wasp genomes. They are composed of domesticated genes from a nudivrius, coding viral particles in which wasp DNA circles are packaged. BVs are viewed as possible vectors of horizontal transfer of genetic material (HT) from wasp to their hosts because they are injected, together with wasp eggs, by female wasps into their host larvae, and because they undergo massive chromosomal integration in multiple host tissues. Here, we show that chromosomal integrations of the Cotesia typhae BV (CtBV) persist up to the adult stage in individuals of its natural host, Sesamia nonagrioides, that survived parasitism. However, while reproducing host adults can bear an average of nearly two CtBV integrations per haploid genome, we were unable to retrieve any of these integrations in 500 of their offspring using Illumina sequencing. This suggests either that host gametes are less targeted by CtBVs than somatic cells or that gametes bearing BV integrations are nonfunctional. We further show that CtBV can massively integrate into the chromosomes of other lepidopteran species that are not normally targeted by the wasp in the wild, including one which is divergent by at least 100 million years from the natural host. Cell entry and chromosomal integration of BVs are thus unlikely to be major factors shaping wasp host range. Together, our results shed new light on the conditions under which BV-mediated wasp-to-host HT may occur and provide information that may be helpful to evaluate the potential risks of uncontrolled HT associated with the use of parasitoid wasps as biocontrol agents.
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Affiliation(s)
- Héloïse Muller
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Camille Heisserer
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France.,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
| | - Florence Mougel
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, 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
| | - Laure Kaiser
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
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5
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Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
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6
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Zhang X, Zhang F, Lu X. Diversity and Functional Roles of the Gut Microbiota in Lepidopteran Insects. Microorganisms 2022; 10:microorganisms10061234. [PMID: 35744751 PMCID: PMC9231115 DOI: 10.3390/microorganisms10061234] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023] Open
Abstract
Lepidopteran insects are one of the most widespread and speciose lineages on Earth, with many common pests and beneficial insect species. The evolutionary success of their diversification depends on the essential functions of gut microorganisms. This diverse gut microbiota of lepidopteran insects provides benefits in nutrition and reproductive regulation and plays an important role in the defence against pathogens, enhancing host immune homeostasis. In addition, gut symbionts have shown promising applications in the development of novel tools for biological control, biodegradation of waste, and blocking the transmission of insect-borne diseases. Even though most microbial symbionts are unculturable, the rapidly expanding catalogue of microbial genomes and the application of modern genetic techniques offer a viable alternative for studying these microbes. Here, we discuss the gut structure and microbial diversity of lepidopteran insects, as well as advances in the understanding of symbiotic relationships and interactions between hosts and symbionts. Furthermore, we provide an overview of the function of the gut microbiota, including in host nutrition and metabolism, immune defence, and potential mechanisms of detoxification. Due to the relevance of lepidopteran pests in agricultural production, it can be expected that the research on the interactions between lepidopteran insects and their gut microbiota will be used for biological pest control and protection of beneficial insects in the future.
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Affiliation(s)
- Xiancui Zhang
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310029, China;
| | - Fan Zhang
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China
- Correspondence: (F.Z.); (X.L.)
| | - Xingmeng Lu
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310029, China;
- Correspondence: (F.Z.); (X.L.)
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7
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Gasmi L, Sieminska E, Okuno S, Ohta R, Coutu C, Vatanparast M, Harris S, Baldwin D, Hegedus DD, Theilmann DA, Kida A, Kawabata M, Sagawa S, Takatsuka J, Tateishi K, Watanabe K, Inoue MN, Kunimi Y, Kim Y, Erlandson MA, Herrero S, Nakai M. Horizontally transmitted parasitoid killing factor shapes insect defense to parasitoids. Science 2021; 373:535-541. [PMID: 34326235 DOI: 10.1126/science.abb6396] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 12/19/2020] [Accepted: 06/17/2021] [Indexed: 01/02/2023]
Abstract
Interkingdom competition occurs between hymenopteran parasitoids and insect viruses sharing the same insect hosts. It has been assumed that parasitoid larvae die with the death of the infected host or as result of competition for host resources. Here we describe a gene family, parasitoid killing factor (pkf), that encodes proteins toxic to parasitoids of the Microgastrinae group and determines parasitism success. Pkfs are found in several entomopathogenic DNA virus families and in some lepidopteran genomes. We provide evidence of equivalent and specific toxicity against endoparasites for PKFs found in entomopoxvirus, ascovirus, baculovirus, and Lepidoptera through a mechanism that elicits apoptosis in the cells of susceptible parasitoids. This highlights the evolutionary arms race between parasitoids, viruses, and their insect hosts.
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Affiliation(s)
- Laila Gasmi
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.,Department of Genetics and Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, Burjassot, 46100 Valencia, Spain
| | - Edyta Sieminska
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Shohei Okuno
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.,Arysta Life Science Corporation, Tsukuba, Ibaraki 305-0832, Japan
| | - Rie Ohta
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | | | - Stephanie Harris
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Doug Baldwin
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - David A Theilmann
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, 4200 Highway #97 South, Summerland, BC V0H 1Z0, Canada
| | - Aki Kida
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.,Kumiai Chemical Industry Co., Ltd., Taitou, Tokyo 110-8782, Japan
| | - Mio Kawabata
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Shiori Sagawa
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Jun Takatsuka
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Ken Tateishi
- National Agriculture and Food Research Organization, Kannondai 3-1-1, Tsukuba, Ibaraki 305-8517, Japan
| | - Kazuyo Watanabe
- National Agriculture and Food Research Organization, Kannondai 3-1-1, Tsukuba, Ibaraki 305-8517, Japan
| | - Maki N Inoue
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yasuhisa Kunimi
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yonggyun Kim
- Department of Plant Medicals, Andong National University, Andong 36729, Korea
| | - Martin A Erlandson
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada. .,Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Salvador Herrero
- Department of Genetics and Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, Burjassot, 46100 Valencia, Spain.
| | - Madoka Nakai
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
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Arai T, Yamauchi A, Miura A, Kondo H, Nishimiya Y, Sasaki YC, Tsuda S. Discovery of Hyperactive Antifreeze Protein from Phylogenetically Distant Beetles Questions Its Evolutionary Origin. Int J Mol Sci 2021; 22:3637. [PMID: 33807342 PMCID: PMC8038014 DOI: 10.3390/ijms22073637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022] Open
Abstract
Beetle hyperactive antifreeze protein (AFP) has a unique ability to maintain a supercooling state of its body fluids, however, less is known about its origination. Here, we found that a popular stag beetle Dorcus hopei binodulosus (Dhb) synthesizes at least 6 isoforms of hyperactive AFP (DhbAFP). Cold-acclimated Dhb larvae tolerated -5 °C chilled storage for 24 h and fully recovered after warming, suggesting that DhbAFP facilitates overwintering of this beetle. A DhbAFP isoform (~10 kDa) appeared to consist of 6-8 tandem repeats of a 12-residue consensus sequence (TCTxSxNCxxAx), which exhibited 3 °C of high freezing point depression and the ability of binding to an entire surface of a single ice crystal. Significantly, these properties as well as DNA sequences including the untranslated region, signal peptide region, and an AFP-encoding region of Dhb are highly similar to those identified for a known hyperactive AFP (TmAFP) from the beetle Tenebrio molitor (Tm). Progenitor of Dhb and Tm was branched off approximately 300 million years ago, so no known evolution mechanism hardly explains the retainment of the DNA sequence for such a lo-ng divergence period. Existence of unrevealed gene transfer mechanism will be hypothesized between these two phylogenetically distant beetles to acquire this type of hyperactive AFP.
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Affiliation(s)
- Tatsuya Arai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan; (T.A.); (A.M.); (H.K.); (Y.N.)
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan;
| | - Akari Yamauchi
- Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan;
| | - Ai Miura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan; (T.A.); (A.M.); (H.K.); (Y.N.)
| | - Hidemasa Kondo
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan; (T.A.); (A.M.); (H.K.); (Y.N.)
- Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan;
| | - Yoshiyuki Nishimiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan; (T.A.); (A.M.); (H.K.); (Y.N.)
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan;
- OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8563, Japan
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan; (T.A.); (A.M.); (H.K.); (Y.N.)
- Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan;
- OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8563, Japan
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9
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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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10
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Wang CF, Sun W, Zhang Z. Functional characterization of the horizontally transferred 4,5-DOPA extradiol dioxygenase gene in the domestic silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2019; 28:409-419. [PMID: 30537278 DOI: 10.1111/imb.12558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
4,5-DOPA dioxygenase (DODA) is a crucial enzyme in the biosynthetic pathway of betalain. Previous studies have shown that DODA is present in plants, fungi and bacteria. Using updated data, here we show that DODA genes (BmDODA) in the domestic silkworm (Bombyx mori) and other lepidopteran insects are most likely to be horizontally transferred from fungi. A synteny analysis indicated that BmDODA1 is orthologous to other lepidopteran DODAs and that BmDODA2 is a paralogous gene. To explore the function of DODA in Lepidoptera, we first examined the expression patterns of BmDODA1. BmDODA1 showed high transcriptional and translational levels in the midgut and head. Then, we exogenously expressed the BmDODA1 gene, detected 4,5-DOPA ring-cleaving activity and calculated the kinetic parameters of the recombinant BmDODA1. We found that the transcription levels of BmDODA1 were significantly induced by the pathogens Bacillus bombyseptieus and Escherichia coli. Thus, the horizontal transfer of the BmDODA gene in the silkworm may be involved in dopa metabolism and contribute to antimicrobial activity in this species. Our results provide a documented example of functional horizontal gene transfer (HGT) between fungi and animals and expand our knowledge of HGT amongst eukaryotes.
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Affiliation(s)
- C-F Wang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - W Sun
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Z Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
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11
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Wu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes (Basel) 2019; 10:genes10050338. [PMID: 31064091 PMCID: PMC6562904 DOI: 10.3390/genes10050338] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/09/2019] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss.
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Affiliation(s)
- Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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Mason CJ, Jones AG, Felton GW. Co-option of microbial associates by insects and their impact on plant-folivore interactions. PLANT, CELL & ENVIRONMENT 2019; 42:1078-1086. [PMID: 30151965 DOI: 10.1111/pce.13430] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 05/28/2023]
Abstract
Plants possess a suite of traits that make them challenging to consume by insect herbivores. Plant tissues are recalcitrant, have low levels of protein, and may be well defended by chemicals. Insects use diverse strategies for overcoming these barriers, including co-opting metabolic activities from microbial associates. In this review, we discuss the co-option of bacteria and fungi in the herbivore gut. We particularly focus upon chewing, folivorous insects (Coleoptera and Lepidoptera) and discuss the impacts of microbial co-option on herbivore performance and plant responses. We suggest that there are two components to microbial co-option: fixed and plastic relationships. Fixed relationships are involved in integral dietary functions and can be performed by microbial enzymes co-opted into the genome or by stably transferred associates. In contrast, the majority of gut symbionts appear to be looser and perform more facultative, context-dependent functions. This more plastic, variable co-option of bacteria likely produces a greater number of insect phenotypes, which interact differently with plant hosts. By altering plant detection of herbivory or mediating insect interactions with plant defensive compounds, microbes can effectively improve herbivore performance in real time within and between generations.
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Affiliation(s)
- Charles J Mason
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania
| | - Asher G Jones
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania
| | - Gary W Felton
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania
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Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot. PLoS Genet 2019; 15:e1007965. [PMID: 30707693 PMCID: PMC6373975 DOI: 10.1371/journal.pgen.1007965] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/13/2019] [Accepted: 01/16/2019] [Indexed: 12/24/2022] Open
Abstract
More than any other genome components, Transposable Elements (TEs) have the capacity to move across species barriers through Horizontal Transfer (HT), with substantial evolutionary consequences. Previous large-scale surveys, based on full-genomes comparisons, have revealed the transposition mode as an important predictor of HT rates variation across TE superfamilies. However, host biology could represent another major explanatory factor, one that needs to be investigated through extensive taxonomic sampling. Here we test this hypothesis using a field collection of 460 arthropod species from Tahiti and surrounding islands. Through targeted massive parallel sequencing, we uncover patterns of HT in three widely-distributed TE superfamilies with contrasted modes of transposition. In line with earlier findings, the DNA transposons under study (TC1-Mariner) were found to transfer horizontally at the highest frequency, closely followed by the LTR superfamily (Copia), in contrast with the non-LTR superfamily (Jockey), that mostly diversifies through vertical inheritance and persists longer within genomes. Strikingly, across all superfamilies, we observe a marked excess of HTs in Lepidoptera, an insect order that also commonly hosts baculoviruses, known for their ability to transport host TEs. These results turn the spotlight on baculoviruses as major potential vectors of TEs in arthropods, and further emphasize the importance of non-vertical TE inheritance in genome evolution. Transposable elements are chunks of DNA that can produce copies of themselves. New copies usually insert in the genome of their carrier but are occasionally subject to horizontal transmission between organisms, sometimes belonging to evolutionarily-distant lineages. Previous surveys have established that the probability of such events is largely conditioned by the transposition mechanism. For example, elements with an RNA intermediate tend to be less frequently involved in horizontal transfers. Here we investigate host taxa as another potential explanatory factor of variation in horizontal transfer rates. Using targeted sequencing in hundreds of insects and other arthropod species collected in South Pacific islands, we found that butterflies and moths (Lepidoptera) show an abnormally elevated rate of horizontal transfers. Previous studies have established that Lepidoptera are also commonly attacked by baculoviruses, large viruses that can transport host DNA. Taken together, these findings point to baculoviruses as a major suspect for transposable elements transfers across arthropod species.
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Chevignon G, Periquet G, Gyapay G, Vega-Czarny N, Musset K, Drezen JM, Huguet E. Cotesia congregata Bracovirus Circles Encoding PTP and Ankyrin Genes Integrate into the DNA of Parasitized Manduca sexta Hemocytes. J Virol 2018; 92:e00438-18. [PMID: 29769342 PMCID: PMC6052314 DOI: 10.1128/jvi.00438-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/04/2018] [Indexed: 12/21/2022] Open
Abstract
Polydnaviruses (PDVs) are essential for the parasitism success of tens of thousands of species of parasitoid wasps. PDVs are present in wasp genomes as proviruses, which serve as the template for the production of double-stranded circular viral DNA carrying virulence genes that are injected into lepidopteran hosts. PDV circles do not contain genes coding for particle production, thereby impeding viral replication in caterpillar hosts during parasitism. Here, we investigated the fate of PDV circles of Cotesia congregata bracovirus during parasitism of the tobacco hornworm, Manduca sexta, by the wasp Cotesia congregata Sequences sharing similarities with host integration motifs (HIMs) of Microplitis demolitor bracovirus (MdBV) circles involved in integration into DNA could be identified in 12 CcBV circles, which encode PTP and VANK gene families involved in host immune disruption. A PCR approach performed on a subset of these circles indicated that they persisted in parasitized M. sexta hemocytes as linear forms, possibly integrated in host DNA. Furthermore, by using a primer extension capture method based on these HIMs and high-throughput sequencing, we could show that 8 out of 9 circles tested were integrated in M. sexta hemocyte genomic DNA and that integration had occurred specifically using the HIM, indicating that an HIM-mediated specific mechanism was involved in their integration. Investigation of BV circle insertion sites at the genome scale revealed that certain genomic regions appeared to be enriched in BV insertions, but no specific M. sexta target site could be identified.IMPORTANCE The identification of a specific and efficient integration mechanism shared by several bracovirus species opens the question of its role in braconid parasitoid wasp parasitism success. Indeed, results obtained here show massive integration of bracovirus DNA in somatic immune cells at each parasitism event of a caterpillar host. Given that bracoviruses do not replicate in infected cells, integration of viral sequences in host DNA might allow the production of PTP and VANK virulence proteins within newly dividing cells of caterpillar hosts that continue to develop during parasitism. Furthermore, this integration process could serve as a basis to understand how PDVs mediate the recently identified gene flux between parasitoid wasps and Lepidoptera and the frequency of these horizontal transfer events in nature.
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Affiliation(s)
- Germain Chevignon
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université de Tours, Tours, France
| | - Georges Periquet
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université de Tours, Tours, France
| | - Gabor Gyapay
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope (Centre National de Séquençage), Evry, France
| | - Nathalie Vega-Czarny
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope (Centre National de Séquençage), Evry, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université de Tours, Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université de Tours, Tours, France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université de Tours, Tours, France
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Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Curr Opin Genet Dev 2018; 49:15-24. [PMID: 29505963 DOI: 10.1016/j.gde.2018.02.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/30/2022]
Abstract
It is becoming clear that most eukaryotic transposable elements (TEs) owe their evolutionary success in part to horizontal transfer events, which enable them to invade new species. Recent large-scale studies are beginning to unravel the mechanisms and ecological factors underlying this mode of transmission. Viruses are increasingly recognized as vectors in the process but also as a direct source of genetic material horizontally acquired by eukaryotic organisms. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, we argue that horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated. To support this proposal, we compile a list of examples, including some previously unrecognized, whereby new host functions and phenotypes can be directly attributed to horizontally acquired TE or viral sequences. We predict that the number of examples will rapidly grow in the future as the prevalence of horizontal transfer in the life cycle of TEs becomes even more apparent, firmly establishing this form of non-Mendelian inheritance as a consequential facet of eukaryotic evolution.
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