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Divekar G, Colmant AMG, Furlong MJ, Etebari K. Transcriptome Analysis Reveals a Diverse Range of Novel Viruses in Australian Sugarcane Soldier Fly ( Inopus flavus) Larvae. Viruses 2024; 16:516. [PMID: 38675859 PMCID: PMC11054854 DOI: 10.3390/v16040516] [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: 03/11/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
In Australia, Soldier flies (Inopus spp.) are economically significant pests of sugarcane that currently lack a viable management strategy. Despite various research efforts, the mechanisms underlying the damage caused by soldier fly larvae remain poorly understood. Our study aims to explore whether this damage is associated with the transmission of plant viruses during larval feeding. We also explore the larval transcriptome to identify any entomopathogenic viruses with the potential to be used as biocontrol agents in future pest management programs. Seven novel virus sequences are identified and characterised using de novo assembly of RNA-Seq data obtained from salivary glands of larvae. The novel virus sequences belong to different virus families and are tentatively named SF-associated anphevirus (SFaAV), SF-associated orthomyxo-like virus (SFaOV), SF-associated narna-like virus (SFaNV), SF-associated partiti-like virus (SFaPV), SF-associated toti-like virus (SFaTV-1 and SFaTV-2) and SF-associated densovirus (SFaDV). These newly identified viruses are more likely insect-associated viruses, as phylogenetic analyses show that they cluster with other insect-specific viruses. Small RNA analysis indicates prominent peaks at both 21 nt and 26-29 nt, suggesting the activation of host siRNA and piwiRNA pathways. Our study helps to improve understanding of the virome of soldier flies and could identify insect viruses for deployment in novel pest management strategies.
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Affiliation(s)
- Gayatri Divekar
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton 4343, Australia
| | - Agathe M. G. Colmant
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), 13005 Marseille, France
| | - Michael J. Furlong
- School of the Environment, The University of Queensland, Brisbane 4072, Australia
| | - Kayvan Etebari
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton 4343, Australia
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Santos D, Feng M, Kolliopoulou A, Taning CNT, Sun J, Swevers L. What Are the Functional Roles of Piwi Proteins and piRNAs in Insects? INSECTS 2023; 14:insects14020187. [PMID: 36835756 PMCID: PMC9962485 DOI: 10.3390/insects14020187] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 06/01/2023]
Abstract
Research on Piwi proteins and piRNAs in insects has focused on three experimental models: oogenesis and spermatogenesis in Drosophila melanogaster, the antiviral response in Aedes mosquitoes and the molecular analysis of primary and secondary piRNA biogenesis in Bombyx mori-derived BmN4 cells. Significant unique and complementary information has been acquired and has led to a greater appreciation of the complexity of piRNA biogenesis and Piwi protein function. Studies performed in other insect species are emerging and promise to add to the current state of the art on the roles of piRNAs and Piwi proteins. Although the primary role of the piRNA pathway is genome defense against transposons, particularly in the germline, recent findings also indicate an expansion of its functions. In this review, an extensive overview is presented of the knowledge of the piRNA pathway that so far has accumulated in insects. Following a presentation of the three major models, data from other insects were also discussed. Finally, the mechanisms for the expansion of the function of the piRNA pathway from transposon control to gene regulation were considered.
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Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, 15341 Athens, Greece
| | - Clauvis N. T. Taning
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, 15341 Athens, Greece
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Complete genome analysis of a novel iflavirus from the spotted lanternfly Lycorma delicatula. Arch Virol 2022; 167:2079-2083. [PMID: 35751691 DOI: 10.1007/s00705-022-05503-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/23/2022] [Indexed: 11/02/2022]
Abstract
The spotted lanternfly (Lycorma delicatula) is an invasive pest that causes serious economic losses in fruit and wood production. Here, we identified a novel iflavirus named "Lycorma delicatula iflavirus 1" (LDIV1), in a spotted lanternfly. The full genome sequence of LDIV1 is 10,222 nt in length and encodes a polyprotein containing a picornavirus capsid-protein-domain-like domain, a cricket paralysis virus capsid superfamily domain, an RNA helicase domain, a peptidase C3 superfamily domain, and an RNA-dependent RNA polymerase (RdRp) domain. LDIV1 replicates in the host insect and activates small interfering RNA (siRNA)-based host antiviral immunity. Phylogenetic analysis demonstrated that LDIV1 is most closely related to an unspecified member of the order Picornavirales, with 61.7% sequence identity in the RdRp region and 57.6% sequence identity in the coat protein region, and thus meets the demarcation criteria for new species in the genus Iflavirus. To the best of our knowledge, LDIV1 is the first virus discovered in L. delicatula.
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Carlson CR, ter Horst AM, Johnston JS, Henry E, Falk BW, Kuo YW. High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations. DNA Res 2022; 29:6648404. [PMID: 35866687 PMCID: PMC9338690 DOI: 10.1093/dnares/dsac027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
The Asian citrus psyllid, Diaphorina citri, is the insect vector of the causal agent of huanglongbing (HLB), a devastating bacterial disease of commercial citrus. Presently, few genomic resources exist for D. citri. In this study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C) sequencing to sequence, assemble, and compare three high-quality, chromosome-scale genome assemblies of D. citri collected from California, Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into 13 pseudomolecules—a reduction in assembly size of 41–45% compared with previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and annotated each assembly for repetitive elements, protein-coding genes, transfer RNAs, ribosomal RNAs, piwi-interacting RNA clusters, and endogenous viral elements. Between 19,083 and 20,357 protein-coding genes were predicted. Repetitive DNA accounts for 36.87–38.26% of each assembly. Comparative analyses and mitochondrial haplotype networks suggest that Taiwan and Uruguay D. citri are more closely related, while California D. citri are closely related to Florida D. citri. These high-quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.
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Affiliation(s)
- Curtis R Carlson
- Department of Plant Pathology, University of California Davis , Davis, CA 95616, USA
| | - Anneliek M ter Horst
- Department of Plant Pathology, University of California Davis , Davis, CA 95616, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University , College Station, TX 77843, USA
| | - Elizabeth Henry
- Department of Plant Pathology, University of California Davis , Davis, CA 95616, USA
| | - Bryce W Falk
- Department of Plant Pathology, University of California Davis , Davis, CA 95616, USA
| | - Yen-Wen Kuo
- Department of Plant Pathology, University of California Davis , Davis, CA 95616, USA
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Cerqueira de Araujo A, Huguet E, Herniou EA, Drezen JM, Josse T. Transposable element repression using piRNAs, and its relevance to endogenous viral elements (EVEs) and immunity in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100876. [PMID: 35065285 DOI: 10.1016/j.cois.2022.100876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
The piRNA system controls transposable element (TE) mobility by transcriptional gene silencing and post-transcriptional gene silencing. Dispersed in insect genomes, piRNA clusters contain TE copies, from which they produce piRNAs (specific small RNAs). These piRNAs can both target the nascent transcripts produced by active TE copies and directly repress them by heterochromatinization. They can also target mature transcripts and cleave them following amplification by the so-called 'ping-pong' loop mechanism. Moreover, piRNA clusters contain endogenous viral elements (EVEs), from which they produce piRNAs. The current idea is that these piRNAs could participate in the antiviral response against exogenous viral infection. In this review, we show that among insects, to date, this antiviral response by the piRNA system appears mainly restricted to mosquitoes, but this could be due to the focus of most studies on arboviruses.
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Affiliation(s)
- Alexandra Cerqueira de Araujo
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS - Université de Tours, 37200 Tours, France.
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He YJ, Ye ZX, Chen JP, Zhang CX, Lu G, Li JM. Complete genome analysis of a novel picorna-like virus from a ladybird beetle (Cheilomenes sexmaculata). Arch Virol 2022; 167:1215-1219. [PMID: 35257228 DOI: 10.1007/s00705-022-05400-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022]
Abstract
The ladybird beetle Cheilomenes sexmaculata (family Coccinellidae, order Coleoptera) is a common insect predator of agricultural pests. In this study, the full genome sequence of a novel picorna-like virus, tentatively named "Cheilomenes sexmaculata picorna-like virus 1" (CSPLV1), was identified in C. sexmaculata. The full-length sequence of CSPLV1 is 11,384 nucleotides (nt) in length (excluding the polyA tail), with one predicted open reading frame (ORF) encoding a polyprotein of 3727 amino acids, a 13-nt 5' untranslated region (UTR), and a 187-nt 3' UTR. The ORF of CSPLV1 consists of four distinct domains, including an RNA virus helicase domain (nt 3029-3319), a peptidase domain (nt 5555-6121), an RNA-dependent RNA polymerase domain (nt 7154-8101), and a picorna-like coat protein domain (nt 8606-9283). Phylogenetic analysis based on the conserved RdRP sequence showed that CSPLV1, together with Wuhan house centipede virus 3, Hypera postica associated virus 1, and Diabrotica undecimpunctata virus 1, forms an unclassified group that is closely related to members of the family Solinviviridae. To the best of our knowledge, CSPLV1 is the first picorna-like virus discovered in C. sexmaculata.
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Affiliation(s)
- Yu-Juan He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‑products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.,College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‑products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‑products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.,College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‑products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Gang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‑products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‑products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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Gilbert C, Belliardo C. The diversity of endogenous viral elements in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 49:48-55. [PMID: 34839030 DOI: 10.1016/j.cois.2021.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/02/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
We provide an overview of the currently known diversity of viral sequences integrated into insect genomes. Such endogenous viral elements (EVE) have so far been annotated in at least eight insect orders and can be assigned to at least three families of large double-stranded (ds) DNA viruses, at least 22 families of RNA viruses, and three families of single-stranded DNA viruses. The study of these EVE has already produced important insights into insect-virus interactions, including the discovery of a new form of adaptive antiviral immunity. Insect EVE diversity will continue to increase as new insect genomes and exogenous viruses are sequenced, which will continue to make paleovirology a vibrant research field in this group of animals in the years to come.
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Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, 91198, France.
| | - Carole Belliardo
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, 06903, France; MYCOPHYTO, 540 Avenue de la Plaine, Mougins, 06250, France
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Wang ZZ, Ye XQ, Huang JH, Chen XX. Virus and endogenous viral element-derived small non-coding RNAs and their roles in insect-virus interaction. CURRENT OPINION IN INSECT SCIENCE 2022; 49:85-92. [PMID: 34974161 DOI: 10.1016/j.cois.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
RNA interference pathways mediated by different types of small non-coding RNAs (siRNAs, miRNAs and piRNAs) are conserved biological responses to exotic stresses, including viral infection. Aside from the well-established siRNA pathway, the miRNA pathway and the piRNA pathway process viral sequences, exogenously or endogenously, into miRNAs and piRNAs, respectively. During the host-virus interaction, viral sequences, including both coding and non-coding sequences, can be integrated as endogenous viral elements (EVEs) and thereby become present within the germline of a non-viral organism. In recent years, significant progress has been made in characterizing the biogenesis and function of viruses and EVEs associated with snRNAs. Overall, the siRNA pathway acts as the primarily antiviral defense against a wide range of exogenous viruses; the miRNA pathways associated with viruses or EVEs function in antiviral response and host gene regulation; EVE derived piRNAs with a ping-pong signature have the potential to limit cognate viral infection.
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Affiliation(s)
- Zhi-Zhi 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; 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; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, 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; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Xue-Xin 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; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; State Key Lab of Rice Biology, Zhejiang University, Hangzhou 310058, China.
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