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Eroglu GB, Karimi J. Whole genome analysis of a novel Spodoptera exigua nucleopolyhedrovirus isolate (SeMNPV-IR) to Iran. Biologia (Bratisl) 2023; 78:1-12. [PMID: 37363644 PMCID: PMC10091331 DOI: 10.1007/s11756-023-01399-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/21/2023] [Indexed: 06/28/2023]
Abstract
Baculoviruses are successful microbial control agents used in the biological control of agricultural pest species, especially in the order Lepidoptera. The beet armyworm, Spodoptera exigua is a popular agricultural pest in the world. S exigua larvae, which are active in the all-summer period, cause economic losses by damaging many crops in agricultural production areas. This article aims to analyze the full genome of Spodoptera exigua multiple nucleopolyhedroviruses from Iran (SeMNPV-IR) and to determine the geographical difference between the strains at the genomic level. The full genome of SeMNPV-IR is 135.764 base pairs in length that contained 136 open reading frames (ORFs), and 43.92% G + C content. The seven homologous repeated (hr) regions were identified. In the results of genome-wide phylogenetic analysis, it was determined that the SeMNPV-IR genome isolated from Iran was interestingly close to the genome of the US and Korea isolates. However, there are significant differences in the two hypothetical (Orf 83 and Orf 104) genes. The SeMNPV-IR has a unique homolog repeat region (hr1, 96 bp) that is not found in other SeMNPV genomes, and it also differs in terms of the hr2 region. In silico restriction endonuclease analysis by StuI and SacII enzymes show that there were significant differences between all geographic isolates of SeMNPV. Supplementary Information The online version contains supplementary material available at 10.1007/s11756-023-01399-2.
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Affiliation(s)
- Gozde Busra Eroglu
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, 25200 Turkey
| | - Javad Karimi
- Department of Plant Protection, School of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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2
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El-Salamouny S, Wennmann JT, Kleespies RG, Richert-Pöggeler KR, Mansour A, Awad M, Agamy E, Salama R, Jehle JA. Identification of a new nucleopolyhedrovirus isolated from the olive leaf moth, Palpita vitrealis, from two locations in Egypt. J Invertebr Pathol 2022; 192:107770. [PMID: 35597278 DOI: 10.1016/j.jip.2022.107770] [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: 12/16/2021] [Revised: 05/11/2022] [Accepted: 05/15/2022] [Indexed: 11/25/2022]
Abstract
The olive leaf moth (jasmine moth), Palpita vitrealis (Lepidoptera: Crambidae), is an important insect pest of olives in several Mediterranean countries. A new alphabaculovirus was isolated from diseased larvae of P. vitrealis in Egypt, first in Giza in spring 2005 and again in Marsa Matrouh in 2019.The larvae exhibited typical symptoms of a baculovirus infection. Light and scanning electron microscopy studies revealed polyhedral occlusion bodies. Transmission electron microscopy of ultrathin sections of purified OBs revealed virions with multiple embedded nucleocapsids. The identity of the two virus isolates was confirmed by sequencing the partial polyhedrin and lef-8 genes, and sequence comparison suggested a relationship to group I alphabaculoviruses. Therefore, this virus was termed Palpita vitrealis nucleopolyhedrovirus (PaviNPV). Whole genome sequencing of the PaviNPV isolate from Giza (Gz05) revealed a genome of 117,533 bp, 131 open reading frames (ORFs) and three homologous repeat (hr) regions. Phylogenetic reconstruction and genetic distance analyses using 38 core genes indicated that PaviNPV is most closely related to Thysanoplusia orichalcea nucleopolyhedrovirus (ThorNPV) but should be considered to belong to a novel species within the genus Alphabaculovirus. In bioassays, PaviNPV was highly virulent against second-instar larvae of P. vitrealis. The study reports a novel baculovirus that might have potential as a biological control agent of the olive leaf moth.
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Affiliation(s)
- Said El-Salamouny
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt; Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Katja R Richert-Pöggeler
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Amany Mansour
- Department of Plant Protection Desert Research Center, Ministry of Agriculture, Matariya, 11753 Cairo, Egypt
| | - Mona Awad
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Essam Agamy
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ramadan Salama
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany.
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Peng X, Zhang W, Lei C, Min S, Hu J, Wang Q, Sun X. Genomic analysis of two Chinese isolates of hyphantria cunea nucleopolyhedrovirus reveals a novel species of alphabaculovirus that infects hyphantria cunea drury (lepidoptera: arctiidae). BMC Genomics 2022; 23:367. [PMID: 35562654 PMCID: PMC9107115 DOI: 10.1186/s12864-022-08604-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/05/2022] [Indexed: 11/22/2022] Open
Abstract
Background Baculoviruses act as effective biological control agents against the invasive pest Hyphantria cunea Drury. In this study, two Chinese Hyphantria cunea nucleopolyhedrovirus (HycuNPV) isolates, HycuNPV-BJ and HycuNPV-HB, were deep sequenced and compared with the Japanese isolate, HycuNPV-N9, to determine whole-genome level diversity and evolutionary history. Results The divergence of the phylogenetic tree and the K2P distances based on 38 core-gene concatenated alignment revealed that two Chinese HycuNPV isolates were a novel species of Alphabaculovirus that infected Hyphantria cunea in China. The gene contents indicated significant differences in the HycuNPV genomes between the Chinese and Japanese isolates. The differences included gene deletions, acquisitions and structural transversions, but the main difference was the high number of single nucleotide polymorphisms (SNPs). In total, 10,393 SNPs, corresponding to approximately 8% of the entire HycuNPV-N9 genome sequence, were detected in the aligned reads. By analyzing non-synonymous variants, we found that hotspot mutation-containing genes had mainly unknown functions and most were early expressing genes. We found that the hycu78 gene which had early and late promoter was under positive selection. Biological activity assays revealed that the infectivity of HycuNPV-HB was greater than that of HycuNPV-BJ, and the killing speed of HycuNPV-HB was faster than that of HycuNPV-BJ. A comparison of molecular genetic characteristics indicated that the virulence differences between the two isolates were affected by SNP and structural variants, especially the homologous repeat regions. Conclusions The genomes of the two Chinese HycuNPV isolates were characterized, they belonged to a novel species of Alphabaculovirus that infected Hyphantria cunea in China. We inferred that the loss or gain of genetic material in the HycuNPV-HB and HycuNPV-BJ genomes resulted in new important adaptive capabilities to the H. cunea host. These results extend the current understanding of the genetic diversity of HycuNPV and will be useful for improving the applicability of this virus as a biological control agent. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08604-7.
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Affiliation(s)
- Xiaowei Peng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenying Zhang
- Hubei Ecology Polytechnic College, Wuhan, 430200, Hubei, China
| | - Chengfeng Lei
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Shuifa Min
- Hubei Ecology Polytechnic College, Wuhan, 430200, Hubei, China
| | - Jia Hu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Qinghua Wang
- Institute of Forestry Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Haidian, Beijing, 100091, China.
| | - Xiulian Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
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Williams T, López-Ferber M, Caballero P. Nucleopolyhedrovirus Coocclusion Technology: A New Concept in the Development of Biological Insecticides. Front Microbiol 2022; 12:810026. [PMID: 35145496 PMCID: PMC8822060 DOI: 10.3389/fmicb.2021.810026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023] Open
Abstract
Nucleopolyhedroviruses (NPV, Baculoviridae) that infect lepidopteran pests have an established record as safe and effective biological insecticides. Here, we describe a new approach for the development of NPV-based insecticides. This technology takes advantage of the unique way in which these viruses are transmitted as collective infectious units, and the genotypic diversity present in natural virus populations. A ten-step procedure is described involving genotypic variant selection, mixing, coinfection and intraspecific coocclusion of variants within viral occlusion bodies. Using two examples, we demonstrate how this approach can be used to produce highly pathogenic virus preparations for pest control. As restricted host range limits the uptake of NPV-based insecticides, this technology has recently been adapted to produce custom-designed interspecific mixtures of viruses that can be applied to control complexes of lepidopteran pests on particular crops, as long as a shared host species is available for virus production. This approach to the development of NPV-based insecticides has the potential to be applied across a broad range of NPV-pest pathosystems.
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Affiliation(s)
| | - Miguel López-Ferber
- Hydrosciences Montpellier, Univ Montpellier, IMT Mines Alès, IRD, CNRS, Alès, France
| | - Primitivo Caballero
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra, Pamplona, Spain
- Bioinsectis SL, Noain, Spain
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Raymond B, Erdos Z. Passage and the evolution of virulence in invertebrate pathogens: Fundamental and applied perspectives. J Invertebr Pathol 2021; 187:107692. [PMID: 34798134 DOI: 10.1016/j.jip.2021.107692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 01/05/2023]
Abstract
Understanding the ecological and genetic factors that determine the evolution of virulence has broad value for invertebrate pathology. In addition to helping us understand the fundamental biology of our study organisms this body of theory has important applications in microbial biocontrol. Experimental tests of virulence theory are often carried out in invertebrate models and yet theory rarely informs applied passage experiments that aim to increase or maintain virulence. This review summarizes recent progress in this field with a focus on work most relevant to biological control: the virulence of invertebrate pathogens that are 'obligate killers' and which require cadavers for the production of infectious propagules. We discuss recent theory and fundamental and applied experimental evolution with bacteria, fungi, baculoviruses and nematodes. While passage experiments using baculoviruses have a long history of producing isolates with increased virulence, studies with other pathogens have not been so successful. Recent passage experiments that have applied evolution of virulence frameworks based on cooperation (kin selection) have produced novel methods and promising mutants with increased killing power. Evolution of virulence theory can provide plausible explanations for the varied results of passage experiments as well as a predictive framework for improving artificial selection.
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Affiliation(s)
- Ben Raymond
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK.
| | - Zoltan Erdos
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK
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Fan J, Jehle JA, Wennmann JT. Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation. Virus Evol 2021; 7:veaa073. [PMID: 33505705 PMCID: PMC7816688 DOI: 10.1093/ve/veaa073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Genetic diversity of viruses is driven by genomic mutations and selection through its host, resulting in differences in virulence as well as host responses. For baculoviruses, which are naturally occurring pathogens of insects and which are frequently sprayed on hundred thousands to millions of hectares as biocontrol agents of insect pests, the phenomenon of virus-host co-evolution is of particular scientific interest and economic importance because high virulence of baculovirus products is essential and emergence of host resistance needs to be avoided as much as possible. In the present study, the population structure of twenty isolates of the Cydia pomonella granulovirus (CpGV), including twelve isolates from different geographic origins and eight commercial formulations, were studied on the basis of next-generation sequencing data and by analyzing the distribution of single nucleotide polymorphisms (SNPs). An entirely consensus sequence-free quantitative SNP analysis was applied for the identification of 753 variant SNP sites being specific for single as well as groups of CpGV isolates. Based on the quantitative SNP analysis, homogenous, heterogenous as well as mixed isolates were identified and their proportions of genotypes were deciphered, revealing a high genetic diversity of CpGV isolates from around the world. Based on hierarchical clustering on principal components (HCPC), six distinct isolate/group clusters were identified, representing the proposed main phylogenetic lineages of CpGV but comprising full genome information from virus mixtures. The relative location of different isolates in HCPC reflected the proportion of variable compositions of different genotypes. The established methods provide novel analysis tools to decipher the molecular complexity of genotype mixtures in baculovirus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than consensus based analyses.
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Affiliation(s)
- Jiangbin Fan
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
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7
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Etebari K, Parry R, Beltran MJB, Furlong MJ. Transcription Profile and Genomic Variations of Oryctes Rhinoceros Nudivirus in Coconut Rhinoceros Beetles. J Virol 2020; 94:e01097-20. [PMID: 32878889 PMCID: PMC7592217 DOI: 10.1128/jvi.01097-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/25/2020] [Indexed: 12/21/2022] Open
Abstract
Oryctes rhinoceros nudivirus (OrNV) is a double-stranded DNA (dsDNA) virus which has been used as a biocontrol agent to suppress the coconut rhinoceros beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. A new wave of O. rhinoceros incursions in Oceania is thought to be related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles. In this study, chronically infected beetles were collected from Philippines, Fiji, Papua New Guinea (PNG), and the Solomon Islands (SI). RNA sequencing (RNA-seq) was performed to investigate the global viral gene expression profiles and for comparative genomic analysis of structural variations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the SI and Philippines are closely related, while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. Nonsynonymous mutations were detected in several hypothetical proteins and 15 nudivirus core genes, such as gp034, lef-8, lef-4, and vp91 We found limited evidence of variation in viral gene expression among geographic populations. Only a few genes, such as gp01, gp022, and gp107, were differentially expressed among different strains. Additionally, small RNA sequencing from the SI population suggested that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21-nucleotide small RNAs. Some of these genomic changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation.IMPORTANCE Oryctes rhinoceros nudivirus has been an effective biocontrol agent against the coconut rhinoceros beetle in Southeast Asia and the Pacific Islands for decades. The recent outbreak of these beetles in many South Pacific islands has had a significant impact on livelihoods in the region. It has been suggested that the resurgence and spread of the pest are related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles. We examined viral genomic and transcriptional variations in chronically infected beetles from different geographical populations. A high number of polymorphic sites among several geographical strains of OrNV were identified, but potentially only a few of these variations in the genome are involved in functional changes and can potentially alter the typical function. These findings provide valuable resources for future studies to improve our understanding of the OrNV genetic variations in different geographic regions and their potential link to virus pathogenicity.
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Affiliation(s)
- Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Rhys Parry
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Marie Joy B Beltran
- National Crop Protection Centre, College of Agriculture and Food Science, University of the Philippines Los Baños College, Laguna, Philippines
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
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Fan J, Wennmann JT, Wang D, Jehle JA. Single nucleotide polymorphism (SNP) frequencies and distribution reveal complex genetic composition of seven novel natural isolates of Cydia pomonella granulovirus. Virology 2019; 541:32-40. [PMID: 31826844 DOI: 10.1016/j.virol.2019.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/24/2022]
Abstract
The co-evolution between baculoviruses and their insect hosts results in selection of virus populations. To explore this phenomenon at the molecular level, seven natural isolates of Cydia pomonella granulovirus (CpGV) collected from orchards in northwest China were studied using Illumina next generation sequencing (NGS). A total of 540 genome positions with single nucleotide polymorphisms (SNPs) were detected in comparison with known CpGV isolates. New members of previously defined phylogenetic genome groups A, D and E of CpGV, as well as two novel phylogenetic lines, termed genome group F and G, were identified. Combining SNP frequency distribution with the prevalence of genome group-specific SNPs, revealed that six isolates of CpGV were mixtures of different ratios of at least two genotypes, whereas only one isolate, CpGV-WW, was genetically highly homogeneous. This study significantly extends our current understanding of the genetic diversity of CpGV and opens new lines of application of this virus.
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Affiliation(s)
- Jiangbin Fan
- Institute for Biological Control, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Heinrichstraße 243, 64287, Darmstadt, Germany; State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Jörg T Wennmann
- Institute for Biological Control, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Heinrichstraße 243, 64287, Darmstadt, Germany
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Johannes A Jehle
- Institute for Biological Control, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Heinrichstraße 243, 64287, Darmstadt, Germany.
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Genetic Variation and Biological Activity of Two Closely Related Alphabaculoviruses during Serial Passage in Permissive and Semi-Permissive Heterologous Hosts. Viruses 2019; 11:v11070660. [PMID: 31323893 PMCID: PMC6669732 DOI: 10.3390/v11070660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 01/12/2023] Open
Abstract
Phylogenetic analyses suggest that Mamestra brassicae multiple nucleopolyhedrovirus (MbMNPV) and Helicoverpa armigera multiple nucleopolyhedrovirus (HearMNPV) may be strains of the same virus species. Most of the studies comparing their biological activities have been performed in their homologous hosts. A comparison of host range and stability in alternative hosts was performed. The host range of these viruses was compared using high concentrations of inoculum to inoculate second instars of six species of Lepidoptera. One semi-permissive host (Spodoptera littoralis) and one permissive host (S. exigua) were then selected and used to perform six serial passages involving a concentration corresponding to the ~25% lethal concentration for both viruses. Restriction endonuclease analysis showed fragment length polymorphisms in every host-virus system studied. In S. littoralis, serial passage of MbMNPV resulted in decreased pathogenicity and an increase in speed-of-kill, whereas no significant changes were detected for HearMNPV with respect to the initial inoculum. In contrast, both viruses showed a similar trend in S. exigua. These results highlight the low genetic diversity and a high phenotypic stability of HearMNPV with respect to the original inoculum after six successive passages in both insect hosts. This study concludes that host-baculovirus interactions during serial passage are complex and the process of adaptation to a novel semi-permissive host is far from predictable.
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Chen Y, Qi B, Zheng G, Zhang Y, Deng F, Wan F, Li C. Identification and genomic sequence analysis of a new Spodoptera exigua multiple nucleopolyhedrovirus, SeMNPV-QD, isolated from Qingdao, China. J Invertebr Pathol 2019; 160:8-17. [DOI: 10.1016/j.jip.2018.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/18/2018] [Accepted: 11/26/2018] [Indexed: 01/07/2023]
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11
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Brito AF, Melo FL, Ardisson-Araújo DMP, Sihler W, Souza ML, Ribeiro BM. Genome-wide diversity in temporal and regional populations of the betabaculovirus Erinnyis ello granulovirus (ErelGV). BMC Genomics 2018; 19:698. [PMID: 30249206 PMCID: PMC6154946 DOI: 10.1186/s12864-018-5070-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 09/11/2018] [Indexed: 11/30/2022] Open
Abstract
Background Erinnyis ello granulovirus (ErelGV) is a betabaculovirus infecting caterpillars of the sphingid moth E. ello ello (cassava hornworm), an important pest of cassava crops (Manihot esculenta). In this study, the genome of seven field isolates of the virus ErelGV were deep sequenced and their inter- and intrapopulational sequence diversity were analyzed. Results No events of gene gain/loss or translocations were observed, and indels were mainly found within highly repetitive regions (direct repeats, drs). A naturally occurring isolate from Northern Brazil (Acre State, an Amazonian region) has shown to be the most diverse population, with a unique pattern of polymorphisms. Overall, non-synonymous substitutions were found all over the seven genomes, with no specific gathering of mutations on hotspot regions. Independently of their sizes, some ORFs have shown higher levels of non-synonymous changes than others. Non-core genes of known functions and structural genes were among the most diverse ones; and as expected, core genes were the least variable genes. We observed remarkable differences on diversity of paralogous genes, as in multiple copies of p10, fgf, and pep. Another important contrast on sequence diversity was found on genes encoding complex subunits and/or involved in the same biological processes, as late expression factors (lefs) and per os infectivity factors (pifs). Interestingly, several polymorphisms in coding regions lie on sequences encoding specific protein domains. Conclusions By comparing and integrating information about inter- and intrapopulational diversity of viral isolates, we provide a detailed description on how evolution operates on field isolates of a betabaculovirus. Our results revealed that 35–41% of the SNPs of ErelGV lead to amino acid changes (non-synonymous substitutions). Some genes, especially non-core genes of unknown functions, tend to accumulate more mutations, while core genes evolve slowly and are more conserved. Additional studies would be necessary to understand the actual effects of such gene variations on viral infection and fitness. Electronic supplementary material The online version of this article (10.1186/s12864-018-5070-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A F Brito
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - F L Melo
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasília, DF, 70910-970, Brazil
| | - D M P Ardisson-Araújo
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil
| | - W Sihler
- Embrapa Genetic Resources and Biotechnology, Biological Station Park, Brasília, DF, 70770-917, Brazil
| | - M L Souza
- Embrapa Genetic Resources and Biotechnology, Biological Station Park, Brasília, DF, 70770-917, Brazil
| | - B M Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasília, DF, 70910-970, Brazil.
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Thézé J, Lopez-Vaamonde C, Cory JS, Herniou EA. Biodiversity, Evolution and Ecological Specialization of Baculoviruses: A Treasure Trove for Future Applied Research. Viruses 2018; 10:E366. [PMID: 29997344 PMCID: PMC6071083 DOI: 10.3390/v10070366] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 11/16/2022] Open
Abstract
The Baculoviridae, a family of insect-specific large DNA viruses, is widely used in both biotechnology and biological control. Its applied value stems from millions of years of evolution influenced by interactions with their hosts and the environment. To understand how ecological interactions have shaped baculovirus diversification, we reconstructed a robust molecular phylogeny using 217 complete genomes and ~580 isolates for which at least one of four lepidopteran core genes was available. We then used a phylogenetic-concept-based approach (mPTP) to delimit 165 baculovirus species, including 38 species derived from new genetic data. Phylogenetic optimization of ecological characters revealed a general pattern of host conservatism punctuated by occasional shifts between closely related hosts and major shifts between lepidopteran superfamilies. Moreover, we found significant phylogenetic conservatism between baculoviruses and the type of plant growth (woody or herbaceous) associated with their insect hosts. In addition, we found that colonization of new ecological niches sometimes led to viral radiation. These macroevolutionary patterns show that besides selection during the infection process, baculovirus diversification was influenced by tritrophic interactions, explained by their persistence on plants and interactions in the midgut during horizontal transmission. This complete eco-evolutionary framework highlights the potential innovations that could still be harnessed from the diversity of baculoviruses.
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Affiliation(s)
- Julien Thézé
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, 37200 Tours, France.
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
| | - Carlos Lopez-Vaamonde
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, 37200 Tours, France.
- INRA, UR633 Zoologie Forestière, 45075 Orléans, France.
| | - Jenny S Cory
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, 37200 Tours, France.
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Drezen JM, Josse T, Bézier A, Gauthier J, Huguet E, Herniou EA. Impact of Lateral Transfers on the Genomes of Lepidoptera. Genes (Basel) 2017; 8:E315. [PMID: 29120392 PMCID: PMC5704228 DOI: 10.3390/genes8110315] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 11/25/2022] Open
Abstract
Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of "alien" DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera. Large DNA viruses, such as baculoviruses and the symbiotic viruses of parasitic wasps (bracoviruses), have the potential to mediate these transfers in Lepidoptera. In particular, using ultra-deep sequencing, newly integrated transposons have been identified within baculovirus genomes. Bacterial genes have also been acquired by genomes of Lepidoptera, as in other insects and nematodes. In addition, insertions of bracovirus sequences were present in the genomes of certain moth and butterfly lineages, that were likely corresponding to rearrangements of ancient integrations. The viral genes present in these sequences, sometimes of hymenopteran origin, have been co-opted by lepidopteran species to confer some protection against pathogens.
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Affiliation(s)
- Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Jérémy Gauthier
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Elisabeth Anne Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
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14
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Chan KN, Akepratumchai S, Mekvichitsaeng P, Poomputsa K. In vitro production of Spodoptera exigua multiple nucleopolyhedrovirus with enhanced insecticidal activity using a genotypically defined virus inoculum. J Biotechnol 2017; 259:19-25. [PMID: 28780162 DOI: 10.1016/j.jbiotec.2017.08.001] [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: 02/05/2017] [Revised: 07/10/2017] [Accepted: 08/01/2017] [Indexed: 11/26/2022]
Abstract
Defective virus accumulations during baculovirus passages in insect cell culture are impediments to large scale baculovirus production. A genotypically defined virus inoculum comprises of stable genotypes was proposed for production of a Thailand isolated SeMNPV in Se-UCR1 insect cells. Targeted genotypes were from wild-type SeMNPV containing naturally mixed genotypes. Plaque assays, PCR screening and XbaI restriction analysis were employed for genotype purification, genotype selection and genome analysis, respectively. A selective marker was pif2 encoded per os infection factor which predominantly deleted, along with the adjacent pif1, in defective viruses. A purified, genetically stable pif2+ (and pif1+) genotype, namely SeThpif2+, was the first tryout. SeThpif2+ occlusion bodies (OBs) possessed insecticidal activity but at lower level than the wild-type. When the SeThpif2+ was co-infected with another purified, genetically stable pif1- (and pif2-) genotype, SeThpif2-, at ratio of 3:1, respectively, mixed genotypes OBs had 2.8 times greater insecticidal activity than the SeThpif2+ alone. Dilution of deleterious PIF1 of SeThpif2+ by the pif1 deletion genotypes, SeThpif2-, was the key for this enhanced activity. A promising approach was described for SeMNPV production in vitro using the virus inoculum whose genotypes compositions were designed to mimic virus interactions in the wild-type, to generate per oral infective baculovirus.
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Affiliation(s)
- Khin Nyein Chan
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok 10150, Thailand
| | - Saengchai Akepratumchai
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok 10150, Thailand
| | - Phenjun Mekvichitsaeng
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok 10150, Thailand
| | - Kanokwan Poomputsa
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok 10150, Thailand.
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15
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Martínez-Solís M, Jakubowska AK, Herrero S. Expression of the lef5 gene from Spodoptera exigua multiple nucleopolyhedrovirus contributes to the baculovirus stability in cell culture. Appl Microbiol Biotechnol 2017; 101:7579-7588. [DOI: 10.1007/s00253-017-8495-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/25/2017] [Accepted: 08/03/2017] [Indexed: 12/17/2022]
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16
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Zamora-Avilés N, Murillo R, Lasa R, Pineda S, Figueroa JI, Bravo-Patiño A, Díaz O, Corrales JL, Martínez AM. Genetic and Biological Characterization of Four Nucleopolyhedrovirus Isolates Collected in Mexico for the Control of Spodoptera exigua (Lepidoptera: Noctuidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:1465-1475. [PMID: 28499035 DOI: 10.1093/jee/tox130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Indexed: 06/07/2023]
Abstract
This study describes four multiple nucleocapsid nucleopolyhedrovirus isolates recovered from infected larvae of beet armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), on crops in two different geographical regions of Mexico. Molecular and biological characterization was compared with characterized S. exigua multiple nucleopolyhedrovirus (SeMNPV) isolates from the United States (SeUS1 and SeUS2) and Spain (SeSP2). Restriction endonuclease analysis of viral DNA confirmed that all Mexican isolates were SeMNPV isolates, but molecular differences between the Mexican and the reference isolates were detected using PCR combined with restriction fragment length polymorphism (RFLP). Amplification of the variable region V01 combined with RFLP distinguished the two Mexican isolates, SeSLP6 and SeSIN6. BglII digestions showed that the majority of the isolates contained submolar bands, indicating the presence of genetic heterogeneity. Amplification of the variable regions V04 and V05 distinguished between American and the Spanish isolates. Biological characterization was performed against two laboratory colonies of S. exigua, one from Mexico, and another from Switzerland. Insects from the Mexican colony were less susceptible to infection than insects from Se-Swiss colony. In the Se-Mex colony, SeSP2 was the most pathogenic isolate followed by SeSIN6, although their virulence was similar to most of the isolates tested. In Se-Swiss colony, similar LD50 values were observed for the five isolates, although the virulence was higher for the SeSLP6 isolate, which also had the highest OB (occlusion body) yield. We conclude that the Mexican isolates SeSIN6 and SeSLP6 possess insecticidal traits of value for the development of biopesticides for the control of populations of S. exigua.
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Affiliation(s)
- N Zamora-Avilés
- Instituto de Investigaciones Agropecuarias y Forestales, Tarimbaro, Km 9.5 Carretera Morelia Zinapecuaro 58880, Tarímbaro, Michoacán, Mexico
| | - R Murillo
- Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, Av. Pamplona 123, Navarra 31192, Spain
- Departamento de Producción Agraria, Universidad Pública de Navarra, Navarra 31192, Mutilva Baja, Spain
| | - R Lasa
- Instituto de Ecología AC, Xalapa, 351 Carretera antigua a Coatepec, Veracruz 91070, Mexico
| | - S Pineda
- Instituto de Investigaciones Agropecuarias y Forestales, Tarimbaro, Km 9.5 Carretera Morelia Zinapecuaro 58880, Tarímbaro, Michoacán, Mexico
| | - J I Figueroa
- Instituto de Investigaciones Agropecuarias y Forestales, Tarimbaro, Km 9.5 Carretera Morelia Zinapecuaro 58880, Tarímbaro, Michoacán, Mexico
| | - A Bravo-Patiño
- Centro Multidisciplinario de estudios en Biotecnología, Tarímbaro, Km 9.5 Carretera Morelia Zinapécuaro 58880, Tarímbaro, Michoacán, Mexico
| | - O Díaz
- Facultad de Agronomía, Universidad Autónoma de San Luis Potosí, 64 Álvaro Obregón, San Luís Potosí 78000, Mexico
| | - J L Corrales
- Facultad de Agronomía, Universidad Autónoma de Sinaloa, Prolongación Josefa Ortiz de Domínguez, Sinaloa 80040, Mexico
| | - A M Martínez
- Instituto de Investigaciones Agropecuarias y Forestales, Tarimbaro, Km 9.5 Carretera Morelia Zinapecuaro 58880, Tarímbaro, Michoacán, Mexico
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17
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Williams T, Virto C, Murillo R, Caballero P. Covert Infection of Insects by Baculoviruses. Front Microbiol 2017; 8:1337. [PMID: 28769903 PMCID: PMC5511839 DOI: 10.3389/fmicb.2017.01337] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/03/2017] [Indexed: 12/19/2022] Open
Abstract
Baculoviruses (Baculoviridae) are occluded DNA viruses that are lethal pathogens of the larval stages of some lepidopterans, mosquitoes, and sawflies (phytophagous Hymenoptera). These viruses have been developed as biological insecticides for control of insect pests and as expression vectors in biotechnological applications. Natural and laboratory populations frequently harbor covert infections by baculoviruses, often at a prevalence exceeding 50%. Covert infection can comprise either non-productive latency or sublethal infection involving low level production of virus progeny. Latency in cell culture systems involves the expression of a small subset of viral genes. In contrast, covert infection in lepidopterans is associated with differential infection of cell types, modulation of virus gene expression and avoidance of immune system clearance. The molecular basis for covert infection may reside in the regulation of host-virus interactions through the action of microRNAs (miRNA). Initial findings suggest that insect nudiviruses and vertebrate herpesviruses may provide useful analogous models for exploring the mechanisms of covert infection by baculoviruses. These pathogens adopt mixed-mode transmission strategies that depend on the relative fitness gains that accrue through vertical and horizontal transmission. This facilitates virus persistence when opportunities for horizontal transmission are limited and ensures virus dispersal in migratory host species. However, when host survival is threatened by environmental or physiological stressors, latent or persistent infections can be activated to produce lethal disease, followed by horizontal transmission. Covert infection has also been implicated in population level effects on host-pathogen dynamics due to the reduced reproductive capacity of infected females. We conclude that covert infections provide many opportunities to examine the complexity of insect-virus pathosystems at the organismal level and to explore the evolutionary and ecological relationships of these pathogens with major crop and forest pests.
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Affiliation(s)
| | - Cristina Virto
- Bioinsecticidas Microbianos, Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas, Universidad Pública de NavarraMutilva, Spain
- Laboratorio de Entomología Agrícola y Patología de Insectos, Departamento de Producción Agraria, Universidad Pública de NavarraPamplona, Spain
| | - Rosa Murillo
- Bioinsecticidas Microbianos, Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas, Universidad Pública de NavarraMutilva, Spain
- Laboratorio de Entomología Agrícola y Patología de Insectos, Departamento de Producción Agraria, Universidad Pública de NavarraPamplona, Spain
| | - Primitivo Caballero
- Bioinsecticidas Microbianos, Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas, Universidad Pública de NavarraMutilva, Spain
- Laboratorio de Entomología Agrícola y Patología de Insectos, Departamento de Producción Agraria, Universidad Pública de NavarraPamplona, Spain
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18
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Brito AFD, Braconi CT, Weidmann M, Dilcher M, Alves JMP, Gruber A, Zanotto PMDA. The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV). Genome Biol Evol 2015; 8:94-108. [PMID: 26615220 PMCID: PMC4758234 DOI: 10.1093/gbe/evv231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.
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Affiliation(s)
- Anderson Fernandes de Brito
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Manfred Weidmann
- Department of Virology, University Medical Center, Göttingen, Germany
| | - Meik Dilcher
- Department of Virology, University Medical Center, Göttingen, Germany
| | - João Marcelo Pereira Alves
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
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Barrera GP, Belaich MN, Patarroyo MA, Villamizar LF, Ghiringhelli PD. Evidence of recent interspecies horizontal gene transfer regarding nucleopolyhedrovirus infection of Spodoptera frugiperda. BMC Genomics 2015; 16:1008. [PMID: 26607569 PMCID: PMC4861128 DOI: 10.1186/s12864-015-2218-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Baculoviruses are insect-associated viruses carrying large, circular double-stranded-DNA genomes with significant biotechnological applications such as biological pest control, recombinant protein production, gene delivery in mammals and as a model of DNA genome evolution. These pathogens infect insects from the orders Lepidoptera, Hymenoptera and Diptera, and have high species diversity which is expressed in their diverse biological properties including morphology, virulence or pathogenicity. Spodoptera frugiperda (Lepidoptera: Noctuidae), the fall armyworm, represents a significant pest for agriculture in America; it is a host for baculoviruses such as the Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) (Colombia strain, genotype A) having been classified as a Group II alphabaculovirus making it a very attractive target for bioinsecticidal use. RESULTS Genome analysis by pyrosequencing revealed that SfMNPV ColA has 145 ORFs, 2 of which were not present in the other sequenced genotypes of the virus (SfMNPV-NicB, SfMNPV-NicG, SfMNPV-19 and SfMNPV-3AP2). An in-depth bioinformatics study showed that ORF023 and ORF024 were acquired by a recent homologous recombination process between Spodoptera frugiperda and Spodoptera litura (the Oriental leafworm moth) nucleopolyhedroviruses. Auxiliary genes are numerous in the affected locus which has a homologous region (hr3), a repetitive sequence associated with genome replication which became lost in SfColA along with 1 ORF. Besides, the mRNAs associated with two acquired genes appeared in the virus' life-cycle during the larval stage. Predictive studies concerning the theoretical proteins identified that ORF023 protein would be a phosphatase involved in DNA repair and that the ORF024 protein would be a membrane polypeptide associated with cell transport. CONCLUSIONS The SfColA genome was thus revealed to be a natural recombinant virus showing evidence of recent horizontal gene transfer between different baculovirus species occurring in nature. This feature could be the cause of its high insecticidal power and therefore SfColA becomes a great candidate for bioinsecticide formulations.
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Affiliation(s)
- Gloria Patricia Barrera
- Centro de Investigación Tibaitatá, Corpoica (Corporación Colombiana de Investigación Agropecuaria), Km 14 Vía Mosquera, Cundinamarca, Colombia.
| | - Mariano Nicolás Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular - Área Virosis de Insectos (LIGBCM-AVI), Dto. Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.
| | - Manuel Alfonso Patarroyo
- Departamento de Biología Molecular e Inmunología, Fundación Instituto de Inmunología de Colombia (FIDIC), Avenida 50 N° 26-20, Bogotá, Colombia. .,Departamento de Ciencias Básicas, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Calle 12C N° 6-25, Bogotá, Colombia.
| | - Laura Fernanda Villamizar
- Centro de Investigación Tibaitatá, Corpoica (Corporación Colombiana de Investigación Agropecuaria), Km 14 Vía Mosquera, Cundinamarca, Colombia.
| | - Pablo Daniel Ghiringhelli
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular - Área Virosis de Insectos (LIGBCM-AVI), Dto. Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.
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20
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Abstract
Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%). K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs). Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential.
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21
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Serrano A, Pijlman GP, Vlak JM, Muñoz D, Williams T, Caballero P. Identification of Spodoptera exigua nucleopolyhedrovirus genes involved in pathogenicity and virulence. J Invertebr Pathol 2015; 126:43-50. [PMID: 25644432 DOI: 10.1016/j.jip.2015.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 11/16/2022]
Abstract
Genome sequence analysis of seven different Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) isolates that differed in insecticidal phenotype permitted the identification of genes likely to be involved in pathogenicity of occlusion bodies (OBs) and speed of kill (virulence) of this virus: se4 (hoar), se5 (unknown function), se28 (unknown function), se76 (cg30), se87 (p26) and se129 (p26). To study the role of these genes experimentally on the insecticidal phenotype, a bacmid-based recombination system was constructed to delete selected genes from a SeMNPV isolate, VT-SeAL1, designated as SeBacAL1. All of the knockout viruses were viable and the repair viruses behaved like the wild-type control, vSeBacAL1. Deletion of se4, se5, se76 and se129 resulted in decreased OB pathogenicity compared to vSeBacAL1 OBs. In contrast, deletion of se87 did not significantly affect OB pathogenicity, whereas deletion of se28 resulted in significantly increased OB pathogenicity. Deletion of se4, se28, se76, se87 and se129 did not affect speed of kill compared to the bacmid vSeBacAL1, whereas speed of kill was significantly extended following deletion of se5 and in the wild-type isolate (SeAL1), compared to that of the bacmid. Therefore, biological assays confirmed that several genes had effects on virus insecticidal phenotype. Se5 is an attractive candidate gene for further studies, as it affects both biological parameters of this important biocontrol virus.
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Affiliation(s)
- Amaya Serrano
- Instituto de Agrobiotecnología, CSIC-UPNA, Avda de Pamplona 123, 31192 Mutilva, Spain; Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Delia Muñoz
- Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain
| | | | - Primitivo Caballero
- Instituto de Agrobiotecnología, CSIC-UPNA, Avda de Pamplona 123, 31192 Mutilva, Spain; Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain.
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22
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Virto C, Navarro D, Tellez MM, Herrero S, Williams T, Murillo R, Caballero P. Natural populations of Spodoptera exigua are infected by multiple viruses that are transmitted to their offspring. J Invertebr Pathol 2014; 122:22-7. [DOI: 10.1016/j.jip.2014.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 02/06/2023]
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