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Peterson L, Rozo Dos Santos E, Morais Ribeiro B, Sosa-Gomez D, Ardisson-Araújo DMP. Genomic analyses of a new baculovirus isolated from the wheat armyworm, Mythimna sequax (Franclemont) (Lepidoptera: Noctuidae). J Invertebr Pathol 2024; 204:108127. [PMID: 38729296 DOI: 10.1016/j.jip.2024.108127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
We report the genomic analysis of a novel alphabaculovirus, Mythimna sequax nucleopolyhedrovirus isolate CNPSo-98 (MyseNPV-CNPSo-98), obtained from cadavers of the winter crop pest, Mythimna sequax Franclemont (Lepidoptera: Noctuidae). The insects were collected from rice fields in Southern Brazil in the 1980's and belongs to the 'EMBRAPA-Soja' Virus Collection. High-throughput sequencing reads of DNA from MyseNPV occlusion bodies and assembly of the data yielded an AT-rich circular genome contig of 148,403 bp in length with 163 annotated opening reading frames (ORFs) and four homologous regions (hrs). Phylogenetic inference based on baculovirus core protein sequence alignments indicated that MyseNPV-CNPSo-98 is a member of Alphabaculovirus genus that clustered with other group II noctuid-infecting baculoviruses, including viruses isolated from Helicoverpa armigera and Mamestra spp. The genomes of the clade share strict collinearity and high pairwise nucleotide identity, with a common set of 149 genes, evolving under negative selection, except a bro gene. Branch lengths and Kimura-2-parameter pairwise nucleotide distances indicated that MyseNPV-CNPSo-98 represents a distinct lineage that may not be classified in any of the currently listed species in the genus.
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Affiliation(s)
- Lenen Peterson
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, Brazil; Graduate Program of Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Ethiane Rozo Dos Santos
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, Brazil
| | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, Brazil
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Jin W, Byambasuren M, Ganbold U, Shi H, Liang H, Li M, Wang H, Qin Q, Zhang H. Sequencing, Analysis and Organization of the Complete Genome of a Novel Baculovirus Calliteara abietis Nucleopolyhedrovirus (CaabNPV). Viruses 2024; 16:252. [PMID: 38400028 PMCID: PMC10891889 DOI: 10.3390/v16020252] [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: 12/25/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Baculoviridae, a virus family characterized by a single large double stranded DNA, encompasses the majority of viral bioinsecticides, representing a highly promising and environmentally friendly pesticide approach to insect control. This study focuses on the characterization of a baculovirus isolated from larvae of Calliteara abietis (Erebidae, Lymantriidae) collected in Mongolian pinaceae forests. This new isolate was called Calliteara abietis nucleopolyhedrovirus (CaabNPV). CaabNPV exhibits an irregular polyhedron shape, and significant variation in the diameter of its occlusion bodies (OBs) was observed. Nucleotide distance calculations confirmed CaabNPV as a novel baculovirus. The CaabNPV genome spans 177,161 bp with a G+C content of 45.12% and harbors 150 potential open reading frames (ORFs), including 38 core genes. A comprehensive genomic analysis categorizes CaabNPV within Group II alphabaculovirus, revealing a close phylogenetic relationship with Alphabaculovirus orleucostigmae (OrleNPV). Additionally, repeat sequence analysis identified three highly repetitive sequences consisting of 112 bp repeat units, known as homologous regions (hrs). This research contributes valuable insights into CaabNPV's phylogenetic placement, genomic structure, and its potential applications in insect biocontrol.
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Affiliation(s)
- Wenyi Jin
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Mijidsuren Byambasuren
- Institute of Plant Protection, Mongolian University of Life Science, Ulaanbaatar 627153, Mongolia;
| | - Uranbileg Ganbold
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 101408, China
- Institute of Plant Protection, Mongolian University of Life Science, Ulaanbaatar 627153, Mongolia;
| | - Huixian Shi
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
| | - Hongbin Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Miaomiao Li
- Institute of College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang 712046, China;
| | - Hongtuo Wang
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
| | - Qilian Qin
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
| | - Huan Zhang
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
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3
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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: 3] [Impact Index Per Article: 1.5] [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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Gallet R, Di Mattia J, Ravel S, Zeddam JL, Vitalis R, Michalakis Y, Blanc S. Gene copy number variations at the within-host population level modulate gene expression in a multipartite virus. Virus Evol 2022; 8:veac058. [PMID: 35799884 PMCID: PMC9255600 DOI: 10.1093/ve/veac058] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/02/2022] [Accepted: 06/21/2022] [Indexed: 11/12/2022] Open
Abstract
Multipartite viruses have a segmented genome, with each segment encapsidated separately. In all multipartite virus species for which the question has been addressed, the distinct segments reproducibly accumulate at a specific and host-dependent relative frequency, defined as the 'genome formula'. Here, we test the hypothesis that the multipartite genome organization facilitates the regulation of gene expression via changes of the genome formula and thus via gene copy number variations. In a first experiment, the faba bean necrotic stunt virus (FBNSV), whose genome is composed of eight DNA segments each encoding a single gene, was inoculated into faba bean or alfalfa host plants, and the relative concentrations of the DNA segments and their corresponding messenger RNAs (mRNAs) were monitored. In each of the two host species, our analysis consistently showed that the genome formula variations modulate gene expression, the concentration of each genome segment linearly and positively correlating to that of its cognate mRNA but not of the others. In a second experiment, twenty parallel FBNSV lines were transferred from faba bean to alfalfa plants. Upon host switching, the transcription rate of some genome segments changes, but the genome formula is modified in a way that compensates for these changes and maintains a similar ratio between the various viral mRNAs. Interestingly, a deep-sequencing analysis of these twenty FBNSV lineages demonstrated that the host-related genome formula shift operates independently of DNA-segment sequence mutation. Together, our results indicate that nanoviruses are plastic genetic systems, able to transiently adjust gene expression at the population level in changing environments, by modulating the copy number but not the sequence of each of their genes.
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Affiliation(s)
- Romain Gallet
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
- CBGP, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | - Jérémy Di Mattia
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | - Sébastien Ravel
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | - Jean-Louis Zeddam
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | - Renaud Vitalis
- CBGP, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | | | - Stéphane Blanc
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
- MIVEGEC, Univ Montpellier, CNRS, IRD, Montpellier, France
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Rodrigues DT, Peterson L, de Oliveira LB, Sosa-Gómez DR, Ribeiro BM, Ardisson-Araújo DM. Characterization of a novel alphabaculovirus isolated from the Southern armyworm, Spodoptera eridania (Cramer, 1782) (Lepidoptera: Noctuidae) and the evolution of odv-e66, a bacterium-acquired baculoviral chondroitinase gene. Genomics 2020; 112:3903-3914. [DOI: 10.1016/j.ygeno.2020.06.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/24/2020] [Accepted: 06/28/2020] [Indexed: 11/16/2022]
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Sosa-Gómez DR, Morgado FS, Corrêa RFT, Silva LA, Ardisson-Araújo DMP, Rodrigues BMP, Oliveira EE, Aguiar RWS, Ribeiro BM. Entomopathogenic Viruses in the Neotropics: Current Status and Recently Discovered Species. NEOTROPICAL ENTOMOLOGY 2020; 49:315-331. [PMID: 32358711 DOI: 10.1007/s13744-020-00770-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
The market for biological control of insect pests in the world and in Brazil has grown in recent years due to the unwanted ecological and human health impacts of chemical insecticides. Therefore, research on biological control agents for pest management has also increased. For instance, insect viruses have been used to protect crops and forests around the world for decades. Among insect viruses, the baculoviruses are the most studied and used viral biocontrol agent. More than 700 species of insects have been found to be naturally infected by baculoviruses, with 90% isolated from lepidopteran insects. In this review, some basic aspects of baculovirus infection in vivo and in vitro infection, gene content, viral replication will be discussed. Furthermore, we provide examples of the use of insect viruses for biological pest control and recently characterized baculoviruses in Brazil.
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Affiliation(s)
- D R Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Soja, Londrina, PR, Brasil
| | - F S Morgado
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - R F T Corrêa
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - L A Silva
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - D M P Ardisson-Araújo
- Depto de Bioquímica e Biologia Molecular, Univ Federal de Santa Maria, Santa Maria, RS, Brasil
| | - B M P Rodrigues
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - E E Oliveira
- Depto de Entomologia, Univ Federal de Viçosa, Viçosa, MG, Brasil
| | - R W S Aguiar
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - B M Ribeiro
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil.
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Trentin LB, Santos ER, Oliveira Junior AG, Sosa-Gómez DR, Ribeiro BM, Ardisson-Araújo DMP. The complete genome of Rachiplusia nu nucleopolyhedrovirus (RanuNPV) and the identification of a baculoviral CPD-photolyase homolog. Virology 2019; 534:64-71. [PMID: 31200103 DOI: 10.1016/j.virol.2019.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 02/08/2023]
Abstract
We described a novel baculovirus isolated from the polyphagous insect pest Rachiplusia nu. The virus presented pyramidal-shaped occlusion bodies (OBs) with singly-embed nucleocapsids and a dose mortality response of 6.9 × 103 OBs/ml to third-instar larvae of R. nu. The virus genome is 128,587 bp long with a G + C content of 37.9% and 134 predicted ORFs. The virus is an alphabaculovirus closely related to Trichoplusia ni single nucleopolyhedrovirus, Chrysodeixis chalcites nucleopolyhedrovirus, and Chrysodeixis includens single nucleopolyhedrovirus and may constitute a new species. Surprisingly, we found co-evolution among the related viruses and their hosts at species level. Besides, auxiliary genes with homologs in other baculoviruses were found, e.g. a CPD-photolyase. The gene seemed to be result of a single event of horizontal transfer from lepidopterans to alphabaculovirus, followed by a transference from alpha to betabaculovirus. The predicted protein appears to be an active enzyme that ensures likely DNA protection from sunlight.
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Affiliation(s)
- Luana Beló Trentin
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | - Ethiane R Santos
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | | | | | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil.
| | - Daniel 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.
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Horta AB, Ardisson-Araujo DMP, da Silva LA, de Melo FL, da Silva Morgado F, Franco Lemos MV, Ribeiro ZA, Boiça AL, Wilcken CF, Ribeiro BM. Genomic analysis of a cypovirus isolated from the eucalyptus brown looper, Thyrinteina arnobia (Stoll, 1782) (Lepidoptera: Geometridae). Virus Res 2018; 253:62-67. [DOI: 10.1016/j.virusres.2018.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 11/26/2022]
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