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1.
Viruses ; 13(2)2021 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-33572446

RESUMO

Analysis of pooled genomic short read sequence data revealed the presence of nudivirus-derived sequences from U.S. populations of both southern corn rootworm (SCR, Diabrotica undecimpunctata howardi Barber) and western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte). A near complete nudivirus genome sequence was assembled from sequence data for an SCR population with relatively high viral titers. A total of 147,179 bp was assembled from five contigs that collectively encode 109 putative open reading frames (ORFs) including 20 nudivirus core genes. In contrast, genome sequence recovery was incomplete for a second nudivirus from WCR, although sequences derived from this virus were present in three geographically dispersed populations. Only 48,989 bp were assembled with 48 putative ORFs including 13 core genes, representing about 20% of a typical nudivirus genome. Phylogenetic analysis indicated that both corn rootworm nudiviruses grouped with the third known nudivirus of beetles, Oryctes rhinoceros nudivirus in the genus Alphanudivirus. On the basis of phylogenetic and additional analyses, we propose further taxonomic separation of nudiviruses within Alphanudivirus and Betanudivirus into two subfamilies and five genera. Identification of nudivirus-derived sequences from two species of corn rootworm highlights the diversity of viruses associated with these agricultural insect pests.


Assuntos
Besouros/virologia , Nudiviridae/genética , Animais , Besouros/classificação , DNA Viral/genética , Genes Virais , Genoma Viral/genética , Genômica , Nudiviridae/classificação , Fases de Leitura Aberta , Filogenia , Viroma/genética
2.
Commun Biol ; 4(1): 104, 2021 01 22.
Artigo em Inglês | MEDLINE | ID: mdl-33483589

RESUMO

Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.


Assuntos
Evolução Biológica , Cromossomos de Insetos , Genoma de Inseto , Polydnaviridae/genética , Vespas/genética , Animais , Sequência de Bases , Sequência Conservada , Nudiviridae/genética , Receptores Odorantes/genética , Olfato , Simbiose , Sintenia , Vespas/virologia
3.
J Virol ; 94(22)2020 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-32878889

RESUMO

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.


Assuntos
Besouros/virologia , Genoma Viral , Genômica , Nudiviridae/genética , Animais , Cocos , DNA , Vírus de DNA/genética , Feminino , Regulação Viral da Expressão Gênica , Genes Virais/genética , Haplótipos , MicroRNAs , Oceania , Perissodáctilos , Filogenia , Interferência de RNA , Análise de Sequência de RNA
4.
mBio ; 11(4)2020 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-32788378

RESUMO

Enveloped viruses hijack cellular membranes in order to provide the necessary material for virion assembly. In particular, viruses that replicate and assemble inside the nucleus have developed special approaches to modify the nuclear landscape for their advantage. We used electron microscopy to investigate cellular changes occurring during nudivirus infection and we characterized a unique mechanism for assembly, packaging, and transport of new virions across the nuclear membrane and through the cytoplasm. Our three-dimensional reconstructions describe the complex remodeling of the nuclear membrane necessary to release vesicle-associated viruses into the cytoplasm. This is the first report of nuclear morphological reconfigurations that occur during nudiviral infection.IMPORTANCE The dynamics of nuclear envelope has a critical role in multiple cellular processes. However, little is known regarding the structural changes occurring inside the nucleus or at the inner and outer nuclear membranes. For viruses assembling inside the nucleus, remodeling of the intranuclear membrane plays an important role in the process of virion assembly. Here, we monitored the changes associated with viral infection in the case of nudiviruses. Our data revealed dramatic membrane remodeling inside the nuclear compartment during infection with Oryctes rhinoceros nudivirus, an important biocontrol agent against coconut rhinoceros beetle, a devastating pest for coconut and oil palm trees. Based on these findings, we propose a model for nudivirus assembly in which nuclear packaging occurs in fully enveloped virions.


Assuntos
Núcleo Celular/virologia , Membrana Nuclear/fisiologia , Nudiviridae/fisiologia , Montagem de Vírus , Liberação de Vírus , Animais , Linhagem Celular , Núcleo Celular/ultraestrutura , Microscopia Crioeletrônica , Insetos , Membrana Nuclear/ultraestrutura , Nudiviridae/ultraestrutura
5.
Insect Biochem Mol Biol ; 123: 103405, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32534986

RESUMO

Sequence analysis of the genomic DNA isolated from four biotypes of the soybean aphid, Aphis glycines (AG), revealed that in addition to the commonly observed retrovirus-related retrotransposons, viral sequences derived from multiple RNA and DNA viruses have integrated into the genome. Notably, sequences of more than 60 nudiviral genes were identified from de novo assembled DNA contigs, and mapped to assembled genomic scaffolds of AG, indicating that an ancient nudivirus, named Aphis glycines endogenous nudivirus (AgENV), had integrated into the AG genome. Furthermore, sequences derived from a similar endogenous nudivirus, Melanaphis sacchari endogenous nudivirus (MsENV), were identified from the genomic scaffolds of the sugarcane aphid, Melanaphis sacchari. Analysis of transcriptome and small RNA sequence data derived from AG did not provide evidence for transcription of the integrated AgENV genes. Hence, the genes of AgENV may be present as pseudogenes. Phylogenetic analysis based on nudivirus core genes indicated that these aphid ENVs belong to the genus Alphanudivirus.


Assuntos
Afídeos/genética , Elementos de DNA Transponíveis/genética , Nudiviridae/genética , Animais , Genes Virais , Genoma de Inseto , Filogenia , Pseudogenes , Soja
6.
Genome Biol Evol ; 12(5): 578-588, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32282886

RESUMO

Endogenous viral elements (EVEs), derived from all major types of viruses, have been discovered in many eukaryotic genomes, representing "fossil records" of past viral infections. The endogenization of nudiviruses has been reported in several insects, leading to the question of whether genomic integration is a common phenomenon for these viruses. In this study, genomic assemblies of insects and other arthropods were analyzed to identify endogenous sequences related to Nudiviridae. A total of 359 nudivirus-like genes were identified in 43 species belonging to different groups; however, none of these genes were detected in the known hosts of nudiviruses. A large proportion of the putative EVEs identified in this study encode intact open reading frames or are transcribed as mRNAs, suggesting that they result from recent endogenization of nudiviruses. Phylogenetic analyses of the identified EVEs and inspections of their flanking regions indicated that integration of nudiviruses has occurred recurrently during the evolution of arthropods. This is the first report of a comprehensive screening for nudivirus-derived EVEs in arthropod genomes. The results of this study demonstrated that a large variety of arthropods, especially hemipteran and hymenopteran insects, have previously been or are still infected by nudiviruses. These findings have greatly extended the host range of Nudiviridae and provide new insights into viral diversity, evolution, and host-virus interactions.


Assuntos
Artrópodes/genética , Artrópodes/virologia , Genoma de Inseto , Nudiviridae/fisiologia , Fenômenos Fisiológicos Virais , Animais , Evolução Molecular , Interações Hospedeiro-Patógeno
7.
Virology ; 542: 34-39, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32056666

RESUMO

Polydnaviruses are obligate mutualists of parasitoid wasps and are divided into two genera, Bracovirus and Ichnovirus. Bracoviruses are thought to originate from a single integration of an ancestral nudivirus into the ancestor of microgastroid complex ~100 million years ago. However, all the known nudiviruses are only distantly related to bracoviruses, and much remains obscure about the origin of bracoviruses. Here we employ a paleovirological method to screen endogenous nudivirus-like elements across arthropods. Interestingly, we identify many endogenous nudivirus-like elements within the genome of Eurytoma brunniventris, a species of the Chalcidoidea superfamily. Among them, we find 14 core gene sequences are likely to be derived from a betanudivirus (designated EbrENV-ß), suggesting that betanudivirus has been circulating in parasitoid wasps. Phylogenomic analysis suggests that EbrENV-ß is the known closest relative of bracoviruses. Synteny analyses show the order of core genes is not well conserved between EbrENV-ß and nudiviruses, revealing the dynamic nature of the evolution of nudivirus genome structures. Our findings narrow down the evolutionary gap between bracoviruses and nudiviruses and provide novel insights into the origin and evolution of polydnaviruses.


Assuntos
Nudiviridae/classificação , Nudiviridae/genética , Polydnaviridae/classificação , Polydnaviridae/genética , Vespas/virologia , Animais , Evolução Molecular , Genoma de Inseto , Genoma Viral , Interações entre Hospedeiro e Microrganismos/genética , Nudiviridae/fisiologia , Filogenia , Polydnaviridae/fisiologia , Simbiose/genética , Integração Viral/genética , Vespas/genética , Vespas/fisiologia
8.
J Gen Virol ; 101(1): 3-4, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31935180

RESUMO

Members of the family Nudiviridae are large dsDNA viruses with distinctive rod-shaped nucleocapsids and circular genomes of 96-232 kbp. Nudiviruses have been identified from a diverse range of insects and crustaceans and are closely related to baculoviruses. This is a summary of the International Committee on Taxonomy of Viruses Report on the taxonomy of the family Nudiviridae, which is available at ictv.global/report/nudiviridae.


Assuntos
Nudiviridae/classificação , Nudiviridae/genética , Animais , Baculoviridae/genética , Crustáceos/virologia , Genoma Viral/genética , Insetos/virologia , Vírion/genética
9.
Virus Res ; 278: 197864, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31945420

RESUMO

Oryctes rhinoceros nudivirus (OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations. We detected OrNV infection in O. rhinoceros from Solomon Islands and used Oxford Nanopore Technologies (ONT) long-read sequencing to determine the full length of the virus genomic sequence isolated from an individual belonging to a mitochondrial lineage (CRB-G) that was previously reported as resistant to OrNV. The complete circular genome of the virus consisted of 125,917 nucleotides, 1.698 bp shorter than the originally-described full genome sequence of Ma07 strain from Malaysia. We found 130 out of 139 previously annotated ORFs (seven contained interrupted/non-coding sequences, two were identified as duplicated versions of the existing genes), as well as a putatively inverted regions containing four genes. These results demonstrate the usefulness of a long-read sequencing technology for resolving potential structural variations when describing new virus isolates. While the Solomon Islands isolate exhibited 99.41 % nucleotide sequence identity with the originally described strain, we found several genes, including a core gene (vlf-1), that contained multiple amino acid insertions and/or deletions as putative polymorphisms of large effect. Our complete annotated genome sequence of a newly found isolate in Solomon Islands provides a valuable resource to help elucidate the mechanisms that compromise the efficacy of OrNV as a biocontrol agent against the coconut rhinoceros beetle.


Assuntos
Besouros/virologia , Genoma Viral , Nudiviridae/genética , Animais , Agentes de Controle Biológico , Cocos , Feminino , Melanesia , Fases de Leitura Aberta , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
10.
ISME J ; 14(2): 531-543, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31676854

RESUMO

Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.


Assuntos
Microbioma Gastrointestinal/genética , Nephropidae/microbiologia , Nephropidae/virologia , Nudiviridae/isolamento & purificação , Animais , Bactérias/classificação , Suscetibilidade a Doenças/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Interações Microbianas , Filogenia , Alimentos Marinhos/microbiologia , Alimentos Marinhos/virologia , Viroses
11.
G3 (Bethesda) ; 9(11): 3575-3582, 2019 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-31455677

RESUMO

Copy number variants (CNV) are associated with phenotypic variation in several species. However, properly detecting changes in copy numbers of sequences remains a difficult problem, especially in lower quality or lower coverage next-generation sequencing data. Here, inspired by recent applications of machine learning in genomics, we describe a method to detect duplications and deletions in short-read sequencing data. In low coverage data, machine learning appears to be more powerful in the detection of CNVs than the gold-standard methods of coverage estimation alone, and of equal power in high coverage data. We also demonstrate how replicating training sets allows a more precise detection of CNVs, even identifying novel CNVs in two genomes previously surveyed thoroughly for CNVs using long read data.


Assuntos
Variações do Número de Cópias de DNA , Aprendizado Profundo , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Animais , Drosophila melanogaster/genética , Genoma de Inseto , Genoma Viral , Nudiviridae/genética
12.
Sci Rep ; 9(1): 10086, 2019 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-31300678

RESUMO

Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters (Homarus gammarus). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.


Assuntos
Doenças dos Peixes/virologia , Nephropidae/virologia , Nudiviridae/classificação , Nudiviridae/genética , Animais , Genoma Viral/genética , Hepatopâncreas/virologia , Microscopia Eletrônica de Transmissão , Nudiviridae/isolamento & purificação , Penaeidae/virologia , Filogenia , Frutos do Mar/virologia
13.
Curr Opin Insect Sci ; 32: 28-35, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-31113628

RESUMO

Endogenous Viral Elements (EVEs) are remnants of viral genomes that are permanently integrated into the genome of another organism. Parasitoid wasps have independently acquired nudivirus-derived EVEs in three lineages. Each parasitoid produces virions or virus-like particles (VLPs) that are injected into hosts during parasitism to function in subversion of host defenses. Comparing the inventory of nudivirus-like genes in different lineages of parasitoids can provide insights into the importance of each encoded function in virus or VLP production and parasitism success. Comparisons revealed the following conserved features: first, retention of genes encoding a viral RNA polymerase and infectivity factors; second, loss of the ancestral DNA polymerase gene; and third, signatures of viral ancestry in patterns of gene retention.


Assuntos
Nudiviridae/genética , Vespas/genética , Vespas/virologia , Animais , RNA Polimerases Dirigidas por DNA/genética , Insetos/parasitologia , Insetos/virologia , Vírion
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