Sequencing of the large dsDNA genome of Oryctes rhinoceros nudivirus using multiple displacement amplification of nanogram amounts of virus DNA

The brown planthopper (BPH), Nilaparvata lugens (Hemiptera:Delphacidae), is one of the most destructive insect pests of rice crops in Asia. Nudivirus-like sequences were identified during the whole-genome sequencing of BPH. PCR examination showed that the virus sequences were present in all of the 22 BPH populations collected from East, Southeast, and South Asia. Thirty-two of the 33 nudivirus core genes were identified, including 20 homologues of baculovirus core genes. In addition, several gene clusters that were arranged collinearly with those of other nudiviruses were found in the partial virus genome. In a phylogenetic tree constructed using the supermatrix method, the original virus was grouped with other nudiviruses and was closely related to polydnavirus. Taken together, these data indicated that the virus sequences belong to a new member of the family Nudiviridae. More specifically, the virus sequences were integrated into the chromosome of its insect host during coevolution. This study is the first report of a large double-stranded circular DNA virus genome in a sap-sucking hemipteran insect. IMPORTANCEThis is the first report of a large double-stranded DNA virus integrated genome in the planthopper, a plant sap-sucking hemipteran insect. It is an exciting addition to the evolutionary story of bracoviruses (polydnaviruses), nudiviruses, and baculoviruses. The results on the virus sequences integrated in the chromosomes of its insect host also represent a story of successful coevolution of an invertebrate virus and a plant sap-sucking insect. Brown planthoppers (BPH) (Nilaparvata lugens) are insect herbivores that feed mainly on rice. They damage rice plants by sucking sap from the vascular bundle and by transmitting the rice ragged stunt virus (RRSV) and rice grassy stunt virus (RGSV) (1). In addition, three commensal viruses have been characterized in BPH, i.e., Nilaparvata lugens reovirus (NLRV) (2), himetobi P virus (HiPV), and Nilaparvata lugens commensal X virus (NLCXV) (3). Recently, an iflavirus found in the honeydews of BPH was reported as Nilaparvata lugens honeydew virus 1 (NLHV-1) (4). These viruses infect BPH without visible symptoms, raising the question of how the insect host copes with various foreign microbes.In our study on the whole genome sequence of BPH, sequences that likely belonged to a previously unknown virus were identified (5). Homology analysis indicated that the sequences came from an uncharacterized virus that was related to the family Nudiviridae. Nudiviruses (Latin nudi ϭ naked) are a highly diverse group of invertebrate viruses that have rod-shaped nucleocapsids and large, double-stranded DNA (dsDNA) genomes. They were once described as "nonoccluded baculoviruses" but were later excluded from the family Baculoviridae (6). These baculovirus-like particles have been reported in a wide range of host species of insects and other arthropods (7, 8); however, although related to baculoviruses, they form a distinct lineage.To date, only a few nudiviruses have been well ...

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“…Subsequently, the genomes of GbNV (23), OrNV (24,25), and HzNV-2 (26) have been completely sequenced. Nudiviruses have large genomes.…”

Section: Resultsmentioning

confidence: 99%

Brown Planthopper Nudivirus DNA Integrated in Its Host Genome

Cheng

Lou

et al. 2014

J Virol

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“…To obtain a better picture of the evolution and diversity of arthropod large dsDNA viruses, we sequenced the complete genome of the O. rhinoceros NV (OrNV) [16]. As this was the first Coleopteran specific nudivirus to be sequenced, it should help to clarify the emerging picture of nudivirus genome plasticity.…”

Section: Introductionmentioning

confidence: 99%

“…OrNV was originally discovered in 1963 in Malaysia and has achieved great success as effective bio-control agents of the rhinoceros beetle, O. rhinoceros (Coleoptera: Scarabaeidae), a severe pest in coconut and oil palm cultivations in South-East Asia and the Pacific Islands [17]. Starting with six OrNV infected, field-collected beetles, which had provided a few nanograms of DNA, the OrNV DNA was then successfully amplified using multiple displacement amplification (MDA) to obtain enough DNA for sequencing the complete genome of OrNV [16]. Here, we report the in-depth analysis of the OrNV genome, including a comprehensive genome comparison with other large invertebrate DNA viruses.…”

Section: Introductionmentioning

confidence: 99%

The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses

et al. 2011

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The Oryctes rhinoceros nudivirus (OrNV) is a dsDNA virus with enveloped, rod-shaped virions. Its genome is 127,615 bp in size and contains 139 predicted protein-coding open reading frames (ORFs). In-depth genome sequence comparisons revealed a varying number of shared gene homologues, not only with other nudiviruses (NVs) and baculoviruses, but also with other arthropod-specific large dsDNA viruses, including the so-called Monodon baculovirus (MBV), the salivary gland hypertrophy viruses (SGHVs) and white spot syndrome virus (WSSV). Nudivirus genomes contain 20 baculovirus core gene homologues associated with transcription (p47, lef-8, lef-9, lef-4, vlf-1, and lef-5), replication (dnapol and helicase), virus structure (p74, pif-1, pif-2, pif-3, 19kda/pif-4, odv-e56/pif-5, vp91, vp39, and 38K), and unknown functions (ac68, ac81, and p33). Most strikingly, a set of homologous genes involved in peroral infection (p74, pif-1, pif-2, and pif-3) are common to baculoviruses, nudiviruses, SGHVs, and WSSV indicating an ancestral mode of infection in these highly diverged viruses. A gene similar to polyhedrin/granulin encoding the baculovirus occlusion body protein was identified in non-occluded NVs and in Musca domestica SGHV evoking the question of the evolutionary origin of the baculovirus polyhedrin/granulin gene. Based on gene homologies, we further propose that the shrimp MBV is an occluded member of the nudiviruses. We conclude that baculoviruses, NVs and the shrimp MBV, the SGHVs and WSSV share the significant number of conserved genetic functions, which may point to a common ancestry of these viruses.

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“…Moreover, our method provides a simple phase-sensitive probe of gap anisotropy that can be applied to other superconductors with other forms of anisotropic gap, such as p-wave and extended s-wave superconductors. Another variant on this method is to examine the coherence factors for scattering off conventional impurities at temperatures above T c : This approach may provide a viable way to probe the nature of the order that develops in the pseudogap normal state (24,25). Lastly, we note that Fourier-transform SI-STM is currently the only method to study the evolution of kdependent electronic states as a function of magnetic field and, in this respect, offers a useful tool for the study of a wide range of fieldinduced quantum phenomena (26).…”

mentioning

confidence: 99%

“…The genomes of HzNV-1; of Gryllus bimaculatus nudivirus (GbNV), a virus infecting the fat body of crickets; and of Oryctes rhinoceros nudivirus (OrNV), a biological control agent used to protect palm trees against the rhinoceros beetle have been sequenced (15,23,24). Partial data are also available for a shrimp nudivirus, designated here as PmV (GenBank accession number: 160432003).…”

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confidence: 99%