The Commensal Viruses In The Brown Planthopper, Nilaparvata Lugens

The brown planthopper (BPH), Nilaparvata lugens, is one of the most destructive insect pests of rice crops in Asia. They damage rice plants by sucking sap from the vascular bundle and by transmitting the rice viruses. In addition, many commensal viruses have been characterized in BPH, which infect BPH without visible symptoms and co-evolution with their host. Based on the massive data produced by high-throughput sequencing, we carried out a study on the commensal viruses in BPH, and identified two kind of uncharacterized viruses through sequence assembly and analysis. Moreover, as the increasing availability of bioinformatics databases, we performed data mining with the transcriptome and genome assembly of other insects and arthropods to discover sequences that derived from viruses. The mainly results are listed as followings:(1) Various kinds of RNA virus sequences were identified in the transcriptome of BPH, and their distribution in different tissues were compared. Some of these sequences were derived from known commensal viruses of BPH, including a dsRNA virus and several ss(+)RNA viruses. Besides, sequences with similarity to ss(-)RNA viruses were also found in the BPH transcriptome. Phylogenetic analysis suggested that the sequence might belong to an uncharacterized virus of the Quaranjavirus genus.(2) A Cripavirus-like long unique sequence was obtained from the transcriptome data of BPH. This unique sequence demonstrated high similarity with the whole-genome sequence of cricket paralysis virus (CrPV), including 5’and 3’ untranslated regions. We proposed that the virus be named Nilaparvata lugens C virus (N1CV). The plus-strand RNA genome spanned 9,144 nucleotides, excluding a 3’poly (A) tail with 2 large open reading frames (ORF) encoding structural and non-structural proteins, respectively. N1CV was detected in BPH honeydew, and could transmit through feeding. Besides, the virus was detected in eggs laid by viruliferous female insects using nested PCR method, indicating the possibility of vertical transmission as well. N1CV could multiply in the insect but no significant symptom was detected in the viruliferous BPH. Thus N1CV is considered a new commensal virus of BPH. Interestingly, this virus was also detected in other two hemipteran insects, the white backed planthopper and the horned gall aphid, indicating that N1CV might be present in many other hemipteran insects and have a wide host range.(3) Using the known dicistrovirus sequences as probes, we identified large numbers of novel dicistrovirus-like sequences in the NCBI TSA (Transcriptome shotgun assembly) database. These 93 sequences were from 22 insect species belonging to 5 orders,16 other invertebrates and 13 plants. Most viral sequences obtained showed limited similarity to known viruses and might present previously undescribed virus species. Phylogenetic analysis indicated complicated interaction and evolutional relationship between virus and their hosts or vectors. These sequences were valuable resources for us to better understand viral diversity, host range and the possible way of transmission.(4) Nudivirus-like sequences were identified in the genome assembly of BPH. A total of 66 viral ORFs were predicted, which distributed in 15 scaffolds or contigs. Thirty-two of the 33 nudivirus core genes were identified, including 20 genes homologous to baculovirus core genes. In addition, several gene clusters that arranged collinearly with other nudiviruses were found in the partial genome of the original virus. In a phylogenetic tree constructed using the supermatrix method, the original virus was grouped with other nudivirus and closely related to bracoviruses of the Polydnaviridae. Taken together, these data indicated that the viral sequences belong to a new member of the family Nudiviridae. More specifically, the virus sequences were integrated into the chromosomes of its host during co-evolution, and represent another kind of endogenous viral elements in insect genomes.(5) We searched for nudivirus-like sequences in 128 sequenced genomes of insects and other arthropods from the WGS (whole genome shotgun) database. A total of 174 sequences that had significant homology to known nudivirus proteins were found out from genome assembly of 28 species. Some of these were endogenous sequences that were integrated into the host genomes. The similarity between these sequences and known viruses were low, so we considered that they were derived from uncharacterized virus. We also investigate the coding ability and expression of these sequences, as well as their relationship to the existing nudiviruses. These results indicated that the virus group was widely distributed in arthropods, and was highly diversed.