Brown planthopper nudivirus DNA integrated in its host genome

Abstract

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.

Importance: This 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.

FIG 1

Organization of NlENV ORFs in BPH scaffolds and contigs. ORFs and their transcriptional directions are indicated as arrows, and predicted BPH cellular genes in the flanking regions are also shown.

FIG 2

PCR examination of NlENV sequences in different BPH populations. (a) PCR survey of NlENV sequences in 22 BPH populations. Lanes A to V, BPH populations from Iloilo, Davao, and Stacruz (Philippines), Nan (Laos), Penang (Malaysia), Maharashtra (India), Nakhonsawan (Thailand), Hochiminh and Hanoi (Vietnam), and Haikou, Kunming, Yulin, Qingyuan, Wushan, Fuzhou, Wenzhou, Sanmen, Zhuji, Hangzhou, Tongxiang, Wuhan, and Yangzhou (China), respectively. (b) PCR examination performed on 10 individual BPH from nine selected populations.

FIG 3

Transcript levels of putative NlENV genes in BPH. Adults (female for ovary, male for testis, and both for fat body and midgut) at the third day after eclosion were used in the experiment. The GAPDH gene of BPH was used as an internal control to allow for normalization. Shown are the means ± standard deviations of triplicate results.

FIG 4

Nudivirus phylogeny. (a) Tree topologies of 4 single and combined PIF proteins (P74/PIF0, PIF1, PIF2, and PIF3) from nudiviruses and baculoviruses. To avoid missing data, a subset of taxa was selected to construct the unrooted trees. Log-likelihood values were calculated by matching all amino acid alignments with every topology and then subjected to Shimodaira-Hasegawa congruence tests. The results (also see Table S2 in the supplemental material) indicated that all topologies were congruent with the phylogenetic signal of each gene (a value of >0.05) and thus can be combined for phylogenetic analysis. (b) The tree of large arthropod DNA viruses based on the combined amino acid sequences of 4 PIF proteins. Multiple-sequence alignments were performed using ClustalX, and the tree was inferred using a mixed-model Bayesian phylogenetic analysis. The Bayesian inference posterior probabilities are presented at the nodes as percent values. Viruses included in this analysis were Autographa californica nucleopolyhedrovirus (AcMNPV), Pieris rapae granulosis virus (PrGV), Culex nigripalpus NPV (CuniNPV), Neodiprion lecontei NPV (NeleNPV), Cotesia congregata bracovirus (CcBV), Chelonus inanitus bracovirus (CiBV), Musca domestica salivary gland hypertrophy virus (MdSGHV), Glossina pallidipes salivary gland hypertrophy (GpSGHV), white spot syndrome virus (WSSV), Gryllus bimaculatus nudivirus (GbNV), Oryctes rhinoceros nudivirus (OrNV), Heliothis zea nudivirus 1 (HzNV-1), and Nilaparvata lugens endogenous nudivirus (NlENV). WSSV was used to root the tree.