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Dicistroviruses are members of a rapidly growing family of small RNA viruses. Related sequences have been discovered in many environmental samples, indicating that our knowledge about dicistrovirus diversity and host range is still limited. In this study, we performed a systematic search against the publicly available transcriptome database, and identified large numbers of dicistrovirus-like sequences in a wide variety of eukaryotic species. The origins of these sequences were 108 invertebrates (including 77 insect species belonging to 18 orders) and 11 plants, revealing new associations between dicistroviruses and hosts. Finally, 83 transcripts corresponding to nearly-complete viral genomes were retrieved from the RNA-seq data, of which most sequences showed limited similarity to known dicistroviruses and might present previously unreported virus species. Phylogenetic analysis suggested that horizontal virus transfer has occurred between diverse hosts and has important implications for dicistrovirus evolution. The results will provide new insight into the hidden diversity of the Dicistroviridae, and help us to better understand the viral evolution, host range and the possible way of transmission.

Nitzschia ZJU1, which originated from the diatom Nitzschia sp. (ash free dry weight of biomass was 0.12 g L−1 and its lipid content was 13.34 %) after 60Co-γ ray irradiation and domestication at high-salinity, was re-mutated by 137Cs-γ irradiation to increase lipid productivity. The lipid yields of the new mutants Nitzschia ZJU2 and Nitzschia ZJU3, which were selected by Nile Red fluorescence, were increased from 209.9 mg L−1 (for the original Nitzschia ZJU1) to 245.5 mg L−1 and 311.6 mg L−1, respectively. The lipid content of the two strains increased to 64.42 and 62.61 % of ash free dry weight, respectively, when the cells were cultured with nitrogen and silicon deprivation. It was found that 3,063 reads of genetic expression including Acetyl-CoA carboxylase and other important genes in lipid synthesis pathway were up-regulated and 4,598 reads of genetic expression were down-regulated in mutant Nitzschia ZJU2, when the cells were cultured in optimized growth medium without nitrogen and silicon. The gene expression levels of ATP-binding cassette transporters, arginine and proline metabolism, and proteasome in metabolic pathways were up-regulated to different degrees in mutant Nitzschia ZJU2 under the same cultivation condition.

The transcriptomes of original diatom strain (wild-type, Nitzschia sp.) and a mutant strain (Nitzschia ZJU2), which exhibited rapid growth and high lipid productivity after two rounds of mutagenesis by γ-rays, were sequenced using the Illumina sequencing platform. Genes in the metabolic pathway and those related to cell growth and lipid synthesis were compared between the two strains. Up to 25 804 and 35 228 transcripts were detected in Nitzschia sp. and Nitzschia ZJU2, respectively. A total of 3939 genes were up-regulated in mutant Nitzschia ZJU2. Nine metabolic pathways involved in cell growth and carbohydrate and protein syntheses obviously changed. Genes involved in lipid synthesis, such as acetyl-CoA carboxylase and diacylgycerol O-acyltransferase, were obviously up-regulated. These phenomena promoted cell growth and lipid synthesis, so as to increase the lipid production of cells. Analysis of single nucleotide polymorphisms revealed the presence of 40 795 nonsynonymous mutations in Nitzschia ZJU2, which indicated that nuclear irradiation triggers algal mutation.

Ge p- and n-MOSFETs with Al 2 O 3 /GeO x /Ge gate stack were fabricated and characterized using a novel sub-1 ns ultra-fast measurement system. Devices operation under the conditions, that applying Vg with the ultra-fast rise edge down to less than 1 ns are confirmed. It is found that the current degradation within the first 10 ns is much more significant than that from 100 ns to longer time due to the fast trapping effect. In additions, the trap density distributions in Ge MOSFETs inside Ec and Ev are measured and calculated.

Bombyx mori nucleopolyhedrovirus (BmNPV) is a baculovirus that selectively infects the domestic silkworm. In this study, six BmNPV strains were compared at the whole genome level. We found that the number of bro genes and the composition of the homologous regions (hrs) are the two primary areas of divergence within these genomes. When we compared the ORFs of these BmNPV variants, we noticed a high degree of sequence divergence in the ORFs that are not baculovirus core genes. This result is consistent with the results derived from phylogenetic trees and evolutionary pressure analyses of these ORFs, indicating that ORFs that are not core genes likely play important roles in the evolution of BmNPV strains. The evolutionary relationships of these BmNPV strains might be explained by their geographic origins or those of their hosts. In addition, the total number of hr palindromes seems to affect viral DNA replication in Bm5 cells.

The brown planthopper (Nilaparvata lugens, BPH), white-backed planthopper (Sogatella furcifera, WBPH) and small brown planthopper (Laodelphax striatellus, SBPH) are important rice pests in Asia. These three species differ in thermal tolerance and exhibit quite different migration and overwintering strategies. To understand the underlying mechanisms, we sequenced and compared the transcriptome of the three species under different temperature treatments. We found that metabolism-, exoskeleton- and chemosensory-related genes were modulated. In high temperature (37 °C), heat shock protein (HSP) genes were the most co-regulated; other genes related with fatty acid metabolism, amino acid metabolism and transportation were also differentially expressed. In low temperature (5 °C), the differences in gene expression of the genes for fatty acid synthesis, transport proteins and cytochrome P450 might explain why SBPH can overwinter in high latitudes, while BPH and WBPH cannot. In addition, other genes related with moulting, and membrane lipid composition might also play roles in resistance to low and high temperatures. Our study illustrates the common responses and different tolerance mechanisms of three rice planthoppers in coping with temperature change, and provides a potential strategy for pest management.

A Cripavirus-like long unique sequence was identified during transcriptome sequencing of the brown planthopper (BPH), Nilaparvata lugens. This unique sequence demonstrated high similarity with the whole-genome sequence of cricket paralysis virus, including 5′ and 3′ untranslated regions; thus we considered it the whole genome of a new virus. We propose that the virus be named Nilaparvata lugens C virus (NlCV). The plus-strand RNA genome spanned 9144 nt, excluding a 3′ poly(A) tail with two large ORFs encoding structural and non-structural proteins, respectively. Detection of NlCV in BPH honeydew raised the hypothesis of horizontal transmission of the virus. Honeydew from viruliferous BPHs was used to feed non-viruliferous insects, the results of which indicated that the BPH could acquire NlCV through feeding and that the virus could multiply in the insect body. A tissue-specific distribution test using real-time quantitative PCR demonstrated that NlCV was mainly present in the reproductive organs, and the virus was detected in eggs laid by viruliferous female insects using nested PCR, indicating the possibility of vertical transmission as well. As no significant symptom was detected in the viruliferous BPH, NlCV is considered a new commensal virus of BPH. Interestingly, this virus was also detected in two other hemipteran insects, the white-backed planthopper and the horned gall aphid, indicating that NlCV might be present in many other hemipteran insects and have a wide host range.

A baculovirus, named BomaNPV S2, was isolated from a diseased larva of the wild silkworm, Bombyx mandarina. Notably, BomaNPV S2 exhibited a distinguishing feature in that its host range covered that of both Bombyx mori nucleopolyhedrosis virus (BmNPV) and Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in cultured cells. It could replicate in cells of B. mori (Bm5 and BmN), Spodoptera frugiperda (Sf9) and Trichoplusia ni (Tn-5B1-4). However, occlusion-derived virions of BomaNPV S2 in B. mori cells contained only a single nucleocapsid, whereas they contained multiple nucleocapsids in Tn-5B1-4 cells. The complete genome sequence of BomaNPV S2, including predicted ORFs, was determined and compared with the genome sequence of its close relatives. The comparison results showed that most of the BomaNPV S2 genome sequence was shared with BmNPV (BmNPV T3) or BomaNPV S1, but several regions seemed more similar to regions of AcMNPV. This observation might explain why BomaNPV S2 covers the host ranges of BmNPV and AcMNPV. Further recombinant virus infection experiments demonstrated that GP64 plays an important role in BomaNPV S2 host-range determination.

The Bombyx mori nucleopolyhedrovirus (BmNPV) is a baculovirus that selectively infects domestic silkworm. BmNPV ORF71 (Bm71) is not a core set gene in baculovirus and shares 92 % amino acid sequence identity with Autographa californica multinucleocapsid NPV ORF88 (Ac88/cg30). Previously, it has been reported that virus lacking Ac88 had no striking phenotypes in cell lines or host larvae. However, the exact role of Bm71 during BmNPV life cycle remains unknown. In the present study, we constructed a Bm71-disrupted (Bm71-D) virus and assessed the effect of the Bm71 disruption on viral replication and viral phenotype throughout the viral life cycle. Results showed that the Bm71-D bacmid could successfully transfect Bm5 cell lines and produce infectious budded virus (BV). But the BV titer was 10- to 100-fold lower than that of the wild-type (WT) virus during infection, and the decreased BV titer was rescued by Bm71 gene repair virus (Bm71-R). A larval bioassay showed that Bm71-D virus took 7.5 h longer than the WT to kill Bombyx mori larvae. Transmission electron microscopy analysis indicated that the Bm71-D virus-infected cells had typical virogenic stroma, bundles of nucleocapsids and polyhedra. Taken together, these results suggest that Bm71 has important implications for determining BV yield and virulence in viral life cycle even though it is not an essential gene for replication of BmNPV.

Background The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management. To better understand how a monophagous sap-sucking arthropod herbivore has adapted to its exclusive host selection and to provide insights to improve pest control, we analyzed the genomes of the brown planthopper and its two endosymbionts. Results We describe the 1.14 gigabase planthopper draft genome and the genomes of two microbial endosymbionts that permit the planthopper to forage exclusively on rice fields. Only 40.8% of the 27,571 identified Nilaparvata protein coding genes have detectable shared homology with the proteomes of the other 14 arthropods included in this study, reflecting large-scale gene losses including in evolutionarily conserved gene families and biochemical pathways. These unique genomic features are functionally associated with the animal’s exclusive plant host selection. Genes missing from the insect in conserved biochemical pathways that are essential for its survival on the nutritionally imbalanced sap diet are present in the genomes of its microbial endosymbionts, which have evolved to complement the mutualistic nutritional needs of the host. Conclusions Our study reveals a series of complex adaptations of the brown planthopper involving a variety of biological processes, that result in its highly destructive impact on the exclusive host rice. All these findings highlight potential directions for effective pest control of the planthopper. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0521-0) contains supplementary material, which is available to authorized users.

Bombyx mori nucleopolyhedrovirus (BmNPV) is a typical species of Baculoviridae . The complete genome sequence of a BmNPV strain with cubic occlusion bodies is reported here. The genome of this strain consists of 127,465 nucleotides with a G+C content of 40.36% and is 97.3% and 97.5% identical to those of BmNPV strain T3 and Bombyx mandarina NPV S1, respectively. Despite the abnormal polyhedra it forms, the polyhedrin gene of the BmNPV cubic strain is 100% identical to those of the other two strains. Baculovirus repeated ORFs and homologous repeat regions cause the major differences in genome size of these BmNPV isolates.

Although microarray and expressed sequence tag (EST)-based approaches have been used to profile gene expression during baculovirus infection, the response of host genes to baculovirus infection and the interaction between baculovirus and its host remain largely unknown. To determine the host response to Bombyx mori nucleopolyhedrovirus infection and the dynamic interaction between the virus and its host, eight digital gene expression libraries were examined in a Bm5 cell line before infection and at 1.5, 3, 6, 12, 24, 48, and 96 h postinfection. Gene set enrichment analysis of differentially expressed genes at each time point following infection showed that gene sets including cytoskeleton, transcription, translation, energy metabolism, iron ion metabolism, and the ubiquitin-proteasome pathway were altered after viral infection. In addition, a time course depicting protein-protein interaction networks between the baculovirus and the host were constructed and revealed that viral proteins interact with a multitude of cellular machineries, such as the proteasome, cytoskeleton, and spliceosome. Several viral proteins, including IE2, CG30, PE38, and PK-1/2, were predicted to play key roles in mediating virus-host interactions. Based on these results, we tested the role of the ubiquitin-proteasome pathway and iron ion metabolism in the viral infection cycle. Treatment with a proteasome inhibitor and deferoxamine mesylate in vitro and in vivo confirmed that these pathways regulate viral infection. Taken together, these findings provide new insights into the interaction between the baculovirus and its host and identify molecular mechanisms that can be used to block viral infection and improve baculovirus expression systems.

Bombyx mori nucleopolyhedrovirus (BmNPV) ORF54 (Bm54), a member of the viral desmoplakin N-terminus superfamily, is homologous to Autographa californica nucleopolyhedrovirus (AcMNPV) ORF66, which is required for the efficient egress of nucleocapsids from the nucleus and occlusion body formation. In this paper, we generated a bacmid with the Bm54 gene deleted via homologous recombination in Escherichia coli and characterized the mutant virus using a transfection-infection assay and transmission electron microscopy analysis. Our results demonstrated that the cells transfected with viral DNA lacking Bm54 produced non-infectious budded viruses (BVs). Electron microscopy showed that although the deletion of Bm54 did not affect assembly and release of nucleocapsids, it severely affected polyhedron formation. In conclusion, deletion of Bm54 resulted in non-infectious BV and defective polyhedra. Although the sequences of Bm54 and Ac66 are very similar, the two genes function quite differently in the regulation of viral life cycle.