The Complete Genome Sequence of Plodia Interpunctella Granulovirus: Evidence for Horizontal Gene Transfer and Discovery of an Unusual Inhibitor-of-Apoptosis Gene

Genome comparison of long-circulating field CnmeGV isolates from the same region

Cnaphalocrocis medinalis granulovirus (CnmeGV), belonging to Betabaculovirus cnamedinalis, can infect the rice pest, the rice leaf roller. In 1979, a CnmeGV isolate, CnmeGV-EP, was collected from Enping County, China. In 2014, we collected another CnmeGV isolate, CnmeGV-EPDH3, at the same location and obtained the complete virus genome sequence using Illumina and ONT sequencing technologies. By combining these two virus isolates, we updated the genome annotation of CnmeGV and conducted an in-depth analysis of its genome features. CnmeGV genome contains abundant tandem repeat sequences, and the repeating units in the homologous regions (hrs) exhibit overlapping and nested patterns. The genetic variations within EPDH3 population show the high stability of CnmeGV genome, and tandem repeats are the only region of high genetic variation in CnmeGV genome replication. Some defective viral genomes formed by recombination were found within the population. Comparison analysis of the two virus isolates collected from Enping showed that the proteins encoded by the CnmeGV-specific genes were less conserved relative to the baculovirus core genes. At the genomic level, there are a large number of SNPs and InDels between the two virus isolates, especially in and around the bro genes and hrs. Additionally, we discovered that CnmeGV acquired a segment of non-ORF sequence from its host, which does not provide any new proteins but rather serves as redundant genetic material integrated into the viral genome. Furthermore, we observed that the host's transposon piggyBac has inserted into some virus genes. Together, dsDNA viruses could acquire non-coding genetic material from their hosts to expand the size of their genomes. These findings provide new insights into the evolution of dsDNA viruses.

Regulatory Mechanisms, Protein Expression and Biological Activity of Photolyase Gene from Spodoptera littoralis Granulovirus Genome

One of the most important factor that affects the efficient using of baculoviruses as a biopesticide is their sensitivity to UV irradiation. In this study, a photolyase gene (phr) of 1.4 kbp DNA fragment was cloned and characterized from Spodoptera littoralis granulovirus, an Egyptian isolate (SpliGV-EG1). A sequence of 466 amino acid were deduced when the gene was completely sequenced with a predicted molecular mass of ~ 55 kDa. Transcriptional regulation analyses revealed that phr transcripts were detected early at 6-h post-infection (hpi) and remained detectable until 72 hpi, suggesting their transcriptional regulation from a putative early promoter motif. An approximately ~ 55 kDa protein fragment was expressed from phr-induced bacterial culture and detected by SDS-PAGE and western blotting. In addition, direct exposure to UV irradiation resulted in a twofold decrease in SpliGV-EG1 occlusion bodies activation compared with Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) occlusion bodies which decreased with about 129-fold after exposure to UV irradiation based on median lethal concentration value (LC50). The obtained results suggested that the presence of photolyase gene possibly alters the inactivation of SpliGV-EG1-occluded bodies by UV irradiation. These results support the role and application of the photolyase protein to improve the damaged DNA repair mechanism as well as resistance of SpliGV to UV light inactivation.

Genome analysis of Psilogramma increta granulovirus and its intrapopulation diversity

The complete genome of Psilogramma increta granulovirus (PsinGV), isolated from P. increta (Lepidoptera: Sphingidae), was ultra-deep sequenced with a Novaseq PE150 platform and de novo assembled and annotated. The PsinGV genome is a circular double-stranded DNA, 103,721 bp in length, with a G+C content of 33.0%, the third lowest G+C content in present sequenced baculoviruses. It encodes 123 putative open reading frames, including 38 baculovirus core genes, 42 lepidopteran baculovirus conserved genes, 38 betabaculovirus conserved genes, and 5 genes unique to PsinGV. Meanwhile, 3 homologous repeated regions with the core sequence TTGCAA and 3 direct repeated sequences were identified within the PsinGV genome. Kimura two-parameters distance analysis confirmed that Psilogramma increta granulovirus is a representative of a prospective new species of the genus Betabaculovirus. Phylogenetic analysis based on the baculovirus core genes showed that PsinGV is closely related to Choristoneura fumiferana granulovirus, Clostera anastomosis granulovirus-B, and Erinnyis ello granulovirus. These four species therefore share a common ancestor residing in the Betabaculovirus genus. The genome of the PsinGV isolate contained two p10 copies: p10 and p10-2. Phylogenetic reconstruction of P10 suggests a transfer event of the p10-2 gene from an alphabaculovirus to the aforementioned common ancestor. Analysis of genomic diversity showed that 203 intrahost variants, including 182 single nucleotide variants and 21 short insertions/deletions, are present within the PsinGV isolate. Meanwhile, allele frequency indicated that the isolate contains three major genotypes, implying the archived isolate consists of several P. increta carcasses killed by PsinGV with different genotypes.

The evolution of host specialization in an insect pathogen

Niche breadth coevolution between biotic partners underpins theories of diversity and co-existence and influences patterns of disease emergence and transmission in host-parasite systems. Despite these broad implications, we still do not fully understand how the breadth of parasites' infectivity evolves, the nature of any associated costs, or the genetic basis of specialization. Here, we serially passage a granulosis virus on multiple inbred populations of its Plodia interpunctella host to explore the dynamics and outcomes of specialization. In particular, we collect time series of phenotypic and genetic data to explore the dynamics of host genotype specialization throughout the course of experimental evolution and examine two fitness components. We find that the Plodia interpunctella granulosis virus consistently evolves and increases in overall specialization, but that our two fitness components evolve independently such that lines can specialize in productivity or infectivity. Furthermore, we find that specialization in our experiment is a highly polygenic trait best explained by a combination of evolutionary mechanisms. These results are important for understanding the evolution of specialization in host-parasite interactions and its broader implications for co-existence, diversification, and infectious disease management.

Genome Analysis of a Novel Clade b Betabaculovirus Isolated from the Legume Pest Matsumuraeses phaseoli (Lepidoptera: Tortricidae)

Matsumuraeses phaseoli is a Lepidopteran pest that primarily feeds on numerous species of cultivated legumes, such as Glycine and Phaseolus. It is widely distributed in northeast Asia. A novel granulovirus, designated as Matsumuraeses phaseoli granulovirus (MaphGV), was isolated from pathogenic M. phaseoli larvae that dwell in rolled leaves of Astragalus membranaceus, a Chinese medicinal herb. In this study, using next-generation sequencing, we report the complete genome of MaphGV. MaphGV genome comprises a double-stranded DNA of 116,875 bp, with 37.18% GC content. It has 128 hypothetical open reading frames (ORFs). Among them, 38 are baculovirus core genes, 18 are lepidopteran baculovirus conserved genes, and 5 are unique to Baculoviridae. MaphGV has one baculovirus repeat ORF (bro) and three inhibitors of apoptosis proteins (iap), including a newfound iap-6. We found two atypical baculoviral homologous regions (hrs) and four direct repeats (drs) in the MaphGV genome. Based on phylogenetic analysis, MaphGV belongs to Clade b of Betabaculovirus and is closely related to Cydia pomonellagranulovirus (CpGV) and Cryptophlebia leucotretagranulovirus (CrleGV). This novel baculovirus discovery and sequencing are invaluable in understanding the evolution of baculovirus and MaphGV may be a potential biocontrol agent against the bean ravaging pest.

Transcriptome-Wide Identification of MicroRNAs and Analysis of Their Potential Roles in Development of Indian Meal Moth (Lepidoptera:Pyralidae)

MicroRNAs (miRNAs) have been reported to play indispensable roles in regulating various developmental processes via the posttranscriptional repression of target genes in insect species. In the present paper, we studied the miRNAs in Indian meal moth (Plodia interpunctella (Hübener)), one of the most economically important stored grains pests around the world. In total, 12 small RNA libraries from four developmental stages of P. interpunctella were constructed, and 178 known and 23 novel miRNAs were identified. In addition, the expression profiles of these miRNAs were assessed across different developmental stages and miRNAs that were highly expressed in eggs, larvae, pupae, and adults were identified. Specifically, 100, 61, and 52 miRNAs were differentially expressed between eggs and larvae, larvae and pupae, and pupae and adults, respectively. The KEGG and GO analysis of the predicted target genes suggested the essential roles of miRNAs in the regulation of complex development of P. interpunctella. Importantly, we also found a set of miRNAs might be involved in the larval metamorphic molting process, with their expressions increasing and then decreasing during the larva-pupa-adult stages of P. interpunctella. In conclusion, the current paper has discovered numerous miRNAs, and some key miRNAs that might be responsible for regulating development in P. interpunctella. To our knowledge, this is the first study to document miRNAs and their expression patterns in interpunctella, and those findings would lay an important molecular foundation for future functional analysis of these miRNAs in P. interpunctella.

The complete genome of Rachiplusia nu nucleopolyhedrovirus (RanuNPV) and the identification of a baculoviral CPD-photolyase homolog

We described a novel baculovirus isolated from the polyphagous insect pest Rachiplusia nu. The virus presented pyramidal-shaped occlusion bodies (OBs) with singly-embed nucleocapsids and a dose mortality response of 6.9 × 10³ OBs/ml to third-instar larvae of R. nu. The virus genome is 128,587 bp long with a G + C content of 37.9% and 134 predicted ORFs. The virus is an alphabaculovirus closely related to Trichoplusia ni single nucleopolyhedrovirus, Chrysodeixis chalcites nucleopolyhedrovirus, and Chrysodeixis includens single nucleopolyhedrovirus and may constitute a new species. Surprisingly, we found co-evolution among the related viruses and their hosts at species level. Besides, auxiliary genes with homologs in other baculoviruses were found, e.g. a CPD-photolyase. The gene seemed to be result of a single event of horizontal transfer from lepidopterans to alphabaculovirus, followed by a transference from alpha to betabaculovirus. The predicted protein appears to be an active enzyme that ensures likely DNA protection from sunlight.

Characterization of the RNA Transcription Profile of Bombyx mori Bidensovirus

Bombyx mori bidensovirus (BmBDV) is a single-stranded DNA (ssDNA) virus from the genus Bidensovirus of the Bidnaviridae family, which, thus far, solely infects insects. It has a unique genome that contains bipartite DNA molecules (VD1 and VD2). In this study, we explored the detailed transcription mapping of the complete BmBDV genome (VD1 and VD2) by rapid amplification of cDNA ends (RACE), reverse transcription quantitative real-time PCR (RT-qPCR), and luciferase assays. For the first time, we report the transcription map of VD2. Our mapping of the transcriptional start sites reveals that the NS genes in VD1 have separate transcripts that are derived from overlapping promoters, P5 and P5.5. Thus, our study provides a strategy for alternative promoter usage in the expression of BmBDV genes.

Vgas: A Viral Genome Annotation System

The in-depth study of viral genomes is of great help in many aspects, especially in the treatment of human diseases caused by viral infections. With the rapid accumulation of viral sequencing data, improved, or alternative gene-finding systems have become necessary to process and mine these data. In this article, we present Vgas, a system combining an ab initio method and a similarity-based method to automatically find viral genes and perform gene function annotation. Vgas was compared with existing programs, such as Prodigal, GeneMarkS, and Glimmer. Through testing 5,705 virus genomes downloaded from RefSeq, Vgas demonstrated its superiority with the highest average precision and recall (both indexes were 1% higher or more than the other programs); particularly for small virus genomes (≤ 10 kb), it showed significantly improved performance (precision was 6% higher, and recall was 2% higher). Moreover, Vgas presents an annotation module to provide functional information for predicted genes based on BLASTp alignment. This characteristic may be specifically useful in some cases. When combining Vgas with GeneMarkS and Prodigal, better prediction results could be obtained than with each of the three individual programs, suggesting that collaborative prediction using several different software programs is an alternative for gene prediction. Vgas is freely available at http://cefg.uestc.cn/vgas/ or http://121.48.162.133/vgas/. We hope that Vgas could be an alternative virus gene finder to annotate new genomes or reannotate existing genome.

Dietary Protein and Carbohydrate Levels Affect Performance and Digestive Physiology of Plodia interpunctella (Lepidoptera: Pyralidae)

In this study, life history and nutritional indices of Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae) was evaluated on six food commodities: dried fig, dried wheat germ, dried white mulberry, groundnut, pistachio, and raisin, compared with artificial diet. The influence of dietary macronutrient content on digestive α-amylase was also assessed. A delay in the developmental time of P. interpunctella immature stages was detected when larvae were fed on raisin. The highest survival rate of immature stages was on the artificial diet, and the lowest was on raisin. The highest realized fecundity and fertility were recorded for the females reared on artificial diet. Overall, fourth instar P. interpunctella reared on artificial diet had the highest relative consumed and growth rate, and lowest rates were observed in larvae fed raisin. Amylolytic activity and isoform patterns varied depending on larval instar and diets, but were higher for larvae fed artificial diet with moderate carbohydrate and protein. Zymograms showed the presence of three isoforms of α-amylase in midgut extracts of P. interpunctella fed different diets. Larvae fed dried white mulberry, fig, and raisin had one (A2) α-amylase isoform. The data suggest that dietary carbohydrate and protein content induce changes in nutritional efficiency, development, and α-amylase activity. A survey of the differences in digestive enzyme activity in response to macronutrient balance and imbalance highlight their importance in the nutrition of insects.

A Novel Betabaculovirus Isolated from the Monocot Pest Mocis latipes (Lepidoptera: Noctuidae) and the Evolution of Multiple-Copy Genes

In this report, we described the genome of a novel baculovirus isolated from the monocot insect pest Mocis latipes, the striped grass looper. The genome has 134,272 bp in length with a G + C content of 38.3%. Based on the concatenated sequence of the 38 baculovirus core genes, we found that the virus is a betabaculovirus closely related to the noctuid-infecting betabaculoviruses including Pseudaletia unipuncta granulovirus (PsunGV), Trichoplusia ni granulovirus (TnGV), Helicoverpa armigera granulovirus (HearGV), and Xestia c-nigrum granulovirus (XecnGV). The virus may constitute a new Betabaculovirus species tentatively named Mocis latipes granulovirus (MolaGV). After gene content analysis, five open reading frames (ORFs) were found to be unique to MolaGV and several auxiliary genes were found including iap-3, iap-5, bro-a, bro-b, and three enhancins. The virus genome lacked both chitinase and cathepsin. We then looked at the evolutionary history of the enhancin gene and found that betabaculovirus acquired this gene from an alphabaculovirus followed by several duplication events. Gene duplication also happened to an endonuclease-like gene. Genomic and gene content analyses revealed both a strict collinearity and gene expansion into the genome of the MolaGV-related species. We also characterized the granulin gene using a recombinant Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and found that occlusion bodies were produced into the nucleus of infected cells and presented a polyhedral shape and no occluded virions within. Overall, betabaculovirus genome sequencing is of importance to the field as few genomes are publicly accessible. Mocislatipes is a secondary pest of maize, rice, and wheat crops in Brazil. Certainly, both the discovery and description of novel baculoviruses may lead to development of greener and safer pesticides in order to counteract and effectively control crop damage-causing insect populations

Characterization of transcriptome in the Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) and gene expression analysis during developmental stages

The Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) is a worldwide pest that causes serious damage to stored foods. Although many efforts have been conducted on this species due to its economic importance, the study of genetic basis of development, behavior and insecticide resistance has been greatly hampered due to lack of genomic information. In this study, we used high throughput sequencing platform to perform a de novo transcriptome assembly and tag-based digital gene expression profiling (DGE) analyses across four different developmental stages of P. interpunctella (egg, third-instar larvae, pupae and adult). We obtained approximate 9gigabyte (GB) of clean data and recovered 84,938 unigenes, including 37,602 clusters and 47,336 singletons. These unigenes were annotated using BLAST against the non-redundant protein databases and then functionally classified based on Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes databases (KEGG). A large number of differentially expressed genes were identified by pairwise comparisons among different developmental stages. Gene expression profiles dramatically changed between developmental stage transitions. Some of these differentially expressed genes were related to digestion and cuticularization. Quantitative real-time PCR results of six randomly selected genes conformed the findings in the DGEs. Furthermore, we identified over 8000 microsatellite markers and 97,648 single nucleotide polymorphisms which will be useful for population genetics studies of P. interpunctella. This transcriptomic information provided insight into the developmental basis of P. interpunctella and will be helpful for establishing integrated management strategies and developing new targets of insecticides for this serious pest.

The Complete Genome Sequence of a Second Distinct Betabaculovirus from the True Armyworm, Mythimna unipuncta

The betabaculovirus originally called Pseudaletia (Mythimna) sp. granulovirus #8 (MyspGV#8) was examined by electron microscopy, host barcoding PCR, and determination of the nucleotide sequence of its genome. Scanning and transmission electron microscopy revealed that the occlusion bodies of MyspGV#8 possessed the characteristic size range and morphology of betabaculovirus granules. Barcoding PCR using cytochrome oxidase I primers with DNA from the MyspGV#8 collection sample confirmed that it had been isolated from the true armyworm, Mythimna unipuncta (Lepidoptera: Noctuidae) and therefore was renamed MyunGV#8. The MyunGV#8 genome was found to be 144,673 bp in size with a nucleotide distribution of 49.9% G+C, which was significantly smaller and more GC-rich than the genome of Pseudaletia unipuncta granulovirus H (PsunGV-H), another M. unipuncta betabaculovirus. A phylogeny based on concatenated baculovirus core gene amino acid sequence alignments placed MyunGV#8 in clade a of genus Betabaculovirus. Kimura-2-parameter nucleotide distances suggested that MyunGV#8 represents a virus species different and distinct from other species of Betabaculovirus. Among the 153 ORFs annotated in the MyunGV#8 genome, four ORFs appeared to have been obtained from or donated to the alphabaculovirus lineage represented by Leucania separata nucleopolyhedrovirus AH1 (LeseNPV-AH1) during co-infection of Mythimna sp. larvae. A set of 33 ORFs was identified that appears only in other clade a betabaculovirus isolates. This clade a-specific set includes an ORF that encodes a polypeptide sequence containing a CIDE_N domain, which is found in caspase-activated DNAse/DNA fragmentation factor (CAD/DFF) proteins. CAD/DFF proteins are involved in digesting DNA during apoptosis.