Whole-genome sequencing and comparative transcriptome analysis of Bombyx mori nucleopolyhedrovirus La strain

Differential pathogenicity of heterologous nucleopolyhedroviruses on Spodoptera frugiperda corresponds to modulated expression of immune-response-related genes

The fall armyworm Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) is a notorious invasive pest wreaking havoc on various crops globally. Nucleopolyhedroviruses (NPVs) are viral pathogens that specially target lepidopteran pests. However, the homologous virus, Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV), has not been commercialized in China. Therefore, understanding the molecular mechanisms underlying heterologous virus-host interactions can inform the design of virus-based insecticides for controlling S. frugiperda. The pathogenicity of the four heterologous NPVs on S. frugiperda varied greatly. Mamestra brassicae multiple nucleopolyhedrovirus (MbMNPV) exhibited the most potent virulence on larvae and induced the most robust sublethal effects on adults. Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) infection was characterized by more moderate pathogenicity, and larvae were relatively resistant to Helicoverpa armigera single nucleopolyhedrovirus (HaSNPV) and Spodoptera litura multiple nucleopolyhedrovirus (SlMNPV). Larval mortality was virus-concentration and larval stage dependent. Specifically, the corrected mortality rate of third instar larvae after treatment with 1 × 106, 1 × 107, and 1 × 108 OBs/mL MbMNPV was 88.9 %, 100.0 %, and 100.0 %, respectively. All four NPVs negatively affected the longevity and fecundity of S. frugiperda adults. Female adults surviving treatment with MbMNPV and SeMNPV were unable to lay eggs. Transcriptomic analysis revealed that MbMNPV infection might suppress the antiviral immune response, and dysregulate biological pathways of S. frugiperda larvae to facilitate systemic infection. However, the overall transcript profiles remain unchanged after SlMNPV infection. The results reinforce the potential of NPVs, specifically MbMNPV, as potent biocontrol agents for S. frugiperda. These findings yield valuable insights into the complex arms race between S. frugiperda and NPVs that may advance the development of virus-based strategies to mitigate the destructive impact of this pest.

Genomic Analysis Reveals Novel Genes and Adaptive Mechanisms for Artificial Diet Utilization in the Silkworm Strain Guican No.5

The transition from traditional mulberry leaf feeding to artificial diet cultivation represents a major advancement in modern sericulture, yet the genetic mechanisms driving this adaptation remain largely unexplored. This study investigates the genomic basis of artificial diet adaptation in the silkworm strain Guican No.5 through whole-genome resequencing and transcriptome analysis. We identified 8,935,179 single-nucleotide polymorphisms (SNPs) across all chromosomes, accounting for 2.01% of the genome, with particularly high densities observed in chromosomes 23, 26, and 28. Our analysis also revealed 879 novel transcripts, many of which are involved in digestion, detoxification, and stress response pathways. Key novel genes, including three carboxylesterases, two cytochrome P450s, one heat shock protein, and one copper/zinc superoxide dismutase, exhibited varying degrees of sequence similarity to known proteins, suggesting modifications to existing genetic frameworks. Notably, one novel P450 gene displayed only 74.07% sequence identity with its closest homolog, indicating the emergence of a new protein sequence. Additionally, several key genes showed high similarity to wild silkworm (Bombyx mandarina) proteins, underscoring their evolutionary origins. These findings provide valuable insights into the molecular mechanisms underpinning artificial diet adaptation in silkworms and offer genomic resources to enhance artificial diet formulations and breeding programs in sericulture.

Distribution and genetic diversity of Bombyx mori nucleopolyhedrovirus in mass-reared silkworms in Thailand

Silk is an economically and culturally important product of Thailand that is threatened by the outbreaks of the Bombyx mori nucleopolyhedrovirus (BmNPV) in silkworm rearings. BmNPV infects the larval stages of the silkworm Bombyx mori, causing fatal viral infection and preventing the larvae from reaching the pupal stage. Numerous BmNPV isolates have been described from silk-producing countries from all over the world. In this study, the geographic distribution of BmNPV in Thailand was analyzed by collecting 18 samples from different regions. The BmNPV samples were analyzed by PCR and whole genome sequencing was performed for eight specimens. Their genome size ranged from 125,888 bp to 126,783 bp, comprising 138 open reading frames. Although the sequenced BmNPV genomes could be phylogenetically differentiated, no correlation between geographic and genetic distance was observed, indicating a close relationship between the BmNPV from Thailand.

Complete genome sequence of a nucleopolyhedrovirus isolated from Bombyx mori in Hakozaki, Japan, obtained using Oxford Nanopore Technologies sequencing

I report the complete genome sequence of an isolate of nucleopolyhedrovirus from Bombyx mori, the domesticated silkworm, maintained for the long term at Kyushu University in Hakozaki, Fukuoka Prefecture, Japan. The genome is 127,783 bp long, with a G+C content of 40.3%, and contains 142 open reading frames.

High-Quality de novo Chromosome-Level Genome Assembly of a Single Bombyx mori With BmNPV Resistance by a Combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing

The reference genomes of Bombyx mori (B. mori), Silkworm Knowledge-based database (SilkDB) and SilkBase, have served as the gold standard for nearly two decades. Their use has fundamentally shaped model organisms and accelerated relevant studies on lepidoptera. However, the current reference genomes of B. mori do not accurately represent the full set of genes for any single strain. As new genome-wide sequencing technologies have emerged and the cost of high-throughput sequencing technology has fallen, it is now possible for standard laboratories to perform full-genome assembly for specific strains. Here we present a high-quality de novo chromosome-level genome assembly of a single B. mori with nuclear polyhedrosis virus (BmNPV) resistance through the integration of PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing. In addition, regular bioinformatics analyses, such as gene family, phylogenetic, and divergence analyses, were performed. The sample was from our unique B. mori species (NB), which has strong inborn resistance to BmNPV. Our genome assembly showed good collinearity with SilkDB and SilkBase and particular regions. To the best of our knowledge, this is the first genome assembly with BmNPV resistance, which should be a more accurate insect model for resistance studies.

H3K4me3 histone modification in baculovirus-infected silkworm cells

Baculovirus infection modulates the chromatin states and gene expression of host insect cells. Here we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of H3 trimethylated at Lys4 (H3K4me3) histone modification in Bombyx mori nucleopolyhedrovirus-infected Bombyx mori cells. The ChIP-seq data revealed the changes of the genome-wide distribution and accumulation of euchromatic histone marks in host insect cells during the progression of baculovirus infection.

Genomic Sequence Analysis of Bombyx mori Nucleopolyhedrovirus Isolated from Yunnan Sericulture Region, China

The blood pathogens of grasserie caused by Bombyx mori nucleopolyhedrovirus BmNPV have a serious impact on the sericulture industry. To understand the genetic status of BmNPV endemic strains in the Yunnan sericulture region, the structure and complete genome sequence of BmNPV isolated from Baoshan city of Yunnan Province were described and compared to known strains. The BmNPV-Baoshan isolate was a nucleopolyhedrovirus parasitized in silkworm larvae. Its genome has 128, 452 bp with a G + C content of 40.4%. Phylogenetic analysis clustered the virus with China BmNPV isolates; BmNPV-Baoshan was closely related to BomaNPV-S1 (both strains originated from the same ancestor). BmNPV-Baoshan strain has bro-b gene deletion, hr1 missing 4 repeat units of 30-bp palindrome structure compared to BmNPV-T3 strain. The aim of this study was to elucidate the evolution of the virus further and provide insights for the protection of virus-induced hematologic sepsis.

Global Metabolic Profiling of Baculovirus Infection in Silkworm Hemolymph Shows the Importance of Amino-Acid Metabolism

Viruses rely on host cell metabolism to provide the necessary energy and biosynthetic precursors for successful viral replication. Infection of the silkworm, Bombyx mori, by Bombyx mori nucleopolyhedrovirus (BmNPV), has been studied extensively in the past to unravel interactions between baculoviruses and their lepidopteran hosts. To understand the interaction between the host metabolic responses and BmNPV infection, we analyzed global metabolic changes associated with BmNPV infection in silkworm hemolymph. Our metabolic profiling data suggests that amino acid metabolism is strikingly altered during a time course of BmNPV infection. Amino acid consumption is increased during BmNPV infection at 24 h post infection (hpi), but their abundance recovered at 72 hpi. Central carbon metabolism, on the other hand, particularly glycolysis and glutaminolysis, did not show obvious changes during BmNPV infection. Pharmacologically inhibiting the glycolytic pathway and glutaminolysis also failed to reduce BmNPV replication, revealing that glycolysis and glutaminolysis are not essential during BmNPV infection. This study reveals a unique amino acid utilization process that is implemented during BmNPV infection. Our metabolomic analysis of BmNPV-infected silkworm provides insights as to how baculoviruses induce alterations in host metabolism during systemic infection.