Late-stage lncRNA profiles in Bombyx mori cells infected with BmNPV

Bombyx mori nucleopolyhedrovirus (BmNPV) poses a major threat to sericulture, yet the roles of long non-coding RNAs (lncRNAs) in host-pathogen interactions remain poorly characterized. We performed transcriptome sequencing of BmNPV-infected (NPV) and mock-infected (Ctrl) BmN cells. Differential lncRNA expression was analyzed using DESeq2. Co-expression networks, lncRNA-miRNA interactions, and functional enrichment (GO/KEGG) were systematically investigated. Unsupervised PCA and FPKM analysis revealed distinct lncRNA expression landscapes between NPV and Ctrl groups. We identified 2,715 differentially expressed lncRNAs (1,567 upregulated and 1,148 downregulated). Co-expression network analysis highlighted lncRNA-mRNA hubs (SPARC/LOC101740071, Mmp1) implicated in extracellular matrix organization and metabolism. Functional enrichment linked upregulated lncRNAs to GPCR and MAPK signaling pathways and downregulated lncRNAs to mitochondrial translation/ribosome assembly. An integrated ceRNA network identified lncRNAs (TCONS_00034038 and XR_005245334.1) acting as miRNA sponges for immune-related miRNAs (bmo-miR-3384-3p and bmo-miR-3332), with high-affinity binding sites (energy ≤ -110 kcal/mol). Target mRNAs of these miRNAs were enriched for viral exploitation pathways including lysosome, Notch signaling and ubiquitin proteolysis. Transcription factor family analysis revealed dysregulation of bHLH and Zinc Finger families during infection. Our study provides a comprehensive landscape of lncRNA-mediated regulatory networks in BmNPV-infected silkworm cells, revealing their critical roles in viral manipulation of host immunity, metabolism, and gene expression. Key lncRNAs and hub genes (SPARC, Mmp1) represent potential targets for antiviral strategies; antisense oligos or CRISPR-based silencing of TCONS_00034038 and XR_005245334.1 could be harnessed to enhance BmNPV resistance in silkworm breeding programs.