Endogenous RNA virus–derived elements exhibit functional divergence in modulating development and virus susceptibility in Bombyx mori

Non-retroviral endogenous viral elements (nrEVEs) are increasingly recognized as potential regulators of host biology, but their functional roles in Lepidoptera remain largely unexplored. Bombyx moriis a pivotal lepidopteran model, and identifying genomic loci for economic traits is vital for its genetic breeding. Here, we identified seven nrEVEs from four RNA virus families in its reference genome, which exhibited non-random chromosomal distribution, stage- and tissue-specific transcription, and divergent small RNA profiles. Functional characterization of two representative elements, the Totiviridae-derived BmToEVE and the Chuviridae-derived BmChuEVE3, revealed essential but divergent roles in silkworm biology. Knockdown of either element caused developmental defects and exerted opposite effects on reproduction and cocoon traits, highlighting their differential contributions to growth and silk production. Transcriptomic and interactome analyses revealed that both nrEVEs engage with cuticular and ribosomal protein networks, regulating genes involved in cuticle biogenesis and oogenesis. Notably, BmChuEVE3 knockdown compromised larval cellular homeostasis and immunity, thereby promoting the replication of Bombyx mori nucleopolyhedrovirus(BmNPV) and cytoplasmic polyhedrosis virus(BmCPV). In contrast, BmToEVE knockdown suppressed BmNPV replication and attenuated BmCPV infection by relieving repression of host immune pathways, including Toll/Imd signaling. Our findings establish nrEVEs as key Lepidoptera regulators, advancing host-virus coevolution insights and providing targets for breeding virus-resistant, developmentally optimized silkworms.