Cross-kingdom noncoding RNA regulation facilitates Nosema bombycis proliferation

Microsporidia are obligate intracellular fungal parasites that are widely distributed in natural and agricultural environments and represent an important biological hazard to economically important insects. Nosema bombycis (N. bombycis), the causative agent of pébrine disease, poses a serious threat to silkworm breeding and sericultural sustainability. However, the molecular mechanisms underlying microsporidian proliferation and host-pathogen interactions remain poorly understood. In this study, we systematically characterized the long noncoding RNAs (lncRNAs) and microRNA-like RNAs (milRNAs) of N. bombycis, an important pathogen of Bombyx mori (B. mori). Using the full-length transcriptome and small RNA sequencing data from B. mori midgut tissues infected with N. bombycis at key developmental stages, we identified 30 novel lncRNAs and 12 previously unreported milRNAs in N. bombycis. We further established a competing endogenous RNA regulatory network involving N. bombycis-derived lncRNAs, parasite-specific milRNAs, and host-derived microRNAs (miRNAs), revealing intricate molecular interactions that may be implicated in pathogenicity. Notably, NbLNC2914, a highly expressed lncRNA, was shown to function as a molecular sponge for the host miRNA bmo-miR-2808a-3p, modulating its expression and consequently regulating the downstream N. bombycis gene, NBO_58g0005. Functional validation assays demonstrated that this regulatory axis had an important impact on N. bombycis proliferation. Our findings reveal a previously unrecognized noncoding RNA (ncRNA)-mediated regulatory axis that facilitates N. bombycis proliferation within host cells. This study provides mechanistic insights into the molecular basis of microsporidia pathogenicity and highlights ncRNAs as potential molecular targets for mitigating microsporidia-associated biological hazards in agricultural ecosystems.