From genomes to field diagnostics: Advances in detection and molecular understanding of Pebrine disease in silkworms.

Pebrine, caused by genus Nosema, is one of the most destructive diseases affecting silkworms. Because the pathogen can be transmitted both vertically and horizontally, infection can persist across successive generations, resulting in substantial reductions in cocoon yield and silk quality. Microscopic examination remains the most widely used method for the routine diagnosis of pebrine. However, microscopy has limited sensitivity and can detect the pathogen only when it is in the sporulated form, which may lead to false-negative results during diagnosis. Recent advances in molecular biology and genomics have significantly improved understanding of the pathogen and have enabled the development of more sensitive diagnostic approaches. This review summarizes updated information on the biology and genomic architecture of Nosema species associated with pebrine, including genome organization and virulence-associated genes. The molecular diagnostic strategies such as conventional PCR, quantitative PCR, loop-mediated isothermal amplification (LAMP), and CRISPR-based detection systems offer improved sensitivity and rapid detection. However, the emerging technologies such as biosensors, microfluidic devices, and smartphone-based detection platforms are also discussed as promising tools for field-level diagnosis. In addition, recent omics-based studies involving genomics, transcriptomics, proteomics, and metabolomics are highlighted for their contributions to understanding host-parasite interactions and disease pathogenesis. The review uniquely integrates recent genomic insights with emerging diagnostic technologies, including CRISPR-based assays, biosensors, microfluidics, and smartphone-assisted platforms, highlighting their potential for rapid and field-deployable detection of pebrine disease.