Silkworm Genomics and Its Applications: A Comprehensive Review

Abstract

Bombyx mori, the domesticated silkworm, is one of the most economically significant and scientifically tractable insects. Since the publication of its draft genome sequence in 2004 and the subsequent production of a refined, consortium-level assembly in 2008, silkworm genomics has undergone a transformative evolution encompassing whole-genome resequencing, functional genomics, epigenomics, small RNA biology, and comparative and population genomics. These advances have not only illuminated the molecular mechanisms underlying silk production, development, immunity, and domestication, but have also catalysed a wide range of applications spanning biotechnology and biomedicine. This review synthesises current knowledge on silkworm genomics, tracing the progression from early sequencing initiatives to state-of-the-art genome editing strategies including the CRISPR/Cas9 system. A systematic literature search was conducted to identify peer-reviewed publications relevant to silkworm genomics and its applications. The primary databases consulted were Web of Science, Scopus, PubMed, and Google Scholar.  The primary date range for inclusion was 2006 to 2026, with an exception for foundational studies published before 2006, which were included when they represented seminal contributions to the field. Special attention is given to the genomic architecture of silk protein genes, the regulatory roles of non-coding RNAs, epigenetic landscapes, and comparative genomics with related Lepidoptera. The biotechnological utility of the silkworm is explored in the context of silk-based biomaterials for tissue engineering, silk as a drug delivery scaffold, the production of chimeric spider silk fibres in transgenic silkworms, and the silkworm as an in vivo model for infectious disease research. The review further addresses the improvement of sericulture through molecular breeding, marker-assisted selection, and precision genome editing, as well as the   genomic basis of innate immunity and disease resistance. Future directions in multi-omics integration, single-cell transcriptomics, synthetic biology, and pangenomics are discussed. Together, these developments  affirm the central importance of silkworm genomics at the interface of fundamental biology and applied innovation.