Multiomics analysis of the Silkworm cocoon shell

In this study we combined phenomics, proteomics, metabolomics and lipidomics analyses of historical and contemporary Bombyx mori cocoon shells to case-study the human-driven introduction and diversification of this species in Europe. Prompted by recent findings on the genomic variability that underlies the ancestry and cocoon shell colour of this species, we carried out optical and fluorescence imaging analysis of 148 cocoons shells to identify overt and covert phenotypic traits and employed LC-MS/MS analyses protocols for 80 cocoon shell samples to identify that the cocoon shell of this species contains on average 98 ± 13 (Mean ± SD) proteins, while we identified 141 metabolites and 981 lipids. We validated these generated datasets through multiple validation protocols, through a series of dimensionality reduction methods and clustering algorithms and through narratives from historical archives and manuscripts. Our multiomics datasets provide a valuable foundation for advancing further exploitations of silkworm cocoon shells in multiple scientific perspectives.