Advancing the understanding of the Bombyx mori genome through satellite DNA analysis: low strain differentiation and relationship with transposable elements

Despite the economic and scientific importance of Bombyx mori, its satellite DNA (satDNA) fraction remains poorly characterized. Here, we present the first comprehensive analysis of the B. mori satellitome, revealing its low abundance ([~]0.76%), A+T enrichment, high monomer size variability, and predominantly dispersed chromosomal organization. Comparative analysis with B. mandarina, the wild ancestor of B. mori, demonstrated high satDNA conservation in abundance and sequence composition, despite speciation and domestication events. Divergence landscapes of satDNA sequences indicate predominantly ancient amplifications with few recent homogenization events. SatDNA families exhibited low strain differentiation across five B. mori strains, exemplified by the consistent presence and abundance of BmorSat01-575 and BmorSat29-84. The W chromosome was identified as a hotspot for satDNA accumulation, especially BmorSat24-753, which showed female-specific amplification and higher sequence homogeneity, suggesting functional or structural roles in W chromosome evolution. In contrast, the Z chromosome displayed similar satDNA content to autosomes, with two families being exclusive to this chromosome and conserved in both Bombyx species. Remarkably, some of B. mori satDNAs were found to be derived from transposable elements (TEs), supporting the hypothesis of TE-driven satDNA origin via multiple mechanisms, including tandemization of TE fragments. Our findings underscore the dynamic interplay between satDNAs and TEs in shaping genome architecture, the stability of the satellitome through domestication, and the sex chromosome-specific accumulation patterns. These insights lay the groundwork for future studies investigating the functional roles of satDNAs in genome regulation and chromatin dynamics in Lepidoptera.