Comprehensive analysis of the Bombyx mori satellitome reveals evolutionary stability, dispersed chromosomal...

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, through the analysis of seven strains, plus the analysis of genome reference assembly. A total of 35 satDNAs were detected, all of which were present across the studied strains, with 29 also shared with B. mandarina, its wild ancestor. We revealed low abundance of satDNAs (mean abundance between strains of ~0.85% for males and 0.91% for females), A + T enrichment, high monomer size variability, and predominantly dispersed chromosomal organization. Divergence landscapes of satDNA sequences indicate predominantly ancient amplifications with few recent homogenization events. SatDNA families exhibited low strain differentiation across seven B. mori reference strains. The W sex chromosome was identified as a hotspot for satDNA accumulation, which showed female-specific amplification and higher sequence homogeneity, suggesting functional or structural roles in W sex chromosome evolution. In contrast, the Z sex chromosome displayed similar satDNA content to autosomes, with few families slightly amplified in this chromosome. Remarkably, some of the B. mori satDNAs were found to be derived from transposable elements (TEs), i.e four families covering ~63% of total satDNA content, 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 strains diversification, 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.