Satellitome analysis of the black soldier fly Hermetia illucens reveals genome organization, interstocks dynamics, and insights into centromeric and telomeric repeat composition

Hermetia illucens (Diptera: Stratiomyidae), commonly known as the black soldier fly (BSF), is a species of growing industrial interest due to its efficiency in organic waste conversion and protein-rich biomass production. Despite the availability of extensive genomic resources, chromosomal-level information on repetitive DNA remains scarce. Here, we present the first comprehensive cytogenomic characterization of satellite DNAs (satDNAs) in H. illucens, integrating cytogenetic mapping with genome data to elucidate their organization and potential structural roles.

The karyotype (2n = 14, XY) was confirmed, showing concordance with the assembled pseudochromosomes and revealing heterochromatin polymorphisms between stocks from Brazil and Spain. We identified eleven satDNA families representing approximately 3–4% of the genome in both males and females, with monomer lengths ranging from 7 to 4,166 bp and A + T contents between 43 and 73%. Chromosomal mapping uncovered diverse distribution patterns, ranging from chromosome-specific to broadly dispersed repeats. HillSat03-160 localized to chromosome termini, suggesting a telomere-associated role, whereas HillSat04-7 was enriched in centromeric regions, likely contributing to centromere organization. Other satDNA families, such as HillSat01-162 and HillSat02-4166, showed broad autosomal distributions, whereas HillSat05-196 and HillSat06-109 exhibited stock-specific variation, indicating dynamic repeat evolution. Comparisons between in silico genome assemblies and FISH mapping revealed inconsistencies attributable to the collapse of repetitive regions during assembly.

Overall, our results demonstrate the dynamic and functional significance of satDNAs in the H. illucens genome, highlighting their contribution to genome organization, telomere evolution, and chromosomal diversification, and providing a foundation for future pangenomic and evolutionary studies in this species.