Distinct satellite DNA composition between core and germline restricted chromosomes in Bradysia (Sciara) coprophila

Programmed DNA elimination, a phenomenon wherein cells eliminate a subset of genetic material during certain stages of development, is observed in a broad range of organisms. The fungus gnat Bradysia (formerly Sciara) coprophila undergoes a series of programmed DNA elimination events during their development, including elimination of germline-restricted chromosomes (called L chromosomes) in the soma and elimination of paternal chromosomes during male meiosis. However, a lack of understanding surrounding the nature of eliminated chromosomes poses a barrier to studying programmed DNA elimination in this system. Highly repetitive satellite DNA, which often shows chromosome-specific distribution, is a possible candidate for sequences involved in programmed DNA elimination. In this study, we utilized recent genomic data and genome assemblies to identify new satellite DNA sequences of B. coprophila, and characterized their distribution on chromosomes. The results imply that the X and autosomes do not share centromeric satellite DNA sequence (BcopSat-155) with the L chromosomes. We further provide cytological evidence that confirms a recent finding based on the genome assembly that there are 2 distinct L chromosomes that were not previously distinguished cytologically. Together, our work lays a foundation for future studies to explore the possible connection between satellite DNA and the mechanism of programmed DNA elimination in B. coprophila.