Centromere evolution in Drosophila - CUT&Tag reads

Despite their essential function in chromosome segregation, centromeres reside in rapidly evolving, repeat-rich genomic regions. While the roles of DNA sequences in centromere function and specification are unclear, centromeres evolve rapidly at both the sequence and protein level. One potential explanation for this paradox is that genetic conflicts cause rapid centromere evolution. In this study, we take advantage of the close evolutionary relationships between Drosophila species to study the evolutionary dynamics of centromeric DNA over short evolutionary timescales, important for understanding the balance between conflict and cooperation at centromeric DNA. We reveal dynamic evolution of centromere composition both within the three species of the simulans clade - D. simulans, D. sechellia, and D. mauritiana - and between this clade and its immediate outgroup, D. melanogaster. We discovered categorical shifts in sequence composition: centromeres varied between retroelement-rich and satellite DNA-rich sequences over short evolutionary timescales (2.4 Mya). We also reveal the recent origin (240 Kya) of telocentric chromosomes: D. sechellia X and dot centromeres now sit among retroelements commonly specialized for telomere function in Drosophila. This rapid centromere turnover is consistent with recurrent genetic conflicts over transmission in the female germline and has implications for the role of DNA sequences in centromere function and evolution, as well as karyotype evolution.