Tribolium madens satellitome reveals a network of highly abundant satellite DNAs in megabase-sized regions hallmarked by macro-dyad symmetries

Abstract Background Tandemly repeated satellite DNAs (satDNAs) are among the most copious sequences of eukaryotic genomes. They often reside in centromeric regions, but their diversity among different organisms obscures the properties that centromere-competent satDNAs should possess. Results Here, we explore the satellitome of the satDNA-rich flour beetle Tribolium madens . By combining short-read Illumina and long-read PacBio HiFi sequencing, we identify 124 satDNAs comprising 41.4% of the genome. We find that 38% of the genome sequence originates from a ~ 110 bp element that gives rise to two distinct satDNAs, the major and minor satellites, which occupy multi-megabase regions likely encompassing (peri)centromeres of all chromosomes. Fine-scale analysis of long-range organization reveals that intermingled arrays of the major and minor satDNAs are arranged in macro-dyad symmetries with the potential to form hairpin or cruciform structures spanning tens of kilobases. The inversion sites within macro-dyad symmetries and the transition zones between the major and minor satDNA arrays are highly conserved, indicating structural significance. The organization of the Tribolium madens putative (peri)centromeric satDNAs is comparable to that of the closely related Tribolium freemani and Tribolium castaneum , whose completely different dominant satDNAs also incline toward macro-dyad symmetries. Conclusions We propose that satDNA-related macro-dyad symmetries may affect the organization of (peri)centromeric chromatin, potentially also influencing centromere specification. The analogous pattern in congeners suggests that such symmetries are an intrinsic feature of Tribolium (peri)centromeric regions, implying that repeat organization and potential non-canonical DNA structures could be functionally more significant than the primary sequence of satDNA repeats.