The role of satellite DNAs in repeatome organization and sex chromosome evolution in the owl monkey Aotus infulatus and congeneric species

Abstract Background Multiple sex chromosome systems provide exceptional models for investigating the genomic mechanisms underlying sex chromosome evolution. In Neotropical primates, owl monkeys ( Aotus ) are notable for their extensive karyotypic diversity and recurrent emergence of complex sex chromosome systems. Here, we present a comprehensive cytogenomic analysis of the repeatome of Aotus infulatus , a species exhibiting an X 1 × 2 Y sex chromosome system. Using low-coverage whole-genome sequencing from males and females, combined with comparative analyses of three congeneric species ( A. nancymaae , A. vociferans , and A. trivirgatus ), we characterized the composition, abundance, and evolutionary dynamics of their repeatomes across the genus. Results Repetitive sequences account for approximately 37% of the A. infulatus genome, with satellite DNAs (satDNAs) representing the most variable component among species. Nine satDNA families were identified in A. infulatus , most of which show high sequence conservation across Aotus , consistent with a shared ancestral repeat library followed by lineage-specific amplification. Comparative analyses between sexes revealed a modest enrichment of satDNAs in the male genome. Fluorescence in situ hybridization uncovered differential chromosomal distributions of several satellites, including sex-biased accumulation on the X 1 and Y chromosomes. In contrast, comparative genomic hybridization revealed extensive sharing of repetitive sequences between sexes, indicating limited genomic divergence between the X 1 and Y chromosomes. Conclusions Our results demonstrate that repetitive DNA, particularly satDNAs, has played a central role in reshaping the sex chromosome architecture of A. infulatus . This study establishes Aotus as a compelling primate model for investigating the genomic consequences of sex chromosome fusion and highlights the importance of repeatome dynamics in the evolution of multiple sex chromosome systems.