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

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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.

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