Characterization and comparative genomic analysis of satellite DNAs in the Characidium genus (Teleostei, Characiformes)

Repetitive DNAs, particularly satellite DNA (satDNA), constitute some of the most dynamic elements of eukaryotic genomes; however, their role in evolutionary diversification remains insufficiently understood. They are commonly associated with the organization of centromeres and telomeres, as well as with chromatin modulation. This study presents the first comprehensive satellitome characterization of Characidium zebra , a Neotropical fish exhibiting notable chromosomal stability, exploiting populations from the Paranapanema and Tietê river basins. We delineate and analyze the arrays of satDNA families, characterize their chromosomal distribution, and evaluate population-level variation in satellitome composition. Furthermore, we assess the evolutionary conservation of these repetitive sequences via comparative analyses with the closely related species Characidium gomesi. This comparison revealed that both species share 25.4% of the satDNAs, with C. zebra possessing 39 and C. gomesi 59 satDNAs. Moreover, 10 of these sequences of C. zebra exhibited similarity rates higher than 80% with 11 of C. gomesi and were therefore considered either sequence variants or the same family. Our findings indicate the presence of both shared and population-specific satDNA families, providing support for the library hypothesis, which posits that related taxa preserve a common repertoire of satDNAs that differ in relative abundance. This study also clarifies the ambiguous taxonomic classification of C. zebra and uncovers the interactions among repetitive DNA dynamics, genome architecture, and population divergence. Our findings establish C. zebra as a model for studying satellitome evolution.