Tracing the rhythms of repetitive sequences: Mixed modes of satellite DNA and transposable element evolution in the air-breathing catfish (Clarias)

Repetitive DNA is a major organization component of eukaryotic genomes; however, its evolutionary dynamics in teleosts remain insufficiently understood. Catfish of the family Clariidae provide a valuable model for studying the evolutionary process of repetitive DNA sequences, owing to their genomic diversity and complex chromosomal histories. Here, the evolutionary diversity of satellite DNA (satDNA), transposable elements (TEs), and microsatellites was investigated across multiple clariid catfish species using bioinformatic approaches that integrate genome-wide annotation of repetitive sequences with phylogenetic and chromosomal contexts. The results revealed distinct chromosome-specific patterns of satDNA evolution and demonstrated that, although certain satDNA clusters were conserved across species, their monomer sequences underwent substantial reshuffling over time, contrary to the expectation that their monomer sequences are homologous through closely related species. An ancient burst of TE activity was detected in the common ancestor of Clarias , followed by their recent species-specific proliferation, which is correlated with the overall TE and microsatellite abundances. Although closely related species generally exhibit similar repeatome profiles, notable deviations, such as the unique TE landscape of C. gariepinus and microsatellite distribution of C. batrachus , highlight lineage-specific evolutionary processes. These findings demonstrate the utility of Clarias catfish as a model for understanding repetitive sequence dynamics, genome plasticity, and chromosome evolution in vertebrates.