Comparative Repeatomics Uncovers Genome Diversification in Gasteropelecidae Fishes

Repetitive DNA contributes to genome and chromosome evolution, yet its diversification remains poorly characterized by Neotropical fishes. Gasteropelecidae provides an informative system because its three genera share an ancient ZZ/ZW sex chromosome system despite lineage-specific W chromosome differentiation. Here, we characterized and compared the repeatomes of three Gasteropelecidae species to investigate how repetitive DNA diversification relates to genome and chromosome evolution. We analyzed Carnegiella strigata, Gasteropelecus levis, and Thoracocharax stellatus, with Triportheus auritus as a comparative lineage. Despite ~30–40 Myr of divergence, Gasteropelecidae species showed remarkably conserved repeatome composition, with repetitive DNA accounting for ~25–32% of their genomes and consistently dominated by retroelements. In contrast, T. auritus displayed a distinct repeatome composition, with DNA transposons representing the most abundant annotated repeat class. Satellitomes were more dynamic: 62% of the 235 identified satDNA families showed homology across taxa, consistent with differential amplification of shared satellite sequences. G. levis exhibited 19 female-biased satDNA families, whereas FISH mapping in T. stellatus provided direct cytogenetic evidence of W chromosome enrichment for specific satDNAs. Thus, conserved genome-wide repeat landscapes coexist with rapid satellitome diversification, with lineage-specific satDNA amplification potentially contributing to W chromosome differentiation while the ancestral ZZ/ZW system remains conserved.