Genomic landscape of repetitive DNAs in Neotropical electric fishes

Abstract

The Neotropical electric fishes of the order Gymnotiformes, known for their unique electrogenic and electrosensory systems, provide exceptional models for investigating ecological and evolutionary questions. While their phylogenetic and cytogenetic diversity is well documented, information about the diversity and evolution of repetitive DNA in gymnotiform genomes remains limited. To understand how repetitive DNA has shaped genome evolution in this group, we conducted bioinformatic analyses on raw sequencing data and genome assemblies from multiple species representing three major families. Our analysis revealed that closely related species share similar patterns of repetitive DNA composition, with Gymnotidae and Apteronotidae exhibiting the highest (16.5%) and lowest (9.4%) proportions of repetitive DNA, respectively. We identified 40 satellite DNA families, with five exclusive to Gymnotidae, twenty-two to Hypopomidae, and six shared between Apteronotidae species. Only one satellite DNA (NEFSat3-18) was conserved across all analyzed species, suggesting rapid evolutionary turnover of these sequences. The evolutionary dynamics of transposable elements varied among families, with Gymnotidae showing recent expansion of LINE elements and DNA transposons, while Apteronotidae displayed more ancient patterns of transposon activity. Analysis of transposable element landscapes revealed that all species experienced at least one burst of transposition during their evolution. Our findings demonstrate that repetitive DNA diversification parallels the evolutionary history of gymnotiform species. We also present a comprehensive dataset of repetitive DNA sequences that can be used as cytogenomic markers in comparative and evolutionary studies.