Abstract
BACKGROUND: Repetitive elements, particularly satellite DNA (satDNA), play a significant role in genome evolution and organisation. However, their diversity and evolutionary dynamics remain poorly understood in non-model organisms. Freshwater crayfish (Decapoda, Astacidea) have large genomes with a high chromosome number and are rich in satDNAs. This makes them attractive for studying the impact of satDNA on genome evolution. RESULTS: In this study, we investigated the repetitive genomic landscape of 19 species representing four freshwater crayfish families. Our analysis revealed a high proportion of repetitive DNA in all studied species, with the total repeat content ranging from 30% to 66%. The number of satDNA families was remarkably high (54–622 families per species), with minisatellites (< 100 bp) forming the largest component of the satellitome. Family-specific patterns emerged: Astacidae and Cambaroididae showed the highest satDNA proportions, while Cambaridae and Parastacidae were dominated by Class I transposable elements. Species of the family Parastacidae showed the largest number of unique satDNA clusters and were clearly separated from other families, reflecting their phylogenetic divergence and distinct biogeographic history. We identified specific satDNAs conserved across all species, among them the PlSAT3-411, pointing to their important functional roles as pericentromeric satDNA. CONCLUSION: This study provides the first comprehensive comparative analysis of satDNA in freshwater crayfish. Our results highlight the dynamic nature of repetitive DNA and underscore its importance in genome organisation and evolutionary history. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13100-026-00399-8.