Beyond “Junk DNA”: The Organization, Evolution, and Interplay of Satellite DNA and Transposable Elements

Repetitive DNA sequences, including satellite DNA (satDNA) and transposable elements (TEs), were once considered "junk DNA” or "genomic dark matter” but are now recognized as key components shaping the structure, function, and evolution of eukaryotic genomes. Findings from two contrasting genomic systems highlight the diversity and evolutionary complexity of repetitive DNA. In the beetle Tenebrio molitor, integrative analyses revealed a highly dynamic satellitome. SatDNAs show diverse chromosomal distributions, with one major family predominantly constituting heterochromatin. They follow distinct evolutionary trajectories with different levels of homogenization and turnover. Age analyses identified both ancient and lineage-specific satDNAs, while stage-specific transcription supports their functional relevance. Several satDNAs were also detected in extrachromosomal circular DNA, suggesting a role in their propagation. A distinct yet complex pattern is observed in oysters (family Ostreidae), whose satellitomes contain high numbers of satDNAs and atypical organization. Unlike the classical model of long heterochromatic arrays, majority of oyster satDNAs are highly interspersed throughout the genome. Many are associated with or derived from TEs, particularly Helitrons, which appear to mediate their amplification and dispersal. The most abundant satDNAs exhibit multiple coexisting organizational states, reflecting structural plasticity conserved across the family. SatDNAs and TEs also form interconnected networks shaped by genomic rearrangements, and degraded TE remnants can serve as sources of novel satDNA sequences. Together, these findings demonstrate that satDNAs and TEs are dynamic, interconnected, and functionally relevant genomic elements. Their diversity and plasticity highlight the importance of integrative approaches for understanding genomic "dark matter” and its impact on genome architecture and evolution.

Eva Šatović Vukšić is a Senior Research Associate at the Ruđer Bošković Institute in Zagreb, Croatia, where she works in the Division of Molecular Biology, Laboratory for Molecular Genetics. After completing her PhD at the Ruđer Bošković Institute, she spent two years at the Institute for Biomedical Research, IRB Barcelona, followed by a secondment at the Biomedical Center of Ludwig Maximilian University of Munich. Her current research focuses on repetitive DNA sequences, particularly transposable elements and satellite DNA, across diverse eukaryotic genomes and related species. Once considered "junk DNA,” repetitive DNA sequences are now recognized as key genomic components. She studies their diversity, structure, genomic distribution, organization, and evolutionary age. Her work further addresses the evolutionary processes shaping these elements, their functional interactions, and their impact on genome architecture, with a particular emphasis on the interplay between satellite DNAs and transposable elements.