Abstract
Repetitive DNA sequences are ubiquitous in eukaryotic genomes, significantly influencing their structure, function, and evolution. They can facilitate genomic rearrangements, contributing to chromosomal and genomic diversity. Chrysomelidae (Coleoptera) beetles are known for their highly diverse karyotypes and heterochromatin distribution. In this study, we advanced the understanding of the intricate relationship between satellite DNA-like sequences (named here solely as satDNA) and genome organization/reshuffling using three species of Eumolpinae chrysomelids. We investigated the satellitomes of three species with divergent karyotypes that had undergone independent chromosomal fusions: Colaspis laeta (2n = 22, Xyp), with a conserved karyotype; Endocephalus bigatus (2n = 10, neo-XY); and Iphimeis dives (2n = 14, neo-XY). Our comparative analysis revealed highly divergent patterns of satDNA origin, organization, and evolution. In species with reduced chromosome numbers and neo-sex chromosomes, we observed a high abundance of transposable element-related (TE-related) satDNAs. In Colaspis laeta, the sex chromosomes (Xyp) showed an advanced level of differentiation. However, in the species with a reduction in diploid number, such a level of differential enrichment of repetitive DNAs was not observed in the sex chromosomes, indicating an early stage of differentiation. Our findings support the hypothesis that chromosomal rearrangements and reorganization of repetitive DNA sequences are connected, with extensive reshuffling observed in species with reduced diploid numbers. Moreover, the data reinforce the involvement of TEs in satDNA origin, which could spread widely throughout the genome, including euchromatic areas. This study provides new insights into the evolutionary dynamics of repetitive DNAs in non-model species, emphasizing the impact of chromosomal rearrangements on genome architecture and evolution.
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Data availability
The raw reads used in the project are deposited at NCBI under the Bioproject accession numbers SRX29965143, SRX29965142, and SRX29965141. Monomers of each satDNA family are available on NCBI.
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Acknowledgements
The authors thank the anonymous reviewers for their helpful input. The study was supported by Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP 2023/02581-2 to DCC-d-M and 2024/01521-9 to PM), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq 309979/2023-4 to DCC-d-M), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (CAPES, financial code 001 to DCC-d-M and AEG), and by Universidad de Jaén (through the program “Plan de Apoyo a la Investigación 2021–2022, Acción 1”).
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JMR-P, PM, AEG, and DCC-d-M did the experimental work; JMR-P, PM, PL, and DCC-d-M analyzed the data; JMR-P, PM, VBB, TP, PL, and DCC-d-M interpreted the results; JMR-P and DCC-d-M wrote the manuscript; PM and DCC-d-M made the manuscript revisions; DCC-d-M coordinated the study; all authors read, revised, and approved the manuscript.
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Rico-Porras, J.M., Mora, P., Gasparotto, A.E. et al. Expansion of satellite DNAs derived from transposable elements in beetles with reduced diploid numbers. Heredity 134, 529–541 (2025). https://doi.org/10.1038/s41437-025-00790-w
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DOI: https://doi.org/10.1038/s41437-025-00790-w
