In silico identified satellite DNAs in genomic data of Caretta caretta. Dataset on Zenodo.

In silico identification of putative satDNAs in short reads (SRR15328383, SRR26671777) was performed using RepeatExplorer2 and TAREAN pipelines [Novák et al. 2013; Novák et al. 2017] implemented in the Galaxy platform [Afgan et al. 2016]. For in silico identification of putative satDNA in long reads we used the publicly available genome data for C. caretta (GCF_023653815.1 and GCA_965140235.1). The analysis was performed using TideCluster (version 1.6) implemented in the Galaxy platform [Novák et al. 2017; Gao et al. 2019; Novák et al. 2025] with default parameters. SatDNAs sequences exhibiting more than 90% query coverage and percentage identity were grouped into distinct satDNA families; thus, eighteen satDNA families were identified. Following nomenclature suggested by Ruiz-Ruano et al. (2016) we numbered the satDNA in order of decreasing abundance in GCA_965140235.1 defined with RepeatMasker [Smit et al. 2015]. References: Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10. doi: 10.1093/nar/gkw343. Epub 2016 May 2. PMID: 27137889; PMCID: PMC4987906. Gao Y, Liu B, Wang Y, Xing Y. TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Bioinformatics. 2019 Jul 15;35(14):i200-i207. doi: 10.1093/bioinformatics/btz376. PMID: 31510677; PMCID: PMC6612900. Novák P, Neumann P, Pech J, Steinhaisl J, Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 2013 Mar 15;29(6):792-3. doi: 10.1093/bioinformatics/btt054. Epub 2013 Feb 1. PMID: 23376349. Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res. 2017 Jul 7;45(12):e111. doi: 10.1093/nar/gkx257. PMID: 28402514; PMCID: PMC5499541. Novák P. 2025. kavonrtep/TideCluster: 1.6.2 (1.6.2). Zenodo. https://doi.org/10.5281/zenodo.15855129 Ruiz-Ruano FJ, López-León MD, Cabrero J, Camacho JPM. High-throughput analysis of the satellitome illuminates satellite DNA evolution. Sci Rep. 2016 Jul 7;6:28333. doi: 10.1038/srep28333. PMID: 27385065; PMCID: PMC4935994. Smit, A. F. A., Hubley, R., Green, P. (2015) RepeatMasker Open-4.0. 2013–2015. https://www.repeatmasker.org/