Caracterização e evolução de DNAs satélites em Drosophila antonietae e D. serido (grupo repleta, cluster buzzatii) e em genomas da zona híbrida

Abstract

Repetitive DNAs are among the most abundant components of eukaryotic genomes and can be classified according to their organization in the genome as dispersed or tandemly arranged. Satellite DNAs (satDNAs) are organized in arrays of thousands of tandemly organized copies, predominantly found in heterochromatin. SatDNAs exhibit a pattern of evolution known as concerted evolution, where copies within the same satDNA family display lower intraspecific variability compared to interspecific one. Despite satellites do not encode proteins, they can play functional roles in the genome, such as gene regulation, chromatin modulation, maintenance of functional centromeres, male fertility and spatial organization of chromosomes. The development of new sequencing techniques, such as Next Generation Sequencing (NGS), together with the advent of new bioinformatics tools, have provided new possibilities for a comprehensive and detailed study of satDNAs. In the present work, we used the RepeatExplorer2 pipeline for de novo identification of satDNAs in Drosophila antonietae and D. serido (buzzatii cluster, repleta group). We used raw sequencing reads from both species and from six genomes from the contact zone between them. We identified five satDNAs and one minisatellite shared between the two species. Among the satDNAs, two were previously described in both species (pBuM and DBC-150), one was previously described and found in other species of the repleta group (CDSTR138), and two novel satDNAs were identified for the first time in this study (SAT197/230 and SAT109/104). The minisatellite CDSTR198 was also found in both species. Our FISH experiments revealed that CDSTR138 (and not pBuM, as previously suggested) is the main centromeric component in D. serido, D. seriema, D. gouveai, and D. koepferae. Additionally, the newly identified satDNAs were exclusively found on the sex chromosomes. The SAT197/230 is present on the Y chromosome and organized in three arrays, one of which is centromeric, and the SAT109/104 is present in the centromeric region of the X chromosome. The CDSTR198 was confirmed as a minisatellite in D. serido, visible only on the euchromatic arms of the polytene chromosomes. All the analyzed centromeric satDNAs showed enrichment of small dyads symmetries and were predicted to form stable secondary structures, which are considered essential characteristics for centromeric function. Among the analyzed satDNAs, four exhibited a pattern of concerted evolution and were considered good taxonomic markers. Our analysis of genomes from the hybrid zone suggests that two genomes can be classified as D. antonietae and four as D. serido. Overall, our study confirms the efficiency of the RepeatExplorer2 pipeline for identifying satDNAs in Drosophila and provides new insights into genome evolution and centromere structure in these species. Furthermore, it reveals new genetic markers for species identification, which will be valuable for studies involving the hybrid zone.