Identificação de novo e citogenômica comparativa de DNAs satélites em espécies de Drosophila dos grupos virilis e montium

Abstract

Repetitive DNAs are the most abundant components of the eukaryotic genomes and can be classified as dispersed, as in the case of transposable elements (TEs), or in tandem, as in the case of microsatellites, minisatellites and satellite DNAs (satDNAs). During the pre-genomic era, repetitive DNA studies were often time-consuming, laborious and limited. Currently, the development of massive DNA sequencing techniques and the availability of several bioinformatics tools provide access and automated annotation of virtually all repetitive DNAs present in a genome. Thus, it is necessary to test the capacity of these tools for the correct identification and classification of these repetitive sequences. In the present project, we used the RepeatExplorer and TAREAN pipelines for de novo identification of satDNAs in two closely species of Drosophila from the virilis group (D. virilis and D. americana) and in 23 newly sequenced species from the montium group. While D. virilis and D. americana have been extensively studied in the context of repetitive DNA in the pre-genomic era, no species from the montium group had been previously investigated in this context. In our analyzes, we identified six families of repetitive tandem repeats (TRs) with satDNA features in the virilis group species and 142 satDNA clusters in the montium group species. For D. virilis and D. americana, we studied each of these families in detail, combining data from the literature, data generated by the tested pipelines and new data on chromosomal localization. For the montium group, we carried out the identification with TAREAN and a more detailed investigation of the satDNA families shared between species. We were able to identify and characterize the “real” satDNAs of D. virilis and D. americana, in addition to analyze evolutionary relationships between satDNAs and transposable elements. For the montium group, we did an unprecedented identification of satDNA sequences, demonstrating that some satellites share sequences with transposable elements and that satDNA families can be used as taxonomic and phylogenetic markers within the group. Thus, we confirmed the effectiveness of the RepeatExplorer and TAREAN pipelines for de novo identification of satDNAs in Drosophila, we showed the importance of combining in silico and experimental approaches for the identification and characterization of satDNAs, we reported examples, within the montium group, where satDNAs may be useful as phylogenetic markers and lastly, we reported several types of interesting associations between satDNAs and TEs.