| dc.description.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. | |
