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Several families of transposable elements (TEs) have been described for the nuclear genome of these parasites [2-5].
For this purpose, and in order to generate accurate gene predictions and annotation, a detail identification of repeat elements in the genome is fundamental.Finally, consensus DNA sequences for each repetitive element identified with either methodology were built from multiple sequence alignments with Clustal X .Extensive manual examination of repeat structures and insertion sites was required for novel elements.In addition, as mentioned above, identification of repeat elements is essential for correct gene set generation, since unidentified TEs can affect the quality of gene annotation and annotation-dependent analyses such as microarray-based gene expression studies .For this reason, our initial goal was to identify and map all the TEs that populate these three genomes.We show that repeats and repeat-clusters are found at syntenic break points between E. dispar and hence, could work as recombination hot spots promoting genome rearrangements. Our work shows that transposable elements are organized in clusters, frequently found at syntenic break points providing insights into their contribution to chromosome instability and therefore, to genomic variation and speciation in these parasites.
CONCLUSION: The mapping of all transposable elements found in these parasites shows that repeat coverage is up to three times higher than previously reported. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
On the other hand, class II TEs comprise elements that transpose DNA (transposons).
Even though TEs can represent a large fraction of the nuclear genome of multicellular organisms [6,8], it is only recently that we have a wealth of finished genome information from unicellular eukaryotes to expand the knowledge about the presence of TEs in protozoan parasites such as transposable elements, and gave us the opportunity to discover previously uncharacterized novel repetitive sequences.
We have mapped all known class I and class II transposons in these genomes, revealing that the collection of shared TEs and the abundance of repetitive sequences are much larger than what was previously reported .
In addition, we report the identification and characterization of two novel TEs, one of which is specific for elements from Gen Bank and Repbase  and ran Repeat Masker to map and quantify the elements.
Additionally, we found a putative transposase-coding gene in E. dispar related to the mariner transposon Hydargos from E. The distribution of transposable elements in these genomes is markedly skewed with a tendency of forming clusters.