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In this work we report the first complete whole genome survey of transposable elements for the newly generated assemblies of E. histolytica, E. dispar, and E. invadens.
In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus.
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Jiao Y, Deng XW. (2007) A genome-wide transcriptional activity survey of rice transposable element-related genes.
Indeed, by doing a genome-wide survey of 10402 characterised transposable elements, the authors found that these are most often located in regions of the human genome that contain very few genes, and show a strong preference for residing closest to genes involved in development and transcription regulation.
This analysis is the first comprehensive survey of this family of transposable elements at a genus scale.
Jiao and Deng [ 58] performed a genome-wide survey of transcriptional activity of transposable element-related genes in 15 developmental stages and stress conditions in rice and found no expression of PIF-like transcripts in their test plants, suggesting that the PIF-like ORF1 is not expressed in all rice genotypes.
We propose a new conceptual framework to study the dynamics of transposable elements.
The D. immitis genome was surveyed for the three main classes of transposable elements [DNA transposons, long terminal repeat (LTR) retrotransposons, and non-LTR retrotransposons] with tBLASTn (18) using the transposon-encoded proteins as queries.
The reassembly and reannotation of the E. histolytica nuclear genome and the completion (5×) of the E. dispar and E. invadens genome sequences provided us with the necessary framework to perform a survey of the currently known Entamoeba transposable elements, and gave us the opportunity to discover previously uncharacterized novel repetitive sequences.
In this study, we examined many categories of transposable elements from the RepBase transposable element annotation database.
Fig. 3: Rapid proliferation of transposable elements.
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