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2015

International,  INV (invited talks)

Analysis and Annotation of DNA Repeats and Dark Matter in Eukaryotic Genomes Conference, Tours, France

08 Jul 2015   Deep annotation of the A. thaliana repeatome sheds light on the evolution of paleocentromeres

Florian Maumus and Hadi Quesneville

Eukaryotic genomes contain highly variable amounts of DNA with no apparent function. This so-called junk DNA is composed of two components: repeated and repeat-derived sequences (together referred to as the repeatome), and non-annotated sequences also known as genomic dark matter. Because of their high duplication rates as compared to other genomic features, transposable elements are predominant contributors to the repeatome and the products of their decay is thought to be a major source of genomic dark matter. Determining the origin and composition of junk DNA is thus important to help understanding genome evolution as well as host biology. Here, we have used a combination of tools enabling to show that the repeatome from the small and reducing A. thaliana genome is significantly larger than previously thought. Furthermore, we present the concepts and results from a series of innovative approaches suggesting that a significant amount of the A. thaliana dark matter is of repetitive origin.

Analysis of the density of repeated and repeat-derived sequences along the five A. thaliana chromosomes enables the detection of regions of high repeat content besides those defined by the centromere/pericentromere space. Positioning these results in the context of karyotype evolution, we established that the position of the most intense peak actually corresponds to the one of an ancestral pericentromere preceding the fusion of two chromosomes in this species. Interestingly, we found that this region on A. thaliana chromosome 1 that corresponds to an ancestral pericentromere shows characteristic properties as compared to the remainder of chromosome arms regarding repeat turnover and recombination rates. This result exemplifies the relevance of our approach for deep repeat annotation and more generally illustrates that the search for ancient repeats helps understanding the evolution of modern genomes.

Update: 20 Jul 2015
Creation date: 15 Jul 2015