[show abstract][hide abstract] ABSTRACT: Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements in plants. They strongly impact the structure, function and evolution of their host genome and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in 8 plant genomes for which a high quality sequence is available (i.e. Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these 8 plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in a recent past and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage-specific. These new findings leads us to propose a new model of TE-driven genome evolution in plants.
Genome Biology and Evolution 02/2013; · 4.76 Impact Factor
[show abstract][hide abstract] ABSTRACT: Plant transposable elements are ubiquitous in eukaryotes. Their propensity to densely populate the genomes of many plants and animal species has put them in the focus of both structural and functional genomics. Although a number of bioinformatic software have been recently developed for the annotation of TEs in sequenced genomes, there are very few computational tools strictly dedicated to the identification of active TEs using genome-wide approaches. In this paper, we describe SearchTESV, a pipeline that we have developed to detect Transposable Elements-associated structural variants (TEASVs) using Next Generation Sequencing (NGS) technologies.
Methods in molecular biology (Clifton, N.J.) 01/2013; 1057:265-74.