considering transposable element diversification in de novo annotation approaches考虑转座因子在新创注释方法多样化.pdf

Considering Transposable Element Diversification in De Novo Annotation Approaches ´ 1 2 3 1 Timothee Flutre , Elodie Duprat , Catherine Feuillet , Hadi Quesneville * ´ ´ ´ ´ 1 Unite de Recherche en Genomique-Info, UR 1164, INRA Centre de Versailles-Grignon, Versailles, France, 2 Institut de Mineralogie et de Physique des Milieux Condenses, ´ ´ ´ ´ ´ ´ ¨ UMR 7590, CNRS-UPMC-IPGP-Universite Paris Diderot, Paris, France, 3 Genetique, Diversite et Ecophysiologie des Cereales, UMR 1095, INRA Domaine du Crouel, Clermont- Ferrand, France Abstract Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high- throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination