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Discovering and detecting transposable elements in genome sequences.pdf

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Discovering and detecting transposable elements in genome sequences

Discovering and detecting transposable elements in genome sequences Casey M. Bergman and Hadi Quesneville Submitted: 16th July 2007; Received (in revised form): 17th September 2007 Abstract The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to identify and annotateTEs in the post-genomic era, covering both the discovery of newTE families and the detection of individual TE copies in genome sequences.These approaches span a broad spectrum in computational biology including de novo, homology-based, structure-based and comparative genomic methods.We conclude that the integration and visuali- zation of multiple approaches and the development of new conceptual representations forTE annotation will further advance the computational analysis of this dynamic component of the genome. Keywords: transposable element; genome annotation; repetitive DNA; bioinformatics INTRODUCTION Transposable elements (TEs) are a widespread class of repetitive sequences that can be viewed largely as ‘selfish’ intragenomic parasitic sequences [1, 2]. Owing to their ability to undergo replicative transposition via an RNA or DNA intermediate, TEs can increase in copy number to occupy large fractions of genome sequences, especially in higher eukaryotes. For example,25% and45% of the rice and human genome sequences, respectively, are estimated to be TE in origin [3, 4]. Aside from their unique modes of replication and sheer abundance, TEs are important biological entities for study because of their roles in genome structure [5], genome size [6], genome rearrangement [7] and contribution to host gene [7, 8] and regulatory evolution [8]. More practically, the repetitive nature of TE sequences poses fundamental challenges to genome sequencing [9]