Plant Transposable Elements

Volume 24 of the series Topics in Current Genetics pp 17-39


Transposable Element Annotation in Completely Sequenced Eukaryote Genomes

  • Timothée FlutreAffiliated withINRA, UR 1164, URGI, Unité de Recherche en Génomique-Info
  • , Emmanuelle PermalAffiliated withINRA, UR 1164, URGI, Unité de Recherche en Génomique-Info
  • , Hadi QuesnevilleAffiliated withINRA, UR 1164, URGI, Unité de Recherche en Génomique-Info Email author 

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With the development of new sequencing techniques, the number of sequenced plant genomes is increasing. However, accurate annotation of these sequences remains a major challenge, in particular with regard to transposable elements (TEs). The aim of this chapter is to provide a roadmap for researchers involved in genome projects to address this issue. We list several widely used tools for each step of the TE annotation process, from the identification of TE families to the annotation of TE copies. We assess the complementarities of these tools and suggest that combined approaches, using both de novo and knowledge-based TE detection methods, are likely to produce reasonably comprehensive and sensitive results. Nevertheless, existing approaches still need to be supplemented by expert manual curation. Hence, we describe good practice required for manual curation of TE consensus sequences.


Annotation Bioinformatics Classification Curation Identification Pipeline