A new approach for annotation of transposable elements using small RNA mapping.

Moaine El Baidouri (1) , Kyung Do Kim (2) , Brian Abernathy (2) , Siwaret Arikit (3) , Florian Maumus (4) , Blake C Meyers (3) , Scott A Jackson (2) , Olivier Panaud (1)

1 LGDP - Laboratoire Génome et développement des plantes
2 University of Georgia [USA]
3 PGML - Plant Genome Mapping Laboratory
4 URGI - Unité de Recherche Génomique Info

Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants.Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/.

Mots clés: transposable element; new method for de novo TE Annotation; TASR

Mots clés: DNA

Domaines: Sciences du Vivant [q-bio]; Biochimie, Biologie Moléculaire; Amélioration des plantes; Génétique; Génétique des plantes; Evolution [q-bio.PE]; Systématique, phylogénie et taxonomie; Biochimie [q-bio.BM]; Biologie moléculaire; Biologie structurale [q-bio.BM]; Génomique, Transcriptomique et Protéomique [q-bio.GN]; Réseaux moléculaires [q-bio.MN]; Biologie cellulaire; Bio-Informatique, Biologie Systémique [q-bio.QM]; Biologie végétale

Moaine El Baidouri, Kyung Do Kim, Brian Abernathy, Siwaret Arikit, Florian Maumus, et al.. A new approach for annotation of transposable elements using small RNA mapping.. Nucleic Acids Research, 2015, 43 (13), pp.e84. ⟨10.1093/nar/gkv257⟩. ⟨hal-01215276⟩