title: A new approach for annotation of transposable elements using small RNA mapping.
abstract: 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/.
authors: Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA.
authors: Moaine
authors: M
authors: El Baidouri
authors: Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA.
authors: Kyung Do
authors: KD
authors: Kim
authors: Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA.
authors: Brian
authors: B
authors: Abernathy
authors: Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA.
authors: Siwaret
authors: S
authors: Arikit
authors: INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France.
authors: Florian
authors: F
authors: Maumus
authors: Université de Perpignan Via Domitia. Laboratoire Génome et Développement des Plantes. UMR5096 CNRS/UPVD., 52, avenue Paul Alduy. 66860 Perpignan Cedex, France.
authors: Olivier
authors: O
authors: Panaud
authors: Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA.
authors: Blake C
authors: http://orcid.org/0000-0003-3436-6097
authors: BC
authors: Meyers
authors: Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA sjackson@uga.edu.
authors: Scott A
authors: SA
authors: Jackson
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D018745:Genome, Plant; D020071:Interspersed Repetitive Sequences; D058977:Molecular Sequence Annotation / Q000379:methods*; D012275:Oryza / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D013025:Glycine max / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering