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2014

International,  COM (posters)

March 09-14 2014, Mobile Genetic Elements & Genome Evolution symposium, Santa Fe, New Mexico, USA

09 Mar 2014   De novo TE annotation : tackling the fat genome issue
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 V. Jamilloux, O. Inizan, T. Chaumier, M. Moissette, S. Arnoux, H.Quesneville

Transposable elements (TEs) constitute the most dynamic and the largest component of large plant genomes, e.g. 85% of the maize genome (Schnable et al. 2009), and 88% of the wheat genome (Choulet et al. 2010). De novo TE annotation is therefore a computational challenge. We designed new strategies to this end that built on the functionalities of the REPET package. This package includes 2 pipelines: TEdenovo that builds a TE consensus library, and TEannot that annotates TEs in the genome. For our methodological development, we chose the approx. 1Gb 3B chromosome sequence from the wheat as an experimental model. We describe the principles and the results from three different approaches able to build TE libraries with TEdenovo using (i) a library of known TEs concatenated with a de novo library built from a genome spliced from their known TEs, (ii) A de novo LTR-retrotransposon library obtained with the LTRHarvest software then concatenated with the de novo library built from a genome spliced for the already identified LTR-RNs, and (iii) a de novo TE consensus library obtained from a genome part (300 Mbp longest contigs). In each cases the consensus are classified and used in an iterative process. Our analyses show that all our strategies enable us to overcome the current memory and time limitations for de novo TEs discovery using REPET on large plant genomes, without losing accuracy. This study paves the route towards comprehensive and high quality automatic TE annotation in a number of economically and agronomically important species.


Keywords: element transposable, annotation, genome
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Creation date: 25 Mar 2014