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2009

International,  INV (invited talks)

25th Fungal Genetics Conference, Asilomar, CA, USA. Mar 2009

20 Mar 2009   Comparative analysis of transposable elements in several fungal genomes

Amselem J, Flutre T, Dominguez Del Angel V, Ghignone S, Lebrun M.H, Cuomo C, Dickman M, Martin F.,Rouxel T. Spanu P. and Quesneville H

Transposable Elements (TEs) are repeated sequences whose abundance is usually correlated with genome size. TEs shapes genomes and are a source of genetic variations and mutations. We started a comparative genomic analysis of fungal TEs using a rigorous annotation strategy. The challenge is to detect ab initio TEs and annotate them including nested and degenerated copies. We use the REPET pipeline developed at URGI which efficiently detects and annotates TEs in novel genomes. We will present preliminary results obtained with REPET on Botrytis cinerea, Sclerotinia sclerotiorum, Leptosphaeria maculans, Tuber melanosporum and Blumeria graminis. Searching for B graminis TEs using RepeatMasker against RepBase Update (known TEs) showed that they represent only 10% of this genome whereas REPET analysis showed up to 75%, TEs mainly as novel elements not already described in RepBase, illustrating the interest of such a pipeline.


Keywords: RIP, fungal genomics, Transposable elements
Update: 10 May 2011
Creation date: 05 May 2010