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You are here : Home / Home URGI / About us / Team / Previous staff / Jonathan Kreplak / Fungal Genome Analysis Of Transposable Elements

Jonathan Kreplak

International,  INV (invited talks)

Plant & Animal Genomes XIX Conference, Transposable Element Workshop, January 15-19, 2011, San Diego, CA

16 Jan 2011   Fungal Genome Analysis Of Transposable Elements: Expansion vs RIP Silencing

Amselem J , Flutre T, Dominguez Del Angel V, Kreplak J, Cuomo C, Duplessis S, Martin F, Rouxel,T Spanu P Lebrun MH Quesneville H

In the framework of several international projects, we have analyzed the transposable element (TE) content of several fungal genomes using the REPET pipelines . REPET TEdenovo pipeline detects TEs in genomic sequences, groups them into families and determines the consensus sequence for each family according to functional features (LTR, ITR, RT, transposase). The TEannot pipeline annotates TEs copies in the genome using the consensus TE library resulting from TEdenovo. The challenge is to detect ab initio TEs and annotate them including nested and degenerated copies. TEs play a key role in genome evolution and dynamics and their abundance is usually correlated with genome size. Most fungi have an efficient mechanism able to irreversibly inactivate multi-copy sequences called RIP (Repeat-induced point mutation) that acts as a defence against TE expansion. RIP detects DNA duplications and mutates their C:G into T:A at high efficiency. We have developed a strategy relying on RIPCAL (http://sourceforge.net/projects/ripcal/) to search for RIP evidence among fungal TEs. This analysis suggests a good correlation between invasion of fungal genomes by TEs and reduced RIP efficiency of these invaded species. We will present results obtained with on 8 ascomycetes and basidiomycetes genomes.

Update: 20 Dec 2013
Creation date: 12 Jan 2011
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