2011
CNET 2011 (XVII Congrès national Eléments Transposable), Lyon, France
06 Jul 2011 Fungal genome analysis of transposable elements: genomes dynamics vs Repeat-Induced Point mutation (RIP)Amselem J , Kreplak J, Le Cam B, Lebrun MH, Quesneville H.
We took advantage of several international whole fungal genome sequencing projects where we were involved and of powerful bioinformatic automated analysis tools to perform a comparative genomic analysis of their transposable elements (TEs). The challenge was to detect ab initio TEs and annotate them including nested and degenerated copies. We used a systematic strategy relying on the REPET package to efficiently detect, classify and annotate TEs in ten ascomycetes and basidiomycetes genomes.
TEs play a key role in genome evolution and dynamics. 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 frequency. Moreover, RIP mutation mechanism occurs mostly preferentially at di-nucleotides (ex: CA to TA and reversibly TG to TA) depending on the organism. We have developed a strategy relying on RIPCAL (http://sourceforge.net/projects/ripcal/) and locally developed scripts to search for RIP and RIP di-nucleotide bias evidences among fungal TEs.
We will present the di-nucleotide targets preferentially used by RIP in the different genomes studied. Beside the fact that this analysis suggests a good correlation between the invasion success of fungal genomes by TEs and reduced RIP efficiency in the invaded species, we will show how genome structure can be affected by an efficient TE invasion counter-balanced by RIP forming AT-rich isochores. These analysis also revealed traces of ancient RIP in small and degenerated TE copies in at least two cases studied
Creation date: 08 Jul 2011
eZ PublishPublication supervisor: A-F. Adam-Blondon
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