2014
March 09-14 2014, Mobile Genetic Elements & Genome Evolution symposium, Santa Fe, New Mexico, USA
09 Mar 2014 Whole genome comparative analysis of transposable elements provide new insights on silencing mechanisms in fungal genomesAmselem J, Lebrun MH, Quesneville H
Transposable Elements (TEs) abundance is usually correlated with genome size and organisation. TEs shape genomes and are a source of genetic variations and evolution. Two main defence mechanisms against DNA repeats and particularly TEs are known in fungi, RIP (Repeat-induced point mutation) and MIP (Methylation Induced Premeiotically). Both mechanisms rely on DNA methylation. RIP operates during the sexual cycle. It is an efficient process able to irreversibly inactivate multi-copy sequences by mutating methylated C into T at high rate. MIP involves the methylation of C bases from repeated sequences. We took advantage of the recent burst in fungal genome sequences to evaluate the impact of RIP and MIP on TEs through a comparative analysis. We have searched and annotated TEs from different fungal genomes using a standardized strategy based on the REPET package. This analysis provides a dataset of all TE families with their consensus with and genomic copy sequences. We developed a workflow using RIPCAL to search for TE mutations produced by RIP as well as all dinucleotide bias associated with RIP mutations or other C into T mutation associated process. The results show a strong correlation between the massive TE invasions and RIP deficiency. In addition, we found traces of novel dinucleotide bias in TE abundant genomes, probably associated with MIP-like gene. Finally, the comparative analysis of genes involved in the RIP and MIP silencing mechanisms revealed a strong correlation between dinucleotide abundance patterns and the presence/absence of RIP/MIP genes.
Creation date: 02 Apr 2014
eZ PublishPublication supervisor: A-F. Adam-Blondon
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