Comparative analysis of transposable elements in the Magnaporthe oryzae/grisea clade
Résumé
Magnaporthe oryzae is a successful pathogen of crop plants and a major threat for food production. This species gathers pathogens of different Poaceaes, and causes the main fungal disease of rice worldwide and severe epidemics on wheat in South America. The evolutionary genomics of Magnaporthe oryzae project aims at characterizing genomic determinants and evolutionary events involved in the adaptation of this fungus to different host plants. Such evolution may be driven by variations in Transposable Elements (TEs) and gene content as well as modifications of coding and regulatory sequences. Indeed, TEs are essential for shaping genomes and are a source of mutations and genome re-organizations. We performed a comparative analysis of TEs in 9 isolates from the M. oryzae/grisea clade differing in their host specificity using a reference TEs consensus library (Mg7015_Refs_TE) made from M. oryzae 70-15 reference genome. We used REPET pipelines (http://urgi.versailles.inra.fr/Tools/REPET) to detect ab initio and classify TEs in M. oryzae 70-15 according to functional features (LTR, ITR, RT, transposase, etc.). After manual curation on consensus provided by the TEdenovo pipeline, we used the resulting consensus of TE families (Mg7015_Refs_TE) to annotate the 9 genome copies including nested and degenerated ones using TEannot pipeline. We will present results obtained for Mg7015_Refs_TE classification, their annotation and preliminary comparison in M. oryzae/grisea species studied regarding correlation with phylogeny.