Deciphering genome content and evolutionary relationships of isolates from the fungus Magnaporthe oryzae attacking different host plants

Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants,we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet,wheat,andgoosegrass),andoneMagnaporthegrisea isolate specific of crabgrass. Analysis ofMagnaporthegenomesrevealed small variation in genome sizes (39-43 Mb) and gene content (12,283-14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogywas mostly bifurcating amongthe different host-specific lineages, butwas reticulate inside the rice lineage.Wedetected traces of introgressionfromanonrice genome inthe rice reference70-15genome.AmongM.oryzae isolates andhost-specific lineages, the genome composition in termsof frequenciesofgenesputatively involved in pathogenicity (effectors, secondarymetabolism,cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent fromthe nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).