title: Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants.
abstract: 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, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed 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 genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the 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).
authors.affiliation: INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France helene.chiapello@toulouse.inra.fr elisabeth.fournier@supagro.inra.fr.
authors.forename: Hélène
authors.initials: H
authors.lastname: Chiapello
authors.affiliation: INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Mallet
authors.affiliation: INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France.
authors.forename: Cyprien
authors.initials: C
authors.lastname: Guérin
authors.affiliation: CNRS, UMR 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France Center for Genomic Regulation, Barcelona, Spain.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Aguileta
authors.affiliation: INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France.
authors.forename: Joëlle
authors.initials: J
authors.lastname: Amselem
authors.affiliation: INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kroj
authors.affiliation: CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France.
authors.forename: Enrique
authors.initials: E
authors.lastname: Ortega-Abboud
authors.affiliation: INRA-AgroParisTech, UMR 1190, Biologie et Gestion des Risques en Agriculture BIOGER-CPP, Campus AgroParisTech, Thiverval-Grignon, France.
authors.forename: Marc-Henri
authors.initials: MH
authors.lastname: Lebrun
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques, Université d'Aix Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France.
authors.forename: Annie
authors.initials: A
authors.lastname: Gendrault
authors.affiliation: INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France.
authors.forename: François
authors.initials: F
authors.lastname: Rodolphe
authors.affiliation: CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Tharreau
authors.affiliation: INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Fournier
mesh_terms: D000220:Adaptation, Biological; D001483:Base Sequence; D005075:Biological Evolution; D019117:Burkholderia / Q000235:genetics / Q000302:isolation & purification; D004251:DNA Transposable Elements; D031746:Digitaria / Q000382:microbiology; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics; D005800:Genes, Fungal; D014644:Genetic Variation; D016681:Genome, Fungal; D020082:Magnaporthe / Q000235:genetics* / Q000302:isolation & purification; D012275:Oryza / Q000382:microbiology; D010935:Plant Diseases / Q000382:microbiology; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D005656:Fungal Proteins
keywords: adaptation to the host, rice blast, comparative genomics; http://genome.jouy.inra.fr/gemo