title: Landscape of genomic diversity and host adaptation in Fusarium graminearum.
abstract: Fusarium graminearum is one of the main causal agents of the Fusarium Head Blight, a worldwide disease affecting cereal cultures, whose presence can lead to contaminated grains with chemically stable and harmful mycotoxins. Resistant cultivars and fungicides are frequently used to control this pathogen, and several observations suggest an adaptation of F. graminearum that raises concerns regarding the future of current plant disease management strategies. To understand the genetic basis as well as the extent of its adaptive potential, we investigated the landscape of genomic diversity among six French isolates of F. graminearum, at single-nucleotide resolution using whole-genome re-sequencing.
  
  
  
  A total of 242,756 high-confidence genetic variants were detected when compared to the reference genome, among which 96% are single nucleotides polymorphisms. One third of these variants were observed in all isolates. Seventy-seven percent of the total polymorphism is located in 32% of the total length of the genome, comprising telomeric/subtelomeric regions as well as discrete interstitial sections, delineating clear variant enriched genomic regions- 7.5 times in average. About 80% of all the F. graminearum protein-coding genes were found polymorphic. Biological functions are not equally affected: genes potentially involved in host adaptation are preferentially located within polymorphic islands and show greater diversification rate than genes fulfilling basal functions. We further identified 29 putative effector genes enriched with non-synonymous effect mutation.
  
  
  
  Our results highlight a remarkable level of polymorphism in the genome of F. graminearum distributed in a specific pattern. Indeed, the landscape of genomic diversity follows a bi-partite organization of the genome according to polymorphism and biological functions. We measured, for the first time, the level of sequence diversity for the entire gene repertoire of F. graminearum and revealed that the majority are polymorphic. Those assumed to play a role in host-pathogen interaction are discussed, in the light of the subsequent consequences for host adaptation. The annotated genetic variants discovered for this major pathogen are valuable resources for further genetic and genomic studies.
authors.affiliation: INRA, UR1264 Mycologie et Sécurité des Aliments, bâtiment Qualis, 71 avenue Edouard Bourlaux, CS 20032, F-33882, Villenave d'Ornon cedex, France.
authors.forename: Benoit
authors.initials: B
authors.lastname: Laurent
authors.affiliation: INRA, UR1264 Mycologie et Sécurité des Aliments, bâtiment Qualis, 71 avenue Edouard Bourlaux, CS 20032, F-33882, Villenave d'Ornon cedex, France.
authors.forename: Magalie
authors.initials: M
authors.lastname: Moinard
authors.affiliation: INRA, UR1264 Mycologie et Sécurité des Aliments, bâtiment Qualis, 71 avenue Edouard Bourlaux, CS 20032, F-33882, Villenave d'Ornon cedex, France.
authors.forename: Cathy
authors.initials: C
authors.lastname: Spataro
authors.affiliation: INRA, UR1264 Mycologie et Sécurité des Aliments, bâtiment Qualis, 71 avenue Edouard Bourlaux, CS 20032, F-33882, Villenave d'Ornon cedex, France.
authors.forename: Nadia
authors.initials: N
authors.lastname: Ponts
authors.affiliation: INRA, UR1264 Mycologie et Sécurité des Aliments, bâtiment Qualis, 71 avenue Edouard Bourlaux, CS 20032, F-33882, Villenave d'Ornon cedex, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Barreau
authors.affiliation: INRA, UR1264 Mycologie et Sécurité des Aliments, bâtiment Qualis, 71 avenue Edouard Bourlaux, CS 20032, F-33882, Villenave d'Ornon cedex, France. marie.foulongne-oriol@inra.fr.
authors.forename: Marie
authors.initials: M
authors.lastname: Foulongne-Oriol
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D005670:Fusarium / Q000145:classification / Q000235:genetics*; D063990:Gene Ontology; D014644:Genetic Variation; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D054884:Host-Pathogen Interactions; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide
keywords: Evolution; Fungal pathogen; Fusarium head blight; Genome-wide polymorphism; Host-Pathogen interaction; Single nucleotides polymorphism; Two-speed genome; Whole genome re-sequencing