Landscape of genomic diversity and host adaptation in Fusarium graminearum

• Published in: BMC genomics Vol. 18; no. 1; pp. 203 - 19
• Main Authors: Laurent, Benoit, Moinard, Magalie, Spataro, Cathy, Ponts, Nadia, Barreau, Christian, Foulongne-Oriol, Marie
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 23-02-2017; BioMed Central
• Subjects: Adaptation; Biological diversity; Blight; Chromosomes; Cluster Analysis; Computational Biology - methods; Cultivars; Disease control; DNA sequencing; Evolution; Fungicides; Fusarium; Fusarium - classification; Fusarium - genetics; Fusarium graminearum; Gene Ontology; Gene sequencing; Genes; Genetic aspects; Genetic diversity; Genetic polymorphisms; Genetic variance; Genetic Variation; Genome, Fungal; Genomes; Genomics; Genomics - methods; Host-bacteria relationships; Host-Pathogen Interactions; INDEL Mutation; Life Sciences; Metabolites; Molecular Sequence Annotation; Mutation; Mycotoxins; Nucleotide sequencing; Nucleotides; Organic chemistry; Pathogens; Phenotype; Physiological aspects; Plant diseases; Polymorphism; Polymorphism, Single Nucleotide; Fungal pathogen; Genome-wide polymorphism; Whole genome re-sequencing; Two-speed genome; Host-Pathogen interaction; Evolution; Single nucleotides polymorphism; Fusarium head blight; single nucleotides polymorphism; diversité génomique; evolution; fusarium graminearum; polymorphisme des nucléotides simples; genome-wide polymorphism; two-speed genome; fungal pathogen; mycotoxine; fusarium head blight; Single nucleotide polymorphism; whole genome re-sequencing; host-Pathogen interaction
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-017-3524-x

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.