Abstract
BackgroundFusarium 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.ResultsA 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.ConclusionsOur 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.
Highlights
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
What are the patterns of polymorphism in the regions of the reference genome not covered by reads produced after re-sequencing? Is this genomic organization respected across worldwide isolates? What is the state of the diversity affecting the functional part of the genome, including the genes for which a role for adaptation could be assumed? In order to answer those questions we proposed to re-sequence six strains of F. graminearum originally isolated from various locations in France
Single nucleotide polymorphism (SNP) and Insertion or deletion (InDel) discovery Our strategy of genome re-sequencing applied to six F. graminearum strains generated a total of 125 million of read pairs of 100 base pairs in length, corresponding to 37.0–44.7 million raw reads per genome (Additional file 1: Table S1)
Summary
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. The ascomycete Fusarium graminearum (teleomorphe Gibberella zeae) is a hemibiotrophic pathogen commonly described as one of the main causal agent of the Fusarium Head blight (FHB), a devastating disease affecting small grains cereals worldwide [1]. Three chemotypes of TCTB-producing isolates have been described according to their ability to produce deoxynivalenol along with 15-acetyldeoxynivalenol (DON/15-ADON), deoxynivalenol and 3-acetyldeoxyni valenol (DON/3-ADON), and nivalenol and acetylated form (NIV). These chemotypes are associated with quantitative difference in pathogenicity; the strains producing DON instead of NIV are, for example, more aggressive against wheat [8]. Other factors were identified in F. graminearum with the detection of 50 quantitative trait nucleotides linked to aggressiveness variation [11]
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