Landscape of genomic diversity and host adaptation in Fusarium graminearum

BMC Genomics

Research Article

Nadia Ponts¹  Cathy Spataro¹  Magalie Moinard¹  Christian Barreau¹  Marie Foulongne-Oriol¹  Benoit Laurent¹ 

[1] INRA, UR1264 Mycologie et Sécurité des Aliments, bâtiment Qualis, 71 avenue Edouard Bourlaux, CS 20032, F-33882, Villenave d’Ornon cedex, France;

关键词: Fungal pathogen;    Fusarium head blight;    Whole genome re-sequencing;    Genome-wide polymorphism;    Single nucleotides polymorphism;    Host-Pathogen interaction;    Evolution;    Two-speed genome;   

DOI  :  10.1186/s12864-017-3524-x

 received in 2016-10-07, accepted in 2017-01-27,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2017