中文摘要：禾谷镰刀菌是影响谷物栽培的全球性病害赤霉病的主要病原之一，还产生化学性质稳定的有害的霉菌毒素污染粮食。生产中通常使用抗性品种及杀菌剂控制该病菌，但多次观察到禾谷镰刀菌的适应性，这使得当前植物病害管理策略的前景堪忧。为了了解其遗传基础及其适应性强的程度，我们利用全基因组重新测序的单核苷酸分辨率，研究了六株法国禾谷镰刀菌基因组多样性的情况。结果凸显了以特定模式分布的禾谷镰刀菌基因组显著的多态性水平。实际上，根据多态性和生物学功能，基因组多样性情况为基因组的二部组织。我们首次为禾谷镰刀菌的整个基因库测量了序列多样性的水平，显示大多数是多态的。根据宿主适应的后续后果，讨论了宿主-病原体相互作用中发挥作用的假设。为这一主要病原体发现的注释遗传变异是进一步研究遗传和基因组的宝贵资源。
外文摘要：BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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 majorpathogen are valuable resources for further genetic and genomic studies.
 
外文关键词：Fungal pathogen；Fusarium head blight；Whole genome re-sequencing；Genome-wide polymorphism；Single nucleotides polymorphism；Host-Pathogen interaction；Evolution；Two-speed genome
作者：Laurent, B；Moinard, M；Spataro, C；Ponts, N；Barreau, C； Foulongne-Oriol, M
作者单位：INRA
期刊名称：BMC GENOMICS
期刊影响因子：3.867
出版年份：2017
出版刊次：2
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