ANSES Laboratoire de la santé des végétaux, Unité de Mycologie, Malzéville, France.
INRA, UMR1290 BIOGER_CPP, Thiverval-Grignon, France.
PLoS One. 2019 Jan 11;14(1):e0207988. doi: 10.1371/journal.pone.0207988. eCollection 2019.
Fusarium head blight (FHB) is a major cereal disease caused by a complex of Fusarium species. These species vary in importance depending on climatic conditions, agronomic factors or host genotype. In addition, Fusarium species can release toxic secondary metabolites. These mycotoxins constitute a significant food safety concern as they have health implications in both humans and animals. The Fusarium species involved in FHB differ in their pathogenicity, ability to produce mycotoxins, and fungicide sensitivity. Accurate and exhaustive identification of Fusarium species in planta is therefore of great importance. In this study, using a new set of primers targeting the EF1α gene, the diversity of Fusarium species on cereals was evaluated using Illumina high-throughput sequencing. The PCR amplification parameters and bioinformatic pipeline were optimized with mock and artificially infected grain communities and further tested on 65 field samples. Fusarium species were retrieved from mock communities and good reproducibility between different runs or PCR cycle numbers was be observed. The method enabled the detection of as few as one single Fusarium-infected grain in 10,000. Up to 17 different Fusarium species were detected in field samples of barley, durum and soft wheat harvested in France. This new set of primers enables the assessment of Fusarium diversity by high-throughput sequencing on cereal samples. It provides a more exhaustive picture of the Fusarium community than the currently used techniques based on isolation or species-specific PCR detection. This new experimental approach may be used to show changes in the composition of the Fusarium complex or to detect the emergence of new Fusarium species as far as the EF1α sequence of these species show a sufficient amount of polymorphism in the portion of sequence analyzed. Information on the distribution and prevalence of the different Fusarium species in a given geographical area, and in response to various environmental factors, is of great interest for managing the disease and predicting mycotoxin contamination risks.
镰刀菌穗腐病（FHB）是一种由镰刀菌属真菌引起的主要谷类病害。这些物种的重要性因气候条件、农业因素或宿主基因型而异。此外，镰刀菌属真菌可以释放出有毒的次生代谢物。这些真菌毒素构成了一个重大的食品安全问题，因为它们对人类和动物的健康都有影响。参与 FHB 的镰刀菌物种在致病性、产毒能力和杀菌剂敏感性方面存在差异。因此，准确和详尽地鉴定植物中的镰刀菌物种非常重要。在这项研究中，使用针对 EF1α 基因的一组新引物，使用 Illumina 高通量测序评估了谷物上镰刀菌物种的多样性。使用模拟和人工感染谷物群落优化了 PCR 扩增参数和生物信息学流程，并在 65 个田间样本上进行了进一步测试。从模拟群落中检索到了镰刀菌物种，并且在不同运行或 PCR 循环数之间观察到了良好的重现性。该方法能够在 10000 个中检测到一个单一的感染谷物。在法国收获的大麦、硬质小麦和软小麦的田间样本中检测到多达 17 种不同的镰刀菌物种。这组新引物能够通过高通量测序对谷物样本进行评估。与目前基于分离或种特异性 PCR 检测的技术相比，它提供了更详尽的镰刀菌群落图片。这种新的实验方法可用于显示镰刀菌复合体组成的变化，或检测新的镰刀菌物种的出现，只要这些物种的 EF1α 序列在分析的序列部分显示出足够多的多态性。在给定地理区域内，不同镰刀菌物种的分布和流行情况以及对各种环境因素的响应信息对于管理病害和预测真菌毒素污染风险非常重要。
