Nanopore technologies for Septoria Surveillance

小麦黑斑病是影响北欧小麦生产的最重要的经济病害。STB是通过农艺、遗传抗性和杀菌剂的组合来控制的，然而，对潜在病原菌种群的选择和随后的适应可能导致寄主抗性和对化学防治的抗性的崩溃。随着病原菌的适应，我们需要了解害虫种群(或致病类型)的组成，以便能够描述同一物种成员之间的具体差异，以及这些差异如何影响受STB影响的小麦品种的范围。STB的有效和经济高效的解决方案将直接取决于我们对潜在病原体(ZymosepVictoria Tritici)的了解。使用先进的测序技术有可能快速有效地筛选许多单独的病原体分离物，以低成本提供丰富的信息。这种方法已经被证明是小麦黄锈病的有力工具。然而，购买进行测序所需的机器的成本往往令人望而却步，而且运行可能需要24-48小时才能完成。还需要高性能的计算设施和有经验的操作员进行相关分析，以便将测序数据安排成实用的格式。NanoPath将使用牛津纳米孔技术公司的Minion测序仪作为监测工具，以提高研究人员识别和调查田间新害虫的速度和简便性。这将首先评估Minion的效用，并帮助开发一个模型和计算平台，将纳米孔测序应用于更广泛的作物病原体。Minion设备是便携的，能够在相对容易使用的过程中产生测序数据。我们还建议实施一个数据分析管道，该管道将利用一些开放源码的主要数据软件工具，这些工具针对发现和表征这种作物病原体的遗传变异而进行了优化。

Septoria tritici blotch (STB) of wheat is the most economically important disease affecting wheat production in Northern Europe. STB is controlled using a combination of agronomy, genetic resistance and fungicides however, selection and subsequent adaptation of the underlying pathogen populations can lead to breakdowns in host resistance and resistance to chemical controls. As the pathogen adapts we will need to understand the composition of the pest population (or pathotypes) to be able to describe specific differences between members of the same species and how these differences affect the range of wheat varieties affected by STB. An effective and cost-efficient solution for STB will directly depend on our understanding of the underlying pathogen (Zymoseptoria tritici). The use of advanced sequencing technologies has the potential to quickly and efficiently screen many individual pathogen isolates, providing a wealth of information at a low cost. This type of approach has already been demonstrated to be a powerful tool in yellow rust of wheat. However, the cost of purchasing machinery required to conduct sequencing is often prohibitive and runs can take between 24-48 hours to complete. There are also requirements for high-powered computing facilities and experienced operators to conduct the relevant analyses to arrange sequencing data in to a practical format. NanoPath will employ the MinION sequencer from Oxford Nanopore Technologies as a surveillance tool to improve the speed and ease at which researchers can identify and survey new pests in the field. This will first assess the utility of the MinION and help to develop a model and computational platform to apply nanopore sequencing to a wider range of crop pathogens. The MinION device is portable and able to generate sequencing data following a relatively easy-to-use process. We also propose to implement a data analysis pipeline that will make use of a number of open-source primary data software tools optimised for the discovery and characterisation of genetic variants this crop pathogen.