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Rapid in-field Nanopore-based identification of plant and animal pathogens

基于纳米孔的现场快速植物和动物病原体鉴定

基本信息

批准号：
BB/N023196/1
负责人：
Richard Leggett
金额：
$ 19.23万
依托单位：
Earlham Institute
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2017
资助国家：
英国
起止时间：
2017 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FN023196%2F1
关键词：
Rapid field Nanopore based identification

项目摘要

Airborne crop diseases pose a serious threat to food security and are responsible for devastating loss of yield and over-reliance on pesticides. Early detection enables farmers to take preventative action, drastically reducing damage and cost. Current detection regimes often rely on expert identification of the pathogen from plant damage. More recently, other molecular techniques have emerged. However, these methods suffer the same problems - being specific for a single species and a need for relatively large quantities of pathogenic material. Recently, TGAC has been working on an approach dubbed Air-seq that seeks to identify pathogens through sequencing of biological particles present in air. This overcomes both problems associated with current techniques as it is unbiased (not limited by species) and requires very small quantities of material. Our ultimate aim is to put sample collection, sequencing and analysis in a single box that can be deployed in the field. Key to success is a compact sequencing technology and this has recently emerged in the form of Oxford Nanopore Technologies' (ONT) MinION.The MinION is a new compact, low-cost sequencing technology that offers long reads (thousands of bases of DNA) and a streamed mode of operation enabling analysis of data as it is generated. These attributes make it ideally suited to in-field use. However, part of the process of generating sequencing data involves converting an electrical signal from the DNA sensing pore into a sequence of bases (letters) and this is performed via an internet 'basecalling' service. For in-field deployment, this is unsatisfactory, as we cannot rely on high speed, reliable data connections. We believe a completely new approach is required in which we utilise the raw signal data in order to identify species, instead of searching against basecalled sequence.In this project, we will develop a tool that searches Nanopore signal data looking for the characteristic signal traces of pathogens of interest, building up a report on abundance levels in the process.

空气传播的作物疾病对粮食安全构成严重威胁，造成严重的产量损失和过度依赖农药。早期检测使农民能够采取预防行动，大大减少损失和成本。目前的检测制度往往依赖于专家鉴定植物损害的病原体。最近，出现了其他分子技术。然而，这些方法遇到了相同的问题-对单一物种是特异性的，并且需要相对大量的致病物质。最近，TGAC一直在研究一种名为Air-seq的方法，该方法旨在通过对空气中存在的生物颗粒进行测序来识别病原体。这克服了与当前技术相关的两个问题，因为它是无偏的（不受物种限制）并且需要非常少量的材料。我们的最终目标是将样本采集、测序和分析放在一个可以在现场部署的盒子里。成功的关键是紧凑型测序技术，最近以Oxford Nanopore Technologies（ONT）MinION的形式出现。MinION是一种新的紧凑型低成本测序技术，可提供长读段（数千个DNA碱基）和流式操作模式，从而能够在生成数据时进行分析。这些特性使其非常适合现场使用。然而，生成测序数据的过程的一部分涉及将来自DNA传感孔的电信号转换为碱基（字母）序列，并且这通过互联网“碱基调用”服务来执行。对于现场部署，这是不能令人满意的，因为我们不能依靠高速，可靠的数据连接。我们认为需要一种全新的方法，利用原始信号数据来识别物种，而不是根据碱基序列进行搜索。在这个项目中，我们将开发一种工具，搜索纳米孔信号数据，寻找感兴趣的病原体的特征信号痕迹，并在此过程中建立丰度水平报告。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples.

DOI：
10.1186/s13059-021-02582-x
发表时间：
2022-01-24
期刊：
Genome biology
影响因子：
12.3
作者：
Martin S;Heavens D;Lan Y;Horsfield S;Clark MD;Leggett RM
通讯作者：
Leggett RM

MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.

DOI：
10.12688/f1000research.11354.1
发表时间：
2017
期刊：
F1000Research
影响因子：
0
作者：
Jain M;Tyson JR;Loose M;Ip CLC;Eccles DA;O'Grady J;Malla S;Leggett RM;Wallerman O;Jansen HJ;Zalunin V;Birney E;Brown BL;Snutch TP;Olsen HE;MinION Analysis and Reference Consortium
通讯作者：
MinION Analysis and Reference Consortium

Additional file 3 of Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

Nanopore自适应采样的附加文件3：宏基因组样本中低丰度物种富集的工具