Field Pathogenomics: An Advanced Tool for Wheat Rust Surveillance.
Field Pathogenomics: An Advanced Tool for Wheat Rust Surveillance.
复制标题
现场病理基因组学：小麦锈病监测的高级工具。
DOI：
10.1007/978-1-4939-7249-4_2
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Bueno-Sancho V
中科院分区：
文献类型：
--
作者：
Bueno-Sancho V
传统上，植物病原体的诊断工具限于对经过表型表征和/或基于PCR的基因型分析的纯化的病原体分离物的分析。然而，这些方法仅检测已知的病原体，可能并不总是识别新的种族，并且可能在结果中引入偏差。下一代测序技术的最新进展为将高分辨率基因型数据整合到病原体监测计划中提供了新的机会。在这里，我们描述了一些关键的生物信息学分析中使用的新开发的“田间病原体组学”病原体监测技术。该技术基于从田间收集的病原体感染的植物叶片样品直接生成的RNA-seq数据，提供了直接在自然环境中表征病原体种群及其宿主的独特机会。我们描述了两个主要的分析：（1）已收集的病原体分离株的系统发育分析，以了解它们是如何相互关联的，以及（2）种群结构分析，以提供对病原体种群内遗传亚结构的洞察。这提供了一个高分辨率的代表性病原体种群动态直接在外地，提供新的见解病原体生物学，种群结构和发病机制。
Traditionally, diagnostic tools for plant pathogens were limited to the analysis of purified pathogen isolates subjected to phenotypic characterization and/or PCR-based genotypic analysis. However, these approaches detect only already known pathogenic agents, may not always recognize novel races, and can introduce bias in the results. Recent advances in next-generation sequencing technologies have provided new opportunities to integrate high-resolution genotype data into pathogen surveillance programs. Here, we describe some of the key bioinformatics analysis used in the newly developed" Field Pathogenomics" pathogen surveillance technique. This technique is based on RNA-seq data generated directly form pathogen-infected plant leaf samples collected in the field, providing a unique opportunity to characterize the pathogen population and its host directly in their natural environment. We describe two main analyses:(1) a phylogenetic analysis of the pathogen isolates that have been collected to understand how they are related to each other, and (2) a population structure analysis to provide insight into the genetic substructure within the pathogen population. This provides a high-resolution representation of pathogen population dynamics directly in the field, providing new insights into pathogen biology, population structure, and pathogenesis.
影响因子：
7
作者：
Naccache SN;Federman S;Veeraraghavan N;Zaharia M;Lee D;Samayoa E;Bouquet J;Greninger AL;Luk KC;Enge B;Wadford DA;Messenger SL;Genrich GL;Pellegrino K;Grard G;Leroy E;Schneider BS;Fair JN;Martínez MA;Isa P;Crump JA;DeRisi JL;Sittler T;Hackett J Jr;Miller S;Chiu CY
通讯作者：
Chiu CY
影响因子：
5.4
作者：
Islam MT;Croll D;Gladieux P;Soanes DM;Persoons A;Bhattacharjee P;Hossain MS;Gupta DR;Rahman MM;Mahboob MG;Cook N;Salam MU;Surovy MZ;Sancho VB;Maciel JL;NhaniJúnior A;Castroagudín VL;Reges JT;Ceresini PC;Ravel S;Kellner R;Fournier E;Tharreau D;Lebrun MH;McDonald BA;Stitt T;Swan D;Talbot NJ;Saunders DG;Win J;Kamoun S
通讯作者：
Kamoun S