Field pathogenomics reveals the emergence of a diverse wheat yellow rust population.
Field pathogenomics reveals the emergence of a diverse wheat yellow rust population.
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DOI：
10.1186/s13059-015-0590-8
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发表时间：
2015-02-25
期刊：
影响因子：
12.3
通讯作者：
Saunders DG
中科院分区：
文献类型：
--
作者：
Hubbard A;Lewis CM;Yoshida K;Ramirez-Gonzalez RH;de Vallavieille-Pope C;Thomas J;Kamoun S;Bayles R;Uauy C;Saunders DG
新出现和再出现的病原体危及公共卫生和全球粮食安全。应对这些威胁需要改进监测和诊断系统。尽管基因组工具具有潜力，但还没有很好地应用于新出现或再出现的植物病原体，如小麦黄（条）锈病病原体小麦条锈病（PST）。这主要是由于PST的专性寄生性质，因为培养PST分离物用于DNA提取仍然缓慢而繁琐。为了克服与培养PST相关的局限性，我们开发并应用了一种田间病理基因组学方法，通过对2013年从田间收集的受感染小麦叶片进行转录组测序。这使我们能够迅速了解这种新出现的病原体种群。我们发现，近年来，英国（UK）的PST人口发生了重大变化。群体遗传结构分析揭示了四个不同的谱系，这些谱系与通过传统的基于病理的毒力分析确定的表型组相关。此外，2013年所有PST野外样本的单个种群群成员之间的遗传多样性远高于英国历史分离株，表明PST群体更加多样化。我们的现场病理基因组学方法揭示了英国PST人群的巨大变化，这可能是由于最近引入了一组不同的外来PST谱系。本文所描述的方法加速了病原体种群的遗传分析，并规避了与专性植物病原体相关的困难。原则上，该策略可广泛应用于多种植物病原体。本文的在线版本（doi:10.1186/s13059-015-0590-8）包含补充材料，授权用户可使用。
Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens. The online version of this article (doi:10.1186/s13059-015-0590-8) contains supplementary material, which is available to authorized users.
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影响因子：
3
作者：
Ali, Sajid;Leconte, Marc;de Vallavieille-Pope, Claude
通讯作者：
de Vallavieille-Pope, Claude
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
3
作者：
Goyeau, Henriette;Halkett, Fabien;Lannou, Christian
通讯作者：
Lannou, Christian
影响因子：
3.2
作者：
Linde, CC;Zhan, J;McDonald, BA
通讯作者：
McDonald, BA