Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing.
Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing.
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DOI：
10.1371/journal.pone.0143665
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Smart CD
中科院分区：
文献类型：
--
作者：
Summers CF;Gulliford CM;Carlson CH;Lillis JA;Carlson MO;Cadle-Davidson L;Gent DH;Smart CD
利用RNA测序（RNA-seq）和测序基因分型（GBS）技术对两种重要的经济专性植物病原菌（黄瓜霜霉病菌和草霜霉病菌）进行单核苷酸多态性（SNP）鉴定。使用RNA-seq和GBS对20株古巴假单胞菌和19株Humuli假单胞菌进行基因分型。主成分分析（PCA）的每个数据集显示两个物种之间的遗传分离。此外，结果支持先前的发现，即来自南瓜的古巴疫霉分离物与黄瓜和哈密瓜分离物在遗传上不同。使用基于PCA的程序来鉴定与两个物种分离相关的SNP，在RNA-seq和GBS数据中分别发现了994和4，231个PCA相关的SNP。相应的unigenes（n = 800）含有这些潜在的物种特异性SNP进行了注释，并确定了135个推定的致病性基因，包括3个效应基因。含有区分这两种密切相关的霜霉病物种的SNP的基因的表征可能有助于改进检测和诊断策略的发展，并提高我们对宿主特异性途径的理解。
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data set showed genetic separation between the two species. Additionally, results supported previous findings that P. cubensis isolates from squash are genetically distinct from cucumber and cantaloupe isolates. A PCA-based procedure was used to identify SNPs correlated with the separation of the two species, with 994 and 4,231 PCA-correlated SNPs found within the RNA-seq and GBS data, respectively. The corresponding unigenes (n = 800) containing these potential species-specific SNPs were then annotated and 135 putative pathogenicity genes, including 3 effectors, were identified. The characterization of genes containing SNPs differentiating these two closely related downy mildew species may contribute to the development of improved detection and diagnosis strategies and improve our understanding of host specificity pathways.