Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races
Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races
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草莓病原菌草莓疫霉的基因组研究表明致病性与三个关键种族的转录变异有关
DOI：
10.1101/860619
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Adams T
中科院分区：
文献类型：
--
作者：
Adams T
草莓疫霉（Phytophthora fragariae）是草莓栽培种上的一种极具破坏性的病原菌，可引起草莓的根腐病--“红心病”。宿主-病原体相互作用有一个很好的描述基因对基因的抗性关系，但迄今为止，既没有候选无毒或抗性基因已被确定。我们对一组美国、加拿大和英国已知小种类型的分离株以及与树莓（Rubus idaeus）密切相关的病原体P.鲁比的三个代表沿着进行了测序，发现了一个清晰的种群结构，在一些小种类型之间观察到高度的核苷酸差异，以及与小种类型4和5相关的丰富的私人变异。相比之下，定义为英国种族1，2和3（UK 1 -2-3）之间的分离株，没有证据表明基因丢失或获得;或插入/缺失（INDEL）或单核苷酸多态性（SNP）的存在内或附近的推定致病性基因可以发现与种族变异。代表性UK 1 -2-3分离株的转录组学分析显示，与病原体小种相关的关键效应子家族基因存在丰富的表达变异;然而，进一步的长读段测序未显示任何与小种UK 2或UK 3抗性的无毒力相关的长范围多态性，这表明控制转基因或其他稳定形式的表观遗传修饰调节基因表达。这项工作揭示了群体重测序揭示致病系统中的种族结构和植物转录组学分析识别候选无毒基因的综合能力。这项工作的影响，在相关的表达数据的情况下，对卵菌植物病原体的效应调控和沉默的机制，需要详细的分子特征的鉴定推定无毒基因。
The oomycetePhytophthora fragariaeis a highly destructive pathogen of cultivated strawberry (Fragaria×ananassa), causing the root rotting disease, “red core”. The host-pathogen interaction has a well described gene-for-gene resistance relationship, but to date neither candidate avirulence nor resistance genes have been identified. We sequenced a set of American, Canadian, and United Kingdom isolates of known race type, along with three representatives of the closely related pathogen of the raspberry (Rubus idaeus),P. rubi, and found a clear population structure, with a high degree of nucleotide divergence seen between some race types and abundant private variation associated with race types 4 and 5. In contrast, between isolates defined as United Kingdom races 1, 2, and 3 (UK1-2-3) there was no evidence of gene loss or gain; or the presence of insertions/deletions (INDELs) or Single Nucleotide Polymorphisms (SNPs) within or in proximity to putative pathogenicity genes could be found associated with race variation. Transcriptomic analysis of representative UK1-2-3 isolates revealed abundant expression variation in key effector family genes associated with pathogen race; however, further long read sequencing did not reveal any long range polymorphisms to be associated with avirulence to race UK2 or UK3 resistance, suggesting either control intransor other stable forms of epigenetic modification modulating gene expression. This work reveals the combined power of population resequencing to uncover race structure in pathosystems andin plantatranscriptomic analysis to identify candidate avirulence genes. This work has implications for the identification of putative avirulence genes in the absence of associated expression data and points toward the need for detailed molecular characterisation of mechanisms of effector regulation and silencing in oomycete plant pathogens.