Transcriptomic analysis of the phytopathogenic oomycete Phytophthora cactorum provides insights into infection-related effectors.
Transcriptomic analysis of the phytopathogenic oomycete Phytophthora cactorum provides insights into infection-related effectors.
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植物病原卵菌 Phytophthora cactorum 的转录组分析提供了对感染相关效应子的见解
DOI：
10.1186/1471-2164-15-980
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发表时间：
2014-11-18
期刊：
影响因子：
4.4
通讯作者：
Xu JY
中科院分区：
文献类型：
--
作者：
Chen XR;Zhang BY;Xing YP;Li QY;Li YP;Tong YH;Xu JY
仙人掌疫霉（Phytophthora cactorum）是一种半生物营养型卵菌病原体，可对全世界多种作物造成破坏性病害，每年造成严重的经济损失。然而，人们对其分子致病机制知之甚少。为了深入了解其效应子库，使用 Illumina RNA-seq 对 P. cactorum 转录组进行了研究。我们首先展示了一种体外接种方法，可用于模拟宿主植物上自然胞囊萌发。获得了五个生命周期阶段（菌丝体、孢子囊、游动孢子、胞囊和萌发胞囊）超过 2800 万个 cDNA 读数，并从头组装成 21,662 个独特基因。通过与11个公共数据库的比较，88.99%的独特基因被注释，其中15,845个映射到注释的近缘致病疫霉的基因模型。使用 TribeMCL，确定了 P. cactorum 和其他三种已完全测序的疫霉属病原体物种中保守的 5,538 个基因家族。计算机分析显示，620 个 P. cactorum 效应子同源物（包括 94 个 RXLR 效应子候选物）与其他卵菌中已知或推定的毒力基因相匹配。预计大约一半的 RXLR 效应子候选者共享一个保守的结构单元，称为 WY 结构域折叠。通过 PCR 扩增检查和验证效应基因的子集。转录实验表明，效应基因在P. cactorum的生命周期和宿主感染阶段存在差异表达。本塞姆氏烟草中的异位表达表明 RXLR、elicitin 和 NLP 效应子可以触发植物细胞死亡。这些效应器在卵菌物种中高度保守。在来自不同国家和宿主的一组 P. cactorum 分离株中检测到 RXLR 效应子的单核苷酸多态性。本研究展示了对 P. cactorum 生命周期阶段的转录组的全面测序、从头组装和分析。在缺乏基因组序列的情况下，转录组数据对于发现 P. cactorum 感染相关基因非常重要，正如此处针对效应基因所证明的那样。对 P. cactorum 转录组和效应器库的首次观察为阐明这种广泛宿主范围病原体的致病性基础提供了有价值的数据。本文的在线版本 (doi:10.1186/1471-2164-15-980) 包含补充材料，可供授权用户使用。
Phytophthora cactorum, a hemibiotrophic oomycete pathogen, can cause destructive diseases on numerous crops worldwide, leading to essential economic losses every year. However, little has been known about its molecular pathogenicity mechanisms. To gain insight into its repertoire of effectors, the P. cactorum transcriptome was investigated using Illumina RNA-seq. We first demonstrated an in vitro inoculation method that can be used to mimic natural cyst germination on host plants. Over 28 million cDNA reads were obtained for five life cycle stages (mycelium, sporangium, zoospore, cyst and germinating cyst) and de novo assembled into 21,662 unique genes. By comparisons with 11 public databases, 88.99% of the unique genes were annotated, including 15,845 mapped to the gene models of the annotated relative Phytophthora infestans. Using TribeMCL, 5,538 gene families conserved across P. cactorum and other three completely sequenced Phytophthora pathogen species were determined. In silico analyses revealed that 620 P. cactorum effector homologues including 94 RXLR effector candidates matched known or putative virulence genes in other oomycetes. About half of the RXLR effector candidates were predicted to share a conserved structure unit, termed the WY-domain fold. A subset of the effector genes were checked and validated by PCR amplification. Transcriptional experiments indicated that effector genes were differentially expressed during the life cycle and host infection stages of P. cactorum. Ectopic expression in Nicotiana benthamiana revealed that RXLR, elicitin and NLP effectors can trigger plant cell death. These effectors are highly conserved across oomycete species. Single nucleotide polymorphisms for RXLR effectors were detected in a collection of P. cactorum isolates from different countries and hosts. This study demonstrates the comprehensive sequencing, de novo assembly, and analyses of the transcriptome of P. cactorum life cycle stages. In the absence of genome sequence, transcriptome data is important for infection-related gene discovery in P. cactorum, as demonstrated here for the effector genes. The first look at the transcriptome and effector arsenal of P. cactorum provides valuable data to elucidate the pathogenicity basis of this broad-host-range pathogen. The online version of this article (doi:10.1186/1471-2164-15-980) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
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