Transcriptomic analysis of the phytopathogenic oomycete Phytophthora cactorum provides insights into infection-related effectors

Abstract

BackgroundPhytophthora 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.ResultsWe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-980) contains supplementary material, which is available to authorized users.

SCR96, a small cysteine‐rich secretory protein of Phytophthora cactorum, can trigger cell death in the Solanaceae and is important for pathogenicity and oxidative stress tolerance

“…Recently, we have assembled the transcriptome of P. cactorum life cycle stages containing 21 662 unique genes (Chen et al ., ). About 620 effectors, including PcF and three SCR proteins (SCR96, SCR99 and SCR121), were identified (Chen et al ., ) (Table ).…”

“…Recently, we have assembled the transcriptome of P. cactorum life cycle stages containing 21 662 unique genes (Chen et al ., ). About 620 effectors, including PcF and three SCR proteins (SCR96, SCR99 and SCR121), were identified (Chen et al ., ) (Table ). To understand the transcriptional profiles of these unique genes during life cycle stages, three cDNA libraries representing mycelia (MY), swimming zoospores (ZO) and germinating cysts with germ tubes (GC) were separately constructed and sequenced in this study using the Illumina Genome Analyzer IIx platform (Illumina, San Diego, CA, USA).…”

“…The expansion of PcF/SCR gene families in oomycetes has been noted in whole‐genome analyses and the size of the family in several species, such as P. infestans ( n = 16), P. sojae ( n = 19), P. ramorum ( n = 4), Pythium ultimum ( n = 3) and Hyaloperonospora arabidopsidis ( n = 2), has been estimated through annotation (Baxter et al ., ; Haas et al ., ; Lévesque et al ., ; Tyler et al ., ). In our recent work, three SCR genes plus PcF were detected in the P. cactorum transcriptome (Chen et al ., ). Comparative structural and functional characterization of PcF and several homologues from P. infestans highlighted a surface‐exposed conserved amino acid stretch SK(E/C)C as a possible structural determinant responsible for the differential phytotoxicity (Orsomando et al ., ).…”

“…Plant receptor‐like kinase, such as Nicotiana benthamiana BAK1/SERK3, contributes to elicitin‐mediated necrosis, and kinase gene silencing leads to enhanced plant susceptibility to P. infestans (Chaparro‐Garcia et al ., ). Furthermore, elicitin‐, NLP‐ and CBEL‐induced cell death can be suppressed by host‐translocated effectors, demonstrating that oomycetes have evolved delicate mechanisms to counteract the host cell death triggered by necrosis‐inducing elicitors (Bos et al ., ; Chen et al., , ; Gilroy et al ., ; Liu et al ., ). Based on these results, it has been suggested that responses to these proteins could overlap with ETI and play an important role in the outcome of Phytophthora –plant interactions (Thomma et al ., ).…”

Evaluation of phytophthora root rot resistance in avocado

“…The same gene was shown to cooperate with a similar receptor-like kinase (BKK1/SERK4), contributing to the resistance of A. thaliana to the biotrophic oomycete Hyaloperonospora arabidopsidis (Roux et al, 2011), suggesting that BAK1/SERK3 may contribute to basal plant defence against oomycete pathogens. The sequencing and analysis of Phytophthora pathogens including P. cinnamomi is ongoing (Chen et al, 2014).…”