RNA-Seq Reveals Infection-Related Gene Expression Changes in Phytophthora capsici

Abstract

Phytophthora capsici is a soilborne plant pathogen capable of infecting a wide range of plants, including many solanaceous crops. However, genetic resistance and fungicides often fail to manage P. capsici due to limited knowledge on the molecular biology and basis of P. capsici pathogenicity. To begin to rectify this situation, Illumina RNA-Seq was used to perform massively parallel sequencing of three cDNA samples derived from P. capsici mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). Over 11 million reads were generated for each cDNA library analyzed. After read mapping to the gene models of P. capsici reference genome, 13,901, 14,633 and 14,695 putative genes were identified from the reads of the MY, ZO and GC libraries, respectively. Comparative analysis between two of samples showed major differences between the expressed gene content of MY, ZO and GC stages. A large number of genes associated with specific stages and pathogenicity were identified, including 98 predicted effector genes. The transcriptional levels of 19 effector genes during the developmental and host infection stages of P. capsici were validated by RT-PCR. Ectopic expression in Nicotiana benthamiana showed that P. capsici RXLR and Crinkler effectors can suppress host cell death triggered by diverse elicitors including P. capsici elicitin and NLP effectors. This study provides a first look at the transcriptome and effector arsenal of P. capsici during the important pre-infection stages.

Phytophthora cinnamomi

“…Members of the Crinkler (CRN) group of effectors were first identified amongst P. infestans genes that caused crinkling and necrosis when transiently expressed in N. benthamiana cells (Torto et al ., ), although more recent studies have shown that the majority of CRN effectors suppress plant defence (Chen et al ., ; Haas et al ., ; Stam et al ., ). CRN proteins have a conserved N‐terminal domain that includes LFLAK and DWL motifs that function in directing translocation of the CRN proteins from the apoplast into the plant cytoplasm (Schornack et al ., ).…”

The Top 10 oomycete pathogens in molecular plant pathology

“…Natural resistance to P. capsici in pepper and cucurbits appears to be rare (Mallard et al, 2013) but, in tomato, it may be extensive (Quesada-Ocampo and Hausbeck, 2010). Recent molecular studies of the CRN class of effectors have indicated that they are often localized to the host nucleus and play an important role in the infection process (Chen et al, 2013;Stam et al, 2013aStam et al, , 2013b. Transcriptome studies using RNAseq and microarrays have indicated dramatic changes from pre-infective spores through the early biotrophic and later necrotrophic stages of infection (Chen et al, 2013;Jupe et al, 2013).…”

“…Recent molecular studies of the CRN class of effectors have indicated that they are often localized to the host nucleus and play an important role in the infection process (Chen et al, 2013;Stam et al, 2013aStam et al, , 2013b. Transcriptome studies using RNAseq and microarrays have indicated dramatic changes from pre-infective spores through the early biotrophic and later necrotrophic stages of infection (Chen et al, 2013;Jupe et al, 2013). Studies of individual effectors have suggested that some manipulate the host to allow infection, whereas others trigger plant cell death (Chen et al, 2013;Feng and Li, 2013;Feng et al, 2010;Sun et al, 2009).…”

“…Transcriptome studies using RNAseq and microarrays have indicated dramatic changes from pre-infective spores through the early biotrophic and later necrotrophic stages of infection (Chen et al, 2013;Jupe et al, 2013). Studies of individual effectors have suggested that some manipulate the host to allow infection, whereas others trigger plant cell death (Chen et al, 2013;Feng and Li, 2013;Feng et al, 2010;Sun et al, 2009).…”

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

“…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, 2011). 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, 2006;Chen et al, 2013Chen et al, , 2014Gilroy et al, 2011;Liu et al, 2011). 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, 2011).…”