title: Transcriptomic analysis of the phytopathogenic oomycete Phytophthora cactorum provides insights into infection-related effectors.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China. xrchen@yzu.edu.cn.
authors.forename: Xiao-Ren
authors.initials: XR
authors.lastname: Chen
authors.forename: Bo-Yue
authors.initials: BY
authors.lastname: Zhang
authors.forename: Yu-Ping
authors.initials: YP
authors.lastname: Xing
authors.forename: Qi-Yuan
authors.initials: QY
authors.lastname: Li
authors.forename: Yan-Peng
authors.initials: YP
authors.lastname: Li
authors.forename: Yun-Hui
authors.initials: YH
authors.lastname: Tong
authors.forename: Jing-You
authors.initials: JY
authors.lastname: Xu
mesh_terms: D000483:Alleles; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019295:Computational Biology; D015870:Gene Expression; D020869:Gene Expression Profiling; D008018:Life Cycle Stages / Q000235:genetics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family; D010641:Phenotype; D010838:Phytophthora / Q000235:genetics* / Q000254:growth & development; D010935:Plant Diseases / Q000469:parasitology*; D011110:Polymorphism, Genetic; D054730:Protein Interaction Domains and Motifs; D015203:Reproducibility of Results; D016415:Sequence Alignment; D059467:Transcriptome