Transcription profiling and identification of infection-related genes in Phytophthora cactorum

Abstract

Phytophthora cactorum, an oomycete pathogen, infects more than 200 plant species within several plant families. To gain insight into the repertoire of the infection-related genes of P. cactorum, Illumina RNA-Seq was used to perform a global transcriptome analysis of three life cycle stages of the pathogen, mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). From over 9.8 million Illumina reads for each library, 18,402, 18,569 and 19,443 distinct genes were identified for MY, ZO and GC libraries, respectively. Furthermore, the transcriptome difference among MY, ZO and GC stages was investigated. Gene ontology (GO) and KEGG pathway enrichment analyses revealed diverse biological functions and processes. Comparative analysis identified a large number of genes that are associated with specific stages and pathogenicity, including 166 effector genes. Of them, most of RXLR and NLP genes showed induction while the majority of CRN genes were down-regulated in GC, the important pre-infection stage, compared to either MY or ZO. And 14 genes encoding small cysteine-rich (SCR) secretory proteins showed differential expression during the developmental stages and in planta. Ectopic expression in the Solanaceae indicated that SCR113 and one elicitin PcINF1 can trigger cell death on Nicotiana benthamiana, tobacco (N. tabacum) and tomato (Solanum lycopersicum) leaves. Neither conserved domain nor homologues of SCR113 in other organisms can be identified. Collectively, our study provides a comprehensive examination of gene expression across three P. cactorum developmental stages and describes pathogenicity-related genes, all of which will help elucidate the pathogenicity mechanism of this destructive pathogen.

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

“…Genomic resources are available for these hosts [ 84 – 87 ], and recent work has identified resistance-associated QTL for cultivated strawberry [ 19 ]. Despite this, genomic resources for the pathogen are limited to identification of ESTs expressed during infection [ 88 ] and transcript expression during oospore germination characterized [ 49 , 89 ]. We report the sequencing, annotation and assembly of the P .…”

Mixed-Mating Model of Reproduction Revealed in European Phytophthora cactorum by ddRADseq and Effector Gene Sequence Data

“…Three effector gene regions that are potentially polymorphic were chosen: RXLR6, RXLR7 [19] and SCR113 [42]. Only a subset of all P. cactorum isolates were used in this part of the whole study (Table 1).…”

Pathogenic Adaptations Revealed by Comparative Genome Analyses of Two Colletotrichum spp., the Causal Agent of Anthracnose in Rubber Tree

“…Based on their phylogenetic analysis of NLP sequences, Oome and Van den Ackerveken (2014) defined four groups belonging to three phylogenetic types. A great number of newly identified NLP sequences, from a broad range of diverse organisms, have been studied to date, providing much valuable insight into the evolution and functions of these remarkable proteins ( de Oliveira et al, 2012 ; Kleemann et al, 2012 ; Zhou et al, 2012 ; Oome and Van den Ackerveken, 2014 ; Chen et al, 2018 ). Importantly, each NLP type differs in its ability to induce necrosis.…”