Genomics of Clubroot Pathogen and Pathogenesis

The main characteristics of the P. brassicae genome are its small size of 24.2–25.41 Mb with high gene density and compactness. The genome contains genes potentially involved in host hormones manipulation. The enzymes (CAZymes) involved in synthesis, metabolism, and transport of carbohydrates are present. Mitochondrial genome is variable (34–180 kbp) in size because of variation in the intergenic regions and intron content. There is higher G+C content in mitochondrial sequence than in nuclear genome. Molecular mechanisms of pathogenesis revealed expression of Y10 gene during plasmodial stages of P. brassicae. A trehalose-6-phosphate synthase gene and PbSTK L1 genes are expressed during resting spores formation. A serine protease (PRO1) gene is expressed during host infection as well as in dormant and germinating resting spores. More than 58 genes are up-regulated in the secondary zoospores relative to 55 genes down-regulated in primary zoospores. The genes PbPP2A and PbHMG are expressed at the early phases of infection. The gene BjN1T1 expression in B. juncea promotes over production of auxins to form root galls. The main plant hormones pathways modified are cytokinin biosynthesis, auxin homeostasis and salicylic acid, and jasmonic acid metabolism. The methyltransferase gene of P. brassicae acts by methylation of salicylic acid, benzoic acid, and anthranilic acids to suppress salicylic acid-induced defense in the host plant. Bioinformatics have been used to identify putative effectors/genes of P. brassicae for pathogenesis. Transcriptomics analysis has revealed 162 candidates’ enzymes/genes involved in lipid metabolism differentially expressed in the P. brassicae life cycle. The rate of infection and pathogen development is most rapid in susceptible host in comparison to resistant. The transcriptomic and proteomic approaches have elucidated mechanisms of P. brassicae infection and coordination in host reactions. Functional genomics approaches like expressed sequence tags (EST’s), serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS), next generations sequencing (NGS), RNA sequencing (RNA-seq), microarray analysis, and construction of suppression subtractive hybridization (SSHcDNA) liberty have been used to achieve better insight into the molecular mechanisms of host–parasite interaction and expression of functional genes. Microarray chips, two-dimensional electrophoresis, and high-throughput sequencing techniques like metabotyping, laser microdissection, transcriptional profiling, and miRNA sequencing have been exploited to observe expression of genes regulating metabolic pathways, and signal transduction at early events during pathogenesis. Differential expression of genes in host shoot and root has been observed during P. brassicae infection. The members of TF families’, viz., MYB, bHLH, and AP2/EREBP are highly up- or down-regulated in both shoot and root. However, both shoot and root also responded to pathogen in a number of common ways such as induction of JA, ABA, and shikimate pathways metabolism. The hypoxia genes PDC1 and PDC2 are induced during secondary infection in cortical cells of root galls. Several BrSWEET genes of clade 1 and clad III up-regulated on infection suggest close relationship between sugar translocation and P. brassicae growth. RNA’s like arth-mi R160, arth-miR164, and arth-miR167 are involved in pathogenesis and target auxin-response-factor (ARF) in auxin homeostasis at clubroot development. Immunopropilin gene (PbCYP3) is differentially regulated in P. brassicae life stages at germinating, and maturing spores and plasmodial formation in infected Brassica hosts. Hydrolases and peptidases are the most common differentially regulated secreted proteins in P. brassicae-infected B. napus. The Pb3-BSMT gene (benzoic acid/salicylic methyltransferases) inactivates host defense by converting salicylic acid to methyl salicylate.