Abstract
Genomics of host–pathogen interactions have greatly advanced in perception and understanding of molecular and genetical mechanisms of host–pathogen recognition system and pathogenesis. Next-generation sequencing and omics technologies have enabled the sequencing of entire host and pathogen genome or transcriptome more efficiently for better comprehension of host-pathosystem. Pathogenomics have revealed how pathogens adopt a specific host, subvert innate immune responses and change host range, and develop new virulent races/strains/pathotypes. In Brassica–Albugo interactions, the host–R genes control pathogen infection and development in compatible (susceptible) and incompatible (resistant/tolerant) cultivars. Differentially expressed proteins regulate defense reactions in the resistant varieties. The boost in cysteine and GSH levels is crucial for incompatible interaction between Albugo candida and Brassica juncea. In the A. candida–B. juncea pathosystem, the timing of the induction of PR-5 in R and S varieties is crucial for mounting of an effective defense to the pathogen. During infection and pathogenesis of Albugo in Brassica genotypes differing in level of resistance (R, PR, MS, S), R genes regulate functions and molecular mechanisms. In Brassica–Alternaria interactions species-specific genes of Alternaria with putative roles in virulence have been identified. Transcriptomic analysis has revealed six genes strongly associated with A. brassicicola pathogenesis. AbPf2 gene activates pathogenicity in A. brassicicola. AbNPS2 gene plays an important role in disease development and virulence. Among several genes identified as pathogenicity factors, Amr1 gene is important for success of A. brassicicola as competitive saprophyte and plant parasite. Microarray analysis of Brassica infected with Alternaria at 48 hpi revealed differential expression of 87 genes mainly involved in cell response signaling, cell wall degradation, protein degradation, auxins-induced metabolism, being downregulated. The change in host cell ultrastructure and transcriptome reprogramming has been observed in Alternaria-infected Brassica. Defense-related genes are activated also in Brassica–Alternaria susceptible interactions. Mitogen-activated protein (MAP) kinase and CAMP/PKA signaling pathways are involved in fungal growth, conidial formation, stress tolerance, and pathogenesis in Arabidopsis by Colletotrichum higginsianum. During pathogenesis, host peroxisomes, microtubules, and Golgi are novel targets for fungal effector genes. Fus3/Ksi1-related MAPK chMK1 plays a significant role in cell wall integrity. In Brassica–Erysiphe interactions, three closely related genes, MLO2, MLO6, and MLO12, play a role in powdery mildew pathogenesis through suppression of basal defense responses. Powdery mildew effector genes promote pathogenesis through host transcriptional regulation. The WRKY 18/40 regulate induced expression of genes whose products are required for pathogen growth and reproduction. In response to powdery mildew infection, the expression of genes is regulated for different biological functions by transcriptional genes. The powdery mildew pathogenesis and disease development is governed by the genes AtLFG1 and AtLFG2 in A. thaliana. Several genes viz., RSP1, RSP2, DMR1, LRR-RLK, DMR6, and DLO1 govern pathogenesis of Brassica by Hyaloperonospora enabling susceptibility process like attraction and attachment of pathogen to host cells, accommodation of specialized infection and feeding structures inside host cells, and nutrient production and transport from host to pathogen. Haustorium formation is initiated when pathogen secrete hydrolyses to locally degrade the host cell wall and establish an entry point. Haustorial penetration is accompanied by reorganization of GFP-tagged cytoskeleton and organelles in Arabidopsis mesophyll cells.
In Brassica–Leptosphaeria pathosystem, BnMPK9–AvrLm1 interaction enhances cell death caused by BnMPk9. The virulence mechanisms are the transition period from biotrophy to necrotrophy to facilitate the acquisition of host nutrients by the pathogen. The AvrLM1 and AvrLM4-7 contribute to the aggressiveness of L. maculans analysis during leaf infection. Genome and transcriptome analysis during Brassica pathogenesis by Leptosphaeria has revealed several genes for 20 major functional categories. The GFP is expressed by the Cht promoter in stem lesions of Brassica during infection of Leptosphaeria. The gene Pro1 is involved in clubroot pathogenesis by stimulating resting spore germination through its proteolytic activity. The genes PbPP2A and PbHMG are expressed in the early phases of infection in B. rapa roots. The BjN1t1 expression in B. juncea during infection promotes over production of auxins to form galls in infected roots. The role of different genes has been revealed through analysis of P. brassicae genome and life stage specific transcriptomics. Several effectors (genes) involved in the infection process (life cycle) of P. brassicae and subsequent clubroot development in its host have been identified. Plasmodiophora pathogenesis is influenced by lipids in resting spores, glucosinolates content of the host and host resistance level. Gene expression levels of primary and secondary zoospores govern different mechanisms utilized by the pathogen in causing primary and secondary infections of Plasmodiophora. Differential expressions of up- and downregulated genes and functional groups have been determined after 4, 7, and 10 DAI during life cycle stages of Plasmodiophora. In Brassica during Plasmodiophora infections, there is differential expression of several genes in host shoots, and roots regulating different biological, biochemical, and hormonal responses. In Arabidopsis roots infected with Plasmodiophora, hypoxia and SWEET genes are expressed to form galls. Host species-specific genes are expressed during Brassica–Plasmodiophora interactions. The genes Pb-YPT, Pb-Brep9, and Pb-PSA regulate P. brassicae infection. During clubroot development, there is expression of MiRNA and immunophilins. Plasmodiophora manipulates host defense through methyl transferase by inactivating SA to Me SA. The GPCR signal transduction pathways play important roles in the growth, development, and pathogenicity of P. brassicae to crucifers. During Sclerotinia pathogenesis of Brassica, four endo-polygalacturonase genes (sspg1d, sspg3, sspg5, and sspg 6) and two exo-PG genes (ssxpg1 and ssxpg2) are expressed. Molecular analysis of Sclerotinia sclerotiorum has revealed its biology, mycelial growth, virulence, pathogenesis, and signal events for sclerotia formation. Genes like Mats, FoxE2, CAMP, and Nsd1 control apothecial and ascospore development. Sclerotinia infection and pathogenesis is regulated by toxins, CWDEs, ROS, OA, Ssvp1, V263, Svf1, PKs13, and Nacα. During the course of Brassica infections by Sclerotinia transcriptomic analysis revealed genes for functional groups like hydrolytic enzymes, CAZymes, secondary metabolites, detoxification, signaling, development, secreted effectors, oxalic acid, and reactive oxygen species production. The genes SsSvf1 is involved in coping with ROS for pathogenesis of Sclerotinia. There is differential expression of genes during Sclerotinia interaction with R and S genotypes of Brassica. Integrated mRNA, sRNA, and degradome sequencing revealed complex responses to Sclerotinia infection in Brassica. The gene SSITL is an effector which suppresses resistance in the host at early stage of Sclerotinia infection. Oxaloacetate acetyl-hydrolase gene is involved in Sclerotinia pathogenesis. Three Sclerotinia genes (SsCTR1, SsCCS, and SsATX1) are upregulated during infection of B. oleracea. Several spliceosome genes are differentially altered during Sclerotinia infections. P3 proteins are important in the infection cycle of TuMV and involved in virus replication, accumulation, symptomatology, resistance breeding, and cell to cell movement. The BnSGS3 gene in Brassica has differentiated effects on the pathogenesis of viruses. Nitric oxide signaling and calcium protein kinases can modulate NADPH oxidase activity in modulating A. thaliana–TuMV pathosystem. Differential expression of proteins has been identified which are activated in response to Verticillium longisporum in the leaf apoplast and xylem sap of Brassica in relation to disease development, photosynthetic electron transport, gas exchange and nutrient status. The secretion system of Xanthomonas genome regulates pathogenesis of black rot in crucifers. The features and functions of Type III effector genes of Xanthomonas in pathogenesis of crucifers have been characterized. The effectors/genes of Xanthomonas governing virulence and pathogenicity have been identified. Key pathogenicity determinants and virulence genes of Xanthomonas have been characterized and exported by Type ii and Type iii secretion system (T3S). The hormonal signaling in the pathways of Xanthomonas infection and pathogenesis of Brassica has been revealed.
The use of evolutionary genomics on the host–pathogen interaction and its impact can clear road map to combat the continuous threat of pathogens in a changing world. New tools will facilitate to resolve challenges of genomics of host with multiple pathogens interactions. The whole genome analysis approaches offer the potential to reveal new unbiased insight into the genetic basis of host-pathosystem of crucifers’.
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Singh Saharan, G., Mehta, N.K., Meena, P.D. (2023). Genomics of Host–Pathogen Interaction. In: Genomics of Crucifer's Host- Pathosystem . Springer, Singapore. https://doi.org/10.1007/978-981-19-3812-2_3
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