Microarray analyses during early stage of the tomato/ Alternaria solani interaction

Upadhyay, Priti; Rai, Anurag; Kumar, Rajesh; Singh, Mahesh Kumar; Sinha, B.

doi:10.1016/j.gdata.2015.09.006

Cited by 8 publications

(10 citation statements)

References 3 publications

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“…The ΔC t value was calculated for finding the fold change (FC) in the relative gene expression level compared to control and was calculated as follows: ΔC t = C t (target gene) − C t (constitutive control gene). The relative transcript levels were determined following the formula 1000 × 2 – ΔC t [ 50 ]. The differential expression of the replicated count data obtained for the healthy control and Fol challenged tissues were further used for clustering the replicated count data and relative fold change expression values for Bioconductor R [ 51 ] analysis to generate Heatmap for expression profile changes in tissue-specific and temporal manner.…”

Section: Methodsmentioning

confidence: 99%

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

et al. 2018

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The WRKY transcription factors have indispensable role in plant growth, development and defense responses. The differential expression of WRKY genes following the stress conditions has been well demonstrated. We investigated the temporal and tissue-specific (root and leaf tissues) differential expression of plant defense-related WRKY genes, following the infection of Fusarium oxysporum f. sp. lycopersici (Fol) in tomato. The genome-wide computational analysis revealed that during the Fol infection in tomato, 16 different members of WRKY gene superfamily were found to be involved, of which only three WRKYs (SolyWRKY4, SolyWRKY33, and SolyWRKY37) were shown to have clear-cut differential gene expression. The quantitative real time PCR (qRT-PCR) studies revealed different gene expression profile changes in tomato root and leaf tissues. In root tissues, infected with Fol, an increased expression for SolyWRKY33 (2.76 fold) followed by SolyWRKY37 (1.93 fold) gene was found at 24 hrs which further increased at 48 hrs (5.0 fold). In contrast, the leaf tissues, the expression was more pronounced at an earlier stage of infection (24 hrs). However, in both cases, we found repression of SolyWRKY4 gene, which further decreased at an increased time interval. The biochemical defense programming against Fol pathogenesis was characterized by the highest accumulation of H2O2 (at 48 hrs) and enhanced lignification. The functional diversity across the characterized WRKYs was explored through motif scanning using MEME suite, and the WRKYs specific gene regulation was assessed through the DNA protein docking studies The functional WRKY domain modeled had β sheets like topology with coil and turns. The DNA-protein interaction results revealed the importance of core residues (Tyr, Arg, and Lys) in a feasible WRKY-W-box DNA interaction. The protein interaction network analysis revealed that the SolyWRKY33 could interact with other proteins, such as mitogen-activated protein kinase 5 (MAPK), sigma factor binding protein1 (SIB1) and with other WRKY members including WRKY70, WRKY1, and WRKY40, to respond various biotic and abiotic stresses. The STRING results were further validated through Predicted Tomato Interactome Resource (PTIR) database. The CELLO2GO web server revealed the functional gene ontology annotation and protein subcellular localization, which predicted that SolyWRKY33 is involved in amelioration of biological stress (39.3%) and other metabolic processes (39.3%). The protein (SolyWRKY33) most probably located inside the nucleus (91.3%) with having transcription factor binding activity. We conclude that the defense response following the Fol challenge was accompanied by differential expression of the SolyWRKY4(↓), SolyWRKY33(↑) and SolyWRKY37(↑) transcripts. The biochemical changes are occupied by elicitation of H2O2 generation and accumulation and enhanced lignified tissues.

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Section: Methodsmentioning

confidence: 99%

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

et al. 2018

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“…In a recent publication, microarray-based profiling of tomato mRNA during the early stage of A . solani infection has been reported, 10 however, a detailed analysis is not available.…”

Section: Introductionmentioning

confidence: 99%

Integrated miRNA and mRNA expression profiling reveals the response regulators of a susceptible tomato cultivar to early blight disease

et al. 2017

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Early blight, caused by the fungus Alternaria solani, is a devastating foliar disease of tomatoes, causes massive yield loss each year worldwide. Molecular basis of the compatible host–pathogen interaction was elusive. We adopted next generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed during Alternaria-stress in tomato. Some of the interesting findings were also validated by alternative techniques. Our analysis revealed 181 known-miRNAs, belonging to 121 miRNA families, of which 67 miRNAs showed at least 2-fold change in expression level with the majority being downregulated. Concomitantly, 5,450 mRNAs were significantly regulated in the same diseased tissues. Differentially expressed genes were most significantly associated with response to stimulus process, photosynthesis, biosynthesis of secondary metabolites, plant–pathogen interaction and plant hormone signal transduction pathways. GO term enrichment-based categorization of gene-functions further supported this observation, as terms related to pathogen perception, disease signal transduction, cellular metabolic processes including oxidoreductase and kinase activity were over represented. In addition, we have discovered 102 miRNA–mRNA pairs which were regulated antagonistically, and careful study of the targeted mRNAs depicted that multiple transcription factors, nucleotide-binding site leucine-rich repeats, receptor-like proteins and enzymes related to cellular ROS management were profoundly affected. These studies have identified key regulators of Alternaria-stress response in tomato and the subset of genes that are likely to be post-transcriptionally silenced during the infection.

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“…Species of Alternaria, such as A. alternata, A. solani, A. linariae and A. tomatophila have been identified as causal agents of early blight in tomato (Adhikari, Oh, and Panthee 2017). On the plant side, multiple resistance sources have been determined in wild tomato species, like S. habrochaites, S. pimpinellifolium, S. peruvianum and S. arcanum (Upadhyay et al 2015;Chaerani et al 2007).…”

Section: Declarations# Introductionmentioning

confidence: 99%

“…However, infection assays revealed both resistant and susceptible phenotypes for S. habrochaites (Upadhyay et al 2015;L. P. Zhang et al 2003).…”

Section: Declarations# Introductionmentioning

confidence: 99%

Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru Upon Dysbiosis

Runge

Ventura

Kemen

et al. 2021

Preprint

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Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops and trees under controlled and natural conditions. Tomato is one of the world’s most important vegetable crops, however little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over two consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves. Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.

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Microarray analyses during early stage of the tomato/ Alternaria solani interaction

Cited by 8 publications

References 3 publications

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

Integrated miRNA and mRNA expression profiling reveals the response regulators of a susceptible tomato cultivar to early blight disease

Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru Upon Dysbiosis

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