Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico Approach
Plant stresses caused by phytopathogenic bacteria are categorized into biotic stresses. The study aimed to perform a meta-analysis of A. thaliana transcriptomic data in response to infection by P. syringae and P. syringae pv. maculicola. The gene expression and transcription factors (TFs) of A. thal...
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University of Mazandaran
2024-09-01
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| Series: | Journal of Genetic Resources |
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| Online Access: | https://sc.journals.umz.ac.ir/article_5278_1bdd032e2b16ec1ea6ed1b85f0eec2c5.pdf |
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| author | Amir Ghaffar Shahriari Mohamad Hamed Ghodoum Parizipour Yaser Biniaz Aminallah Tahmasebi Fatemeh Gholizadeh |
| author_facet | Amir Ghaffar Shahriari Mohamad Hamed Ghodoum Parizipour Yaser Biniaz Aminallah Tahmasebi Fatemeh Gholizadeh |
| author_sort | Amir Ghaffar Shahriari |
| collection | DOAJ |
| description | Plant stresses caused by phytopathogenic bacteria are categorized into biotic stresses. The study aimed to perform a meta-analysis of A. thaliana transcriptomic data in response to infection by P. syringae and P. syringae pv. maculicola. The gene expression and transcription factors (TFs) of A. thaliana infected by the bacteria were investigated using published RNA-Seq data. Also, critical factors, including hub genes, protein-protein interaction (PPI), and micro RNAs (miRNAs), were analyzed. A total number of 22 biological pathways were significantly enriched with up-/down-regulated differentially expressed genes (DEGs) in the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Also, 39 TFs of A. thaliana were altered during the bacterial infection. Moreover, 5034 DEGs were significantly different from non-stressed plants, of which 2291 and 2743 DEGs were up- and down-regulated, respectively. The expression of genes related to stress response, cellular process, metabolic process, and stimulus response was up-regulated in the bacteria-infected plant. In contrast, the down-regulation of genes involved in the cellular and biosynthesis processes was observed. Regarding molecular function, 412 genes associated with kinase, catalase, and oxidoreductase activities were up-regulated in the bacteria-infected plants, while down-regulation of hydrolase and transferase activity genes was observed. The PPI network showed 107 nodes and 189 edges. The most important hubs genes included MYC2, WRKY40, WRKY33, and other genes. Moreover, the total number of 41 miRNA families was determined during the A. thaliana-bacterium interaction. Infection of A. thaliana by P. syringae and P. syringae pv. maculicola induced the expression of some stress-responsive genes and pathways among which some defense-related hub genes were identified. The results provide a clearer understanding of the strategies applied to program defense pathways in bacterial infection of A. thaliana. |
| format | Article |
| id | doaj-art-63a0c8328b944419ba4fcf68d749f354 |
| institution | Kabale University |
| issn | 2423-4257 2588-2589 |
| language | English |
| publishDate | 2024-09-01 |
| publisher | University of Mazandaran |
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| series | Journal of Genetic Resources |
| spelling | doaj-art-63a0c8328b944419ba4fcf68d749f3542025-01-27T06:11:46ZengUniversity of MazandaranJournal of Genetic Resources2423-42572588-25892024-09-0110220922010.22080/jgr.2025.27951.14065278Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico ApproachAmir Ghaffar Shahriari0Mohamad Hamed Ghodoum Parizipour1Yaser Biniaz2Aminallah Tahmasebi3Fatemeh Gholizadeh4Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, IranDepartment of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, IranPlant Virology Research Center, School of Agriculture, Shiraz University, Shiraz, IranDepartment of Agriculture, Minab Higher Education Center, University of Hormozgan, Bandar Abbas, IranDepartment of Plant Physiology and Metabolomics, Agricultural Institute, HUN-REN Centre for Agricultural Research, Martonvásár 2462, HungaryPlant stresses caused by phytopathogenic bacteria are categorized into biotic stresses. The study aimed to perform a meta-analysis of A. thaliana transcriptomic data in response to infection by P. syringae and P. syringae pv. maculicola. The gene expression and transcription factors (TFs) of A. thaliana infected by the bacteria were investigated using published RNA-Seq data. Also, critical factors, including hub genes, protein-protein interaction (PPI), and micro RNAs (miRNAs), were analyzed. A total number of 22 biological pathways were significantly enriched with up-/down-regulated differentially expressed genes (DEGs) in the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Also, 39 TFs of A. thaliana were altered during the bacterial infection. Moreover, 5034 DEGs were significantly different from non-stressed plants, of which 2291 and 2743 DEGs were up- and down-regulated, respectively. The expression of genes related to stress response, cellular process, metabolic process, and stimulus response was up-regulated in the bacteria-infected plant. In contrast, the down-regulation of genes involved in the cellular and biosynthesis processes was observed. Regarding molecular function, 412 genes associated with kinase, catalase, and oxidoreductase activities were up-regulated in the bacteria-infected plants, while down-regulation of hydrolase and transferase activity genes was observed. The PPI network showed 107 nodes and 189 edges. The most important hubs genes included MYC2, WRKY40, WRKY33, and other genes. Moreover, the total number of 41 miRNA families was determined during the A. thaliana-bacterium interaction. Infection of A. thaliana by P. syringae and P. syringae pv. maculicola induced the expression of some stress-responsive genes and pathways among which some defense-related hub genes were identified. The results provide a clearer understanding of the strategies applied to program defense pathways in bacterial infection of A. thaliana.https://sc.journals.umz.ac.ir/article_5278_1bdd032e2b16ec1ea6ed1b85f0eec2c5.pdfarabidopsisgene expressionhost responsetranscriptomicspseudomonas |
| spellingShingle | Amir Ghaffar Shahriari Mohamad Hamed Ghodoum Parizipour Yaser Biniaz Aminallah Tahmasebi Fatemeh Gholizadeh Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico Approach Journal of Genetic Resources arabidopsis gene expression host response transcriptomics pseudomonas |
| title | Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico Approach |
| title_full | Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico Approach |
| title_fullStr | Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico Approach |
| title_full_unstemmed | Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico Approach |
| title_short | Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico Approach |
| title_sort | transcriptomic response of arabidopsis thaliana to pseudomonas syringae infection an in silico approach |
| topic | arabidopsis gene expression host response transcriptomics pseudomonas |
| url | https://sc.journals.umz.ac.ir/article_5278_1bdd032e2b16ec1ea6ed1b85f0eec2c5.pdf |
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