Agrios, G. (2005). Plant Pathology. 5th eds, Department of Plant Pathology. University of Florida. United States of America.
Almagro Armenteros, J. J., Tsirigos, K. D., Sønderby, C. K., Petersen, T. N., Winther, O., Brunak, S., von Heijne, G., & Nielsen, H. (2019). SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature biotechnology, 37(4), 420-423.
Babicki, S., Arndt, D., Marcu, A., Liang, Y., Grant, J. R., Maciejewski, A., & Wishart, D. S. (2016). Heatmapper: web-enabled heat mapping for all. Nucleic acids research, 44(W1), W147-W153.
Bhadouria, J., & Giri, J. (2022). Purple acid phosphatases: roles in phosphate utilization and new emerging functions. Plant Cell Reports, 41(1), 33-51.
Bigeard, J., & Hirt, H. (2018). Nuclear signaling of plant MAPKs. Frontiers in Plant Science, 9, 469.
Blancard, D. (2012). Tomato diseases: identification, biology and control: a colour handbook. CRC Press.
Bolwell, G. P., & Wojtaszek, P. (1997). Mechanisms for the generation of reactive oxygen species in plant defence–a broad perspective. Physiological and Molecular Plant Pathology, 51(6), 347-366.
Bozzo, G. G., Raghothama, K. G., & Plaxton, W. C. (2002). Purification and characterization of two secreted purple acid phosphatase isozymes from phosphate‐starved tomato (Lycopersicon esculentum) cell cultures. European Journal of Biochemistry, 269(24), 6278-6286.
Brenya, E., Trusov, Y., Dietzgen, R. G., & Botella, J. R. (2016). Heterotrimeric G-proteins facilitate resistance to plant pathogenic viruses in Arabidopsis thaliana (L.) Heynh. Plant signaling & behavior, 11(8), e1212798.
Cheng, Y. T., Zhang, L., & He, S. Y. (2019). Plant-microbe interactions facing environmental challenge. Cell Host & Microbe, 26(2), 183-192.
Chin, C.-H., Chen, S.-H., Wu, H.-H., Ho, C.-W., Ko, M.-T., & Lin, C.-Y. (2014). cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC systems biology, 8(4), 1-7.
Chow, C.-N., Lee, T.-Y., Hung, Y.-C., Li, G.-Z., Tseng, K.-C., Liu, Y.-H., Kuo, P.-L., Zheng, H.-Q., & Chang, W.-C. (2019). PlantPAN3. 0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic acids research, 47(D1), D1155-D1163.
Cristina, M. S., Petersen, M., & Mundy, J. (2010). Mitogen-activated protein kinase signaling in plants. Annual review of plant biology, 61, 621-649.
Derksen, H., Rampitsch, C., & Daayf, F. (2013). Signaling cross-talk in plant disease resistance. Plant science, 207, 79-87.
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., & Smart, A. (2019). The Pfam protein families database in 2019. Nucleic acids research, 47(D1), D427-D432.
Fei, Z., Joung, J.-G., Tang, X., Zheng, Y., Huang, M., Lee, J. M., McQuinn, R., Tieman, D. M., Alba, R., & Klee, H. J. (2010). Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic acids research, 39(suppl_1), D1156-D1163.
Gatahi, D. M. (2020). Challenges and opportunities in tomato production chain and sustainable standards. International Journal of Horticultural Science and Technology, 7(3), 235-262.
Gerszberg, A., Hnatuszko-Konka, K., Kowalczyk, T., & Kononowicz, A. K. (2015). Tomato (Solanum lycopersicum L.) in the service of biotechnology. Plant Cell, Tissue and Organ Culture (PCTOC), 120, 881-902.
Göhre, V., & Robatzek, S. (2008). Breaking the barriers: microbial effector molecules subvert plant immunity. Annu. Rev. Phytopathol., 46, 189-215.
Heberle, H., Meirelles, G. V., da Silva, F. R., Telles, G. P., & Minghim, R. (2015). InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC bioinformatics, 16, 1-7.
Heidari, P., Ahmadizadeh, M., & Najafi-Zarrini, H. (2015). In silico analysis of Cis-regulatory elements on co-expressed genes. Journal of Biological and Environmental Sciences, 9(25).
Henriquez, M. A., Adam, L. R., & Daayf, F. (2012). Alteration of secondary metabolites' profiles in potato leaves in response to weakly and highly aggressive isolates of Phytophthora infestans. Plant Physiology and Biochemistry, 57, 8-14.
Higo, K., Ugawa, Y., Iwamoto, M., & Korenaga, T. (1999). Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic acids research, 27(1), 297-300.
Ishikawa, A. (2009). The Arabidopsis G-protein β-subunit is required for defense response against Agrobacterium tumefaciens. Bioscience, biotechnology, and biochemistry, 73(1), 47-52.
Jones, P., Binns, D., Chang, H.-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., & Nuka, G. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics, 30(9), 1236-1240.
Jwa, N.-S., Agrawal, G. K., Tamogami, S., Yonekura, M., Han, O., Iwahashi, H., & Rakwal, R. (2006). Role of defense/stress-related marker genes, proteins and secondary metabolites in defining rice self-defense mechanisms. Plant Physiology and Biochemistry, 44(5-6), 261-273.
Kim, N. H., & Hwang, B. K. (2015). Pepper heat shock protein 70a interacts with the type III effector AvrBsT and triggers plant cell death and immunity. Plant physiology, 167(2), 307-322.
Kumar, A., & Verma, J. P. (2018). Does plant—microbe interaction confer stress tolerance in plants: a review? Microbiological research, 207, 41-52.
Kumar, M., Tomar, M., Bhuyan, D. J., Punia, S., Grasso, S., Sa, A. G. A., Carciofi, B. A. M., Arrutia, F., Changan, S., & Singh, S. (2021). Tomato (Solanum lycopersicum L.) seed: A review on bioactives and biomedical activities. Biomedicine & Pharmacotherapy, 142, 112018.
Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P., & Rombauts, S. (2002). PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic acids research,30(1),325-327.
Lindquist, S., & Craig, E. A. (1988). The heat-shock proteins. Annual review of genetics, 22(1), 631-677.
Long, T. A., Brady, S. M., & Benfey, P. N. (2008). Systems approaches to identifying gene regulatory networks in plants. Annual review of cell and developmental biology, 24, 81-103.
Maimbo, M., Ohnishi, K., Hikichi, Y., Yoshioka, H., & Kiba, A. (2007). Induction of a small heat shock protein and its functional roles in Nicotiana plants in the defense response against Ralstonia solanacearum. Plant physiology, 145(4), 1588-1599.
Marchler-Bauer, A., Derbyshire, M. K., Gonzales, N. R., Lu, S., Chitsaz, F., Geer, L. Y., Geer, R. C., He, J., Gwadz, M., & Hurwitz, D. I. (2015). CDD: NCBI's conserved domain database. Nucleic acids research, 43(D1), D222-D226.
Martinelli, F., Reagan, R. L., Uratsu, S. L., Phu, M. L., Albrecht, U., Zhao, W., Davis, C. E., Bowman, K. D., & Dandekar, A. M. (2013). Gene regulatory networks elucidating huanglongbing disease mechanisms. PloS one, 8(9), e74256.
Maruta, N., Trusov, Y., Brenya, E., Parekh, U., & Botella, J. R. (2015). Membrane-localized extra-large G proteins and Gβγ of the heterotrimeric G proteins form functional complexes engaged in plant immunity in Arabidopsis. Plant physiology, 167(3), 1004-1016.
McHale, L., Tan, X., Koehl, P., & Michelmore, R. W. (2006). Plant NBS-LRR proteins: adaptable guards. Genome biology, 7, 1-11.
Mehdy, M. C. (1994). Active oxygen species in plant defense against pathogens. Plant physiology, 105(2), 467.
Meng, X., & Zhang, S. (2013). MAPK cascades in plant disease resistance signaling. Annual review of phytopathology, 51, 245-266.
Milosevic, N., & Slusarenko, A. (1996). Active oxygen metabolism and lignification in the hypersensitive response in bean. Physiological and Molecular Plant Pathology, 49(3), 143-158.
Nobori, T., Wang, Y., Wu, J., Stolze, S. C., Tsuda, Y., Finkemeier, I., Nakagami, H., & Tsuda, K. (2020). Multidimensional gene regulatory landscape of a bacterial pathogen in plants. Nature Plants, 6(7), 883-896.
Noctor, G., & Foyer, C. H. (1998). Ascorbate and glutathione: keeping active oxygen under control. Annual review of plant biology, 49(1), 249-279.
Olczak, M., Morawiecka, B., & Watorek, W. (2003). Plant purple acid phosphatases-genes, structures and biological function. Acta Biochimica Polonica, 50(4), 1245-1256.
Pedley, K. F., & Martin, G. B. (2003). Molecular basis of Pto-mediated resistance to bacterial speck disease in tomato. Annual review of phytopathology, 41(1), 215-243.
Piquerez, S. J., Harvey, S. E., Beynon, J. L., & Ntoukakis, V. (2014). Improving crop disease resistance: lessons from research on Arabidopsis and tomato. Frontiers in Plant Science, 5, 671.
Pitzschke, A., Schikora, A., & Hirt, H. (2009). MAPK cascade signalling networks in plant defence. Current opinion in plant biology, 12(4), 421-426.
Ravichandran, S., Stone, S. L., Benkel, B., & Prithiviraj, B. (2013). Purple Acid Phosphatase5 is required for maintaining basal resistance against Pseudomonas syringaein Arabidopsis. BMC plant biology, 13(1), 1-12.
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research, 13(11), 2498-2504.
Sharma, P., Jha, A. B., Dubey, R. S., & Pessarakli, M. (2012). Reactive oxygen species, oxidative damage, and antioxidative defense mechanism in plants under stressful conditions. Journal of botany, 2012.
Singh, K. B., Foley, R. C., & Oñate-Sánchez, L. (2002). Transcription factors in plant defense and stress responses. Current opinion in plant biology, 5(5), 430-436.
Singh, V. K., Singh, A. K., & Kumar, A. (2017). Disease management of tomato through PGPB: current trends and future perspective. 3 Biotech, 7, 1-10.
Sinha, A. K., Jaggi, M., Raghuram, B., & Tuteja, N. (2011). Mitogen-activated protein kinase signaling in plants under abiotic stress. Plant signaling & behavior, 6(2), 196-203.
Solovyev, V., Kosarev, P., Seledsov, I., & Vorobyev, D. (2006). Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome biology, 7(1), 1-12.
Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., & Bork, P. (2019). STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic acids research, 47(D1), D607-D613.
Topcu, Y., Nambeesan, S. U., & van der Knaap, E. (2022). Blossom-end rot: a century-old problem in tomato (Solanum lycopersicum L.) and other vegetables. Molecular Horticulture, 2(1), 1.
Torres, M. A., Morales, J., Sánchez-Rodríguez, C., Molina, A., & Dangl, J. L. (2013). Functional interplay between Arabidopsis NADPH oxidases and heterotrimeric G protein. Molecular Plant-Microbe Interactions, 26(6), 686-694.
Trusov, Y., & Botella, J. R. (2016). Plant G-proteins come of age: breaking the bond with animal models. Frontiers in chemistry, 4, 24.
Urano, D., & Jones, A. M. (2014). Heterotrimeric G protein–coupled signaling in plants. Annual review of plant biology, 65, 365-384.
Wang, C., El-Shetehy, M., Shine, M., Yu, K., Navarre, D., Wendehenne, D., Kachroo, A., & Kachroo, P. (2014). Free radicals mediate systemic acquired resistance. Cell Reports, 7(2), 348-355.
Waters, E. R., & Vierling, E. (2020). Plant small heat shock proteins–evolutionary and functional diversity. New Phytologist, 227(1), 24-37.
Yao, Z., Islam, M. R., Badawi, M. A., El-Bebany, A. F., & Daayf, F. (2015). Overexpression of StRbohA in Arabidopsis thaliana enhances defence responses against Verticillium dahliae. Physiological and Molecular Plant Pathology, 90, 105-114.
Yu, C.-S., Cheng, C.-W., Su, W.-C., Chang, K.-C., Huang, S.-W., Hwang, J.-K., & Lu, C.-H. (2014). CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PloS one, 9(6), e99368.
Yuan, B., Shen, X., Li, X., Xu, C., & Wang, S. (2007). Mitogen-activated protein kinase OsMPK6 negatively regulates rice disease resistance to bacterial pathogens. Planta, 226, 953-960.
Yuqing, W., Zhang, Y., Zhipeng, G., & Wencai, Y. (2018). Breeding for resistance to tomato bacterial diseases in China: challenges and prospects. Horticultural Plant Journal, 4(5), 193-207.
Zamani, K., Lohrasebi, T., Sabet, M. S., Malboobi, M. A., & Mousavi, A. (2014). Expression pattern and subcellular localization of Arabidopsis purple acid phosphatase AtPAP9. Gene Expression Patterns, 14(1), 9-18.
Zhang, S., & Klessig, D. F. (2001). MAPK cascades in plant defense signaling. Trends in plant science, 6(11), 520-527.
Zhang, S., Wang, L., Zhao, R., Yu, W., Li, R., Li, Y., Sheng, J., & Shen, L. (2018). Knockout of SlMAPK3 reduced disease resistance to Botrytis cinerea in tomato plants. Journal of agricultural and food chemistry, 66(34), 8949-8956.