شناسایی ژن‌های کلیدی و عوامل تنظیمی مؤثر در پاسخ به ویروس چروکیدگی قهوه‌ای میوه گوجه‌فرنگی (‏TOBRFV‏) با ‏استفاده از داده‌های ‏RNA-Seq ‏

Akbar, S., Wei, Y., Yuan, Y., Khan, M. T., Qin, L., Powell, C. A., ... & Zhang, M. (2020). Gene expression profiling of reactive oxygen species (ROS) and antioxidant defense system following Sugarcane mosaic virus (SCMV) infection. BMC Plant Biology, 20(1), 532. Alseekh, S., de Souza, L. P., Benina, M., & Fernie, A. R. (2020). The style and substance of plant flavonoid decoration; towards defining both structure and function. Phytochemistry, 174, 112347. Bao, F., Huang, X., Zhu, C., Zhang, X., Li, X., & Yang, S. (2014). Arabidopsis HSP 90 protein modulates RPP 4‐mediated temperature‐dependent cell death and defense responses. New Phytologist, 202(4), 1320-1334. Beltran-Garcia, M. J., Martínez-Rodríguez, A., Olmos-Arriaga, I., Valdes-Salas, B., Di Mascio, P., & White, J. F. (2021). Nitrogen fertilization and stress factors drive shifts in microbial diversity in soils and plants. Symbiosis, 84(3), 379-390. Berry, H. M., & Argueso, C. T. (2022). More than growth: Phytohormone-regulated transcription factors controlling plant immunity, plant development and plant architecture. Current opinion in plant biology, 70, 102309. Bian, Z., Gao, H., & Wang, C. (2020). NAC transcription factors as positive or negative regulators during ongoing battle between pathogens and our food crops. International Journal of Molecular Sciences, 22(1), 81. Bouzroud, S., Gouiaa, S., Hu, N., Bernadac, A., Mila, I., Bendaou, N., ... & Zouine, M. (2018). Auxin response factors (ARFs) are potential mediators of auxin action in tomato response to biotic and abiotic stress (Solanum lycopersicum). PloS one, 13(2), e0193517. Callis, J. (2014). The ubiquitination machinery of the ubiquitin system. The Arabidopsis Book/American Society of Plant Biologists, 12, e0174. Campos, M. D., Félix, M. D. R., Patanita, M., Materatski, P., & Varanda, C. (2021). High throughput sequencing unravels tomato-pathogen interactions towards a sustainable plant breeding. Horticulture research, 8. Caruso, A. G., Tortorici, S., Davino, S., Bertacca, S., Ragona, A., Lo Verde, G., ...& Panno, S. (2024). The invasive tomato pest Tuta absoluta can transmit the emergent tomato brown rugose fruit virus. Entomologia Generalis, 44(2), 289-296. Chen, Q., Niu, F., Yan, J., Chen, B., Wu, F., Guo, X., ... & Jiang, Y. Q. (2017). Oilseed rape NAC56 transcription factor modulates reactive oxygen species accumulation and hypersensitive response‐like cell death. Physiologia Plantarum, 160(2), 209-221. Chen, Y., Liu, X., Zhou, Y., Zheng, Y., Xiao, Y., Yuan, X., ... & Chen, X. (2025 a). Functional characterization of four soybean C2H2 zinc-finger genes in Phytophthora resistance. Plant Signaling & Behavior, 20(1), 2481185. Chen, Y., Cheng, L., Guan, X., Liang, Y., Xue, Y., Zhao, W., ... & Gao, G. (2025 b). StCPP3 interacts with type III secretion protein HrpB7 and negatively regulates plant resistance against Ralstonia solanacearum. Biochemical and Biophysical Research Communications, 742, 151105. 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(Suppl 4), S11. Davino, S., Caruso, A. G., Bertacca, S., Barone, S., & Panno, S. (2020). Tomato brown rugose fruit virus: Seed transmission rate and efficacy of different seed disinfection treatments. Plants, 9(11), 1615. Dong, B., Liu, Y., Huang, G., Song, A., Chen, S., Jiang, J., ... & Fang, W. (2024). Plant NAC transcription factors in the battle against pathogens. BMC Plant Biology, 24(1), 958. Du, Y. C., Wang, Y. B., Fan, W. T., Gai, Z. J., Yu, D. S., Gu, W., Zhang, L. L., & Ma, F. M. (2012). Effect of nitrogen fertilization on nitrate reductase and nitrite reductase activities of sugar beet. Journal of Plant Nutrition and Fertilizers, 18(3), 717-723. Ehlers, J., Nourinejhad Zarghani, S., Liedtke, S., Kroschewski, B., Büttner, C., & Bandte, M. (2023). Analysis of the spatial dispersion of tomato brown rugose fruit virus on surfaces in a commercial tomato production site. Horticulturae, 9(5), 611. Farvardin, A., Llorens, E., Liu-Xu, L., Sánchez-Giménez, L., Wong, A., Biosca, E. G., ... & Vicedo, B. (2023). Solanum lycopersicum heme-binding protein 2 as a potent antimicrobial weapon against plant pathogens. Scientific Reports, 13(1), 20336. Formosa, L. E., Maghool, S., Sharpe, A. J., Reljic, B., Muellner-Wong, L., Stroud, D. A., ... & Maher, M. J. (2022). Mitochondrial COA7 is a heme-binding protein with disulfide reductase activity, which acts in the early stages of complex IV assembly. Proceedings of the National Academy of Sciences, 119(9), e2110357119. García-Estrada, R. S., Diaz-Lara, A., Aguilar-Molina, V. H., & Tovar-Pedraza, J. M. (2022). Viruses of economic impact on tomato crops in Mexico: From diagnosis to management—A review. Viruses, 14(6), 1251. Gull, S., Arfan, M., Uddin, S., Qasim, M., Babar, S., Rajput, N., ... & Iqbal, R. (2024). Identification and characterization of cysteine-rich polycomb-like protein (CPP) gene family in rice (Oryza sativa L.) in response to phytohormones and Xanthomonas oryzae pv. oryzae stress. Plant Stress, 14, 100677. Hak, H., & Spiegelman, Z. (2021). The tomato brown rugose fruit virus movement protein overcomes Tm-22 resistance in tomato while attenuating viral transport. Molecular Plant-Microbe Interactions, 34(9), 1024-1032. Herlihy, J. H., Long, T. A., & McDowell, J. M. (2020). Iron homeostasis and plant immune responses: recent insights and translational implications. Journal of Biological Chemistry, 295(39), 13444-13457. Huang, S., Monaghan, J., Zhong, X., Lin, L., Sun, T., Dong, O. X., & Li, X. (2014). HSP 90s are required for NLR immune receptor accumulation in Arabidopsis. The Plant Journal, 79(3), 427-439. Ishibashi, K., & Ishikawa, M. (2016). Replication of tobamovirus RNA. Annual Review of Phytopathology, 54(1), 55-78. Jagodzik, P., Tajdel-Zielinska, M., Ciesla, A., Marczak, M., & Ludwikow, A. (2018). Mitogen-activated protein kinase cascades in plant hormone signaling. Frontiers in plant science, 9, 1387. Jeandet, P., Hébrard, C., Deville, M. A., Cordelier, S., Dorey, S., Aziz, A., & Crouzet, J. (2014). Deciphering the role of phytoalexins in plant-microorganism interactions and human health. Molecules, 19(11), 18033-18056. Jeandet, P., Trotel-Aziz, P., Jacquard, C., Clément, C., Mohan, C., Morkunas, I., ... & Aziz, A. (2023). Use of elicitors and beneficial bacteria to induce and prime the stilbene phytoalexin response: applications to grapevine disease resistance. Agronomy, 13(9), 2225. Jewehan, A., Salem, N., Tóth, Z., Salamon, P., & Szabó, Z. (2022). Screening of Solanum (sections Lycopersicon and Juglandifolia) germplasm for reactions to the tomato brown rugose fruit virus (ToBRFV). Journal of Plant Diseases and Protection, 129(1), 117-123. Jiao, Y., An, M., Li, X., Yu, M., Zhao, X., Xia, Z., & Wu, Y. (2020). Transcriptomic and functional analyses reveal an antiviral role of autophagy during pepper mild mottle virus infection. BMC Plant Biology, 20(1), 495. Joshi, A., & Pokhrel, C. P. (2022). Assessment of rice blast (Pyricularia Grisea) disease under different concentrations of nitrogen on different rice cultivars. American Journal of Interdisciplinary Research and Innovation, 1(1), 25-33. Kang, B., Liu, L., Liu, L., Liu, M., Wu, H., Peng, B., ... & Gu, Q. (2024). A bifunctional nuclease promotes the infection of zucchini yellow mosaic virus in watermelon by targeting P3. Plants, 13(23), 3431. Karimipour, R., Koolivand, D., Ghorbani, A., Naderpour, M., & Rostami, M. (2025). Integrated gene network analysis and experimental validation identify key hub genes in potato response to Potato Virus Y infection. PLoS One, 20(8), e0329747. Khan, A. A., & Quigley, J. G. (2011). Control of intracellular heme levels: heme transporters and heme oxygenases. Biochimica Et Biophysica Acta (BBA)-Molecular Cell Research, 1813(5), 668-682. Khatri, P., Wally, O., Rajcan, I., & Dhaubhadel, S. (2022). Comprehensive analysis of cytochrome P450 monooxygenases reveals insight into their role in partial resistance against Phytophthora sojae in soybean. Frontiers in Plant Science, 13, 862314. Kim, S. Y., Kim, Y. C., Seong, E. S., Lee, Y. H., Park, J. M., & Choi, D. (2007). The chili pepper CaATL1: an AT‐hook motif‐containing transcription factor implicated in defence responses against pathogens. Molecular plant pathology, 8(6), 761-771. Kong, M., Xu, H., Ali, Q., Jing, H., Wang, F., Xu, Q., ... & Shen, Y. (2024). Nitrate reductase drives nutrition control and disease resistance in tomato (Solanum lycopersicum L.) Cultivars. Journal of Soil Science and Plant Nutrition, 24(1), 818-830. Kyaing, M. S., Gu, L. J., & Cheng, H. M. (2011). The role of nitrate reductase and nitrite reductase in plant. Current Biotechnology, 1, 159-164. Lee, H. J., Mochizuki, N., Masuda, T., & Buckhout, T. J. (2012). Disrupting the bimolecular binding of the haem-binding protein 5 (AtHBP5) to haem oxygenase 1 (HY1) leads to oxidative stress in Arabidopsis. Journal of experimental botany, 63(16), 5967-5978. Levitzky, N., Smith, E., Lachman, O., Luria, N., Mizrahi, Y., Bakelman, H., ... & Dombrovsky, A. (2019). The bumblebee Bombus terrestris carries a primary inoculum of Tomato brown rugose fruit virus contributing to disease spread in tomatoes. PloS one, 14(1), e0210871. Li, M., Chen, J. E., Wang, J. X., Hu, B., & Chen, G. (2008). Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC bioinformatics, 9(1), 398. Li, Y., Pearl, S. A., & Jackson, S. A. (2015). Gene networks in plant biology: approaches in reconstruction and analysis. Trends in plant science, 20(10), 664-675. Li, M., Li, D., Tang, Y., Wu, F., & Wang, J. (2017 a). CytoCluster: a cytoscape plugin for cluster analysis and visualization of biological networks. International journal of molecular sciences, 18(9), 1880. Li, X., Fan, S., Hu, W., Liu, G., Wei, Y., He, C., & Shi, H. (2017 b). Two cassava basic leucine zipper (bZIP) transcription factors (MebZIP3 and MebZIP5) confer disease resistance against cassava bacterial blight. Frontiers in plant science, 8, 2110. Li, T., Cheng, X., Wang, X., Li, G., Wang, B., Wang, W., ... & Xu, Y. (2021). Glyoxalase I‐4 functions downstream of NAC72 to modulate downy mildew resistance in grapevine. The Plant Journal, 108(2), 394-410. Li, X., Niu, G., Fan, Y., Liu, W., Wu, Q., Yu, C., ... & Pei, Y. (2023). Synthetic dual hormone-responsive promoters enable engineering of plants with broad-spectrum resistance. Plant Communications, 4(4). Liu, Z., Zheng, Y., Du, C., Sun, E., Yu, H., Cai, M., ... & Zuo, C. (2025). Genome-wide analysis of C2H2 transcription factors reveals that PbeCH1 and PbeCH4 are associated with Valsa canker resistance in Pyrus betulifolia. Plant Physiology and Biochemistry, 110328. Martinčová, M., & Soukup, A. (2025). Twenty years of AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) gene family research–Their potential in crop improvement. Current Plant Biology, 100460. Matern, U., Grimmig, B., & Kneusel, R. E. (1995). Plant cell wall reinforcement in the disease-resistance response: molecular composition and regulation. Canadian journal of botany, 73(S1), 511-517. Mazzoni-Putman, S. M., Brumos, J., Zhao, C., Alonso, J. M., & Stepanova, A. N. (2021). Auxin interactions with other hormones in plant development. Cold Spring Harbor Perspectives in Biology, 13(10), a039990. McLellan, H., Boevink, P. C., Armstrong, M. R., Pritchard, L., Gomez, S., Morales, J., ... & Birch, P. R. (2013). An RxLR effector from Phytophthora infestans prevents re-localisation of two plant NAC transcription factors from the endoplasmic reticulum to the nucleus. PLoS pathogens, 9(10), e1003670. Meisrimler, C. N., Pelgrom, A. J., Oud, B., Out, S., & Van den Ackerveken, G. (2019). Multiple downy mildew effectors target the stress‐related NAC transcription factor Ls NAC 069 in lettuce. The Plant Journal, 99(6), 1098-1115. Meng, X., & Zhang, S. (2013). MAPK cascades in plant disease resistance signaling. Annual review of phytopathology, 51(1), 245-266. Nabavi, S. M., Šamec, D., Tomczyk, M., Milella, L., Russo, D., Habtemariam, S., ... & Shirooie, S. (2020). Flavonoid biosynthetic pathways in plants: Versatile targets for metabolic engineering. Biotechnology advances, 38, 107316. Naoumkina, M. A., Zhao, Q., Gallego‐Giraldo, L. I. N. A., Dai, X., Zhao, P. X., & Dixon, R. A. (2010). Genome‐wide analysis of phenylpropanoid defence pathways. Molecular plant pathology, 11(6), 829-846. Niu, J., Zhao, J., Guo, Q., Zhang, H., Yue, A., Zhao, J., ... & Du, W. (2024). WGCNA reveals hub genes and key gene regulatory pathways of the response of soybean to infection by Soybean mosaic virus. Genes, 15(5), 566. Oros, G., & Kállai, Z. (2019). Phytoanticipins: The constitutive defense compounds as potential botanical fungicides. In Bioactive Molecules in Plant Defense: Signaling in Growth and Stress (pp. 179-229). Cham: Springer International Publishing. Porameri, Z., Ghorbani, A., Mirsoleymani, Z., Karimi, M., Rostami, M., & Hemmati, S. A. (2025). Key regulatory genes in sugar beet's defense against curly top virus identified by network analysis and qRT-PCR. Biochemistry and Biophysics Reports, 43, 102214. Queitsch, C., Sangster, T. A., & Lindquist, S. (2002). Hsp90 as a capacitor of phenotypic variation. Nature, 417(6889), 618-624. Ramaroson, M. L., Koutouan, C., Helesbeux, J. J., Le Clerc, V., Hamama, L., Geoffriau, E., & Briard, M. (2022). Role of phenylpropanoids and flavonoids in plant resistance to pests and diseases. Molecules, 27(23), 8371. Raza, M. M., Jia, H., Gu, S., Gai, J., & Li, K. (2025). Transcriptome insights into resistance mechanisms against Soybean Mosaic Virus Strain SC4 in Soybean. Agronomy, 15(4), 906. Salem, N., Mansour, A., Ciuffo, M., Falk, B. W., & Turina, M. (2016). A new tobamovirus infecting tomato crops in Jordan. Archives of virology, 161(2), 503-506. Salem, N. M., Cao, M. J., Odeh, S., Turina, M., & Tahzima, R. (2020). First report of tobacco mild green mosaic virus and tomato brown rugose fruit virus infecting Capsicum annuum in Jordan. Plant Disease, 104(2), 601. Salem, N. M., Sulaiman, A., Samarah, N., Turina, M., & Vallino, M. (2022). Localization and mechanical transmission of tomato brown rugose fruit virus in tomato seeds. Plant Disease, 106(1), 275-281. Salem, N. M., Jewehan, A., Aranda, M. A., & Fox, A. (2023). Tomato brown rugose fruit virus pandemic. Annual review of phytopathology, 61(1), 137-164. Samakovli, D., Tichá, T., Vavrdová, T., Ovečka, M., Luptovčiak, I., Zapletalová, V., ... & Šamaj, J. (2020). YODA-HSP90 module regulates phosphorylation-dependent inactivation of SPEECHLESS to control stomatal development under acute heat stress in Arabidopsis. Molecular Plant, 13(4), 612-633. Singh, B. K., Delgado-Baquerizo, M., Egidi, E., Guirado, E., Leach, J. E., Liu, H., & Trivedi, P. (2023). Climate change impacts on plant pathogens, food security and paths forward. Nature Reviews Microbiology, 21(10), 640-656. Sun, Y., Jia, X., Chen, D., Fu, Q., Chen, J., Yang, W., ... & Xu, X. (2023). Genome-wide identification and expression analysis of cysteine-rich polycomb-like protein (CPP) gene family in tomato. International Journal of Molecular Sciences, 24(6), 5762. Thakare, A. P., Della Lucia, M. C., Mulagala, C., Bertoldo, G., Cagnin, M., & Stevanato, P. (2024). Omics based approaches to decipher the leaf ionome and transcriptome changes in Solanum lycopersicum L. upon Tomato Brown Rugose Fruit Virus (ToBRFV) infection. PloS one, 19(11), e0313335. Tonnessen, B. W., Bossa-Castro, A. M., Mauleon, R., Alexandrov, N., & Leach, J. E. (2019). Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice. Scientific reports, 9(1), 1536. Topcu, Y., Yildiz, K., Kayikci, H. C., Aydin, S., Feng, Q., & Sapkota, M. (2025). Deciphering resistance to Tomato brown rugose fruit virus (ToBRFV) using genome-wide association studies. Scientia Horticulturae, 341, 113968. Tripathi, A., Goswami, K., Tiwari, M., Mukherjee, S. K., & Sanan-Mishra, N. (2018). Identification and comparative analysis of microRNAs from tomato varieties showing contrasting response to ToLCV infections. Physiology and Molecular Biology of Plants, 24(2), 185-202. Vanhee, C., Zapotoczny, G., Masquelier, D., Ghislain, M., & Batoko, H. (2011). The Arabidopsis multistress regulator TSPO is a heme binding membrane protein and a potential scavenger of porphyrins via an autophagy-dependent degradation mechanism. The Plant Cell, 23(2), 785-805. Vogt, T. (2010). Phenylpropanoid biosynthesis. Molecular plant, 3(1), 2-20. Wang, Z., Xia, Y., Lin, S., Wang, Y., Guo, B., Song, X., ... & Zhao, H. (2018). Osa‐miR164a targets Os NAC 60 and negatively regulates rice immunity against the blast fungus Magnaporthe oryzae. The Plant Journal, 95(4), 584-597 Wang, J., Zheng, C., Shao, X., Hu, Z., Li, J., Wang, P., ... & Shi, K. (2020). Transcriptomic and genetic approaches reveal an essential role of the NAC transcription factor SlNAP1 in the growth and defense response of tomato. Horticulture Research, 7, 209 Wang, D., Chen, M., Peng, J., Zheng, H., Lu, Y., Wu, G., ... & Rao, S. (2024). Transcriptome analysis of tomato leaves reveals candidate genes responsive to tomato brown rugose fruit virus infection. International journal of molecular sciences, 25(7), 4012. Website. EPPO. (2024). Tomato brown rugose fruit virus. EPPO datasheets on pests recommended for regulation. https://gd.eppo.int Wei, Y., Zhu, B., Liu, W., Cheng, X., Lin, D., He, C., & Shi, H. (2021 a). Heat shock protein 90 co-chaperone modules fine-tune the antagonistic interaction between salicylic acid and auxin biosynthesis in cassava. Cell Reports, 34(5). Wei, Y., Zeng, H., Liu, W., Cheng, X., Zhu, B., Guo, J., & Shi, H. (2021 b). Autophagy‐related genes serve as heat shock protein 90 co‐chaperones in disease resistance against cassava bacterial blight. The Plant Journal, 107(3), 925-937. Werghi, S., Herrero, F. A., Fakhfakh, H., & Gorsane, F. (2021). Auxin drives tomato spotted wilt virus (TSWV) resistance through epigenetic regulation of auxin response factor ARF8 expression in tomato. Gene, 804, 145905. Yan, J., Tong, T., Li, X., Chen, Q., Dai, M., Niu, F., ... & Jiang, Y. Q. (2018). A novel NAC-type transcription factor, NAC87, from oilseed rape modulates reactive oxygen species accumulation and cell death. Plant and Cell Physiology, 59(2), 290-303. Yan, Z. Y., Ma, H. Y., Wang, L., Tettey, C., Zhao, M. S., Geng, C., ... & Li, X. D. (2021). Identification of genetic determinants of tomato brown rugose fruit virus that enable infection of plants harbouring the Tm‐22 resistance gene. Molecular Plant Pathology, 22(11), 1347-1357. Yang, S., Zhang, X., Zhang, X., Bi, Y., & Gao, W. (2022). A bZIP transcription factor, PqbZIP1, is involved in the plant defense response of American ginseng. Peer J, 10, e12939. Yang, J., Wang, D., Zhang, B., Chen, M., Chen, J., Yan, F., & Rao, S. (2025). Comprehensive ubiquitome analysis of Nicotiana benthamiana leaves infected with tomato brown rugose fruit virus. Biology, 14(6), 656. You, M. K., Shin, H. Y., Kim, Y. J., Ok, S. H., Cho, S. K., Jeung, J. U., ... & Shin, J. S. (2010). Novel bifunctional nucleases, OmBBD and AtBBD1, are involved in abscisic acid-mediated callose deposition in Arabidopsis. Plant physiology, 152(2), 1015-1029. Yue, W., Liu, L., Chen, S., Bai, Y., & Li, N. (2022). Effects of water and nitrogen coupling on growth, yield and quality of greenhouse tomato. Water, 14(22), 3665. Zhang, M., Liu, Y., Li, Z., She, Z., Chai, M., Aslam, M., ... & Qin, Y. (2021). The bZIP transcription factor GmbZIP15 facilitates resistance against Sclerotinia sclerotiorum and Phytophthora sojae infection in soybean. Iscience, 24(6). Zhang, S., Griffiths, J. S., Marchand, G., Bernards, M. A., & Wang, A. (2022). Tomato brown rugose fruit virus: An emerging and rapidly spreading plant RNA virus that threatens tomato production worldwide. Molecular Plant Pathology, 23(9), 1262-1277. Zhang, Z., Chang, X., Luo, S., Wang, Y., Xuan, S., Zhao, J., ... & Chen, X. (2023). Transcriptome analysis of two pepper genotypes infected with pepper mild mottle virus. Frontiers in Genetics, 14, 1164730. Zhang, B., Wang, D., Chen, M., Yang, J., Li, J., Chen, J., ... & Rao, S. (2025). Transcriptome analysis of pepper leaves in response to tomato brown rugose fruit virus infection. Plants, 14(9), 1280. Zhou, Z., Duan, Y., Li, Y., Zhang, P., Li, Q., Yu, L., ... & Xiao, Y. (2025). CYP98A monooxygenases: a key enzyme family in plant phenolic compound biosynthesis. Horticulture Research, 12(6), uhaf074. Zhu, H., Li, R., Fang, Y., Zhao, X., Teng, W., Li, H., & Han, Y. (2024). Weighted gene co-expression network analysis uncovers critical genes and pathways involved in soybean response to soybean mosaic virus. Agronomy, 14(11), 2455.