Please use this identifier to cite or link to this item:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/88733Full metadata record
| ???org.dspace.app.webui.jsptag.ItemTag.dcfield??? | Value | Language |
|---|---|---|
| dc.contributor.advisor | 伊藤剛 | zh_TW |
| dc.contributor.advisor | TAKESHI ITOH | en |
| dc.contributor.author | Miguelito F. Isip | zh_TW |
| dc.contributor.author | Miguelito F. Isip | en |
| dc.date.accessioned | 2023-08-15T17:33:54Z | - |
| dc.date.available | 2023-11-09 | - |
| dc.date.copyright | 2023-08-15 | - |
| dc.date.issued | 2023 | - |
| dc.date.submitted | 2023-08-07 | - |
| dc.identifier.citation | Adachi, H., Nakano, T., Miyagawa, N., Ishihama, N., Yoshioka, M., Katou, Y., Yaeno, T., Shirasu, K., & Yoshioka, H. (2015). WRKY transcription factors phosphorylated by MAPK regulate a plant immune NADPH oxidase in Nicotiana benthamiana. The Plant Cell, 27(9), 2645–2663.
Agrios, G. N. (2009). Plant Pathogens and Disease: General Introduction. Akagi, T., Masuda, K., Kuwada, E., Takeshita, K., Kawakatsu, T., Ariizumi, T., Kubo, Y., Ushijima, K., & Uchida, S. (2022). Genome-wide cis-decoding for expression design in tomato using cistrome data and explainable deep learning. The Plant Cell, 34(6), 2174–2187. Ali, S., Ganai, B. A., Kamili, A. N., Bhat, A. A., Mir, Z. A., Bhat, J. A., Tyagi, A., Islam, S. T., Mushtaq, M., Yadav, P., Rawat, S., & Grover, A. (2018b). Pathogenesis-related proteins and peptides as promising tools for engineering plants with multiple stress tolerance. Microbiological Research, 212–213, 29–37. Amorim, L., Santos, R., Neto, J., Guida-Santos, M., Crovella, S., & Benko-Iseppon, A. (2017). Transcription factors involved in plant resistance to pathogens. Current Protein & Peptide Science, 18(4), 335–351. Amos, B., Aurrecoechea, C., Barba, M., Barreto, A., Basenko, E. Y., Bażant, W., Belnap, R., Blevins, A. S., Böhme, U., Brestelli, J., Brunk, B. P., Caddick, M., Callan, D., Campbell, L., Christensen, M. B., Christophides, G. K., Crouch, K., Davis, K., Debarry, J., … Zheng, J. (2022). VEuPathDB: The eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Research, 50(D1), D898–D911. Amselem, J., Cuomo, C. A., van Kan, J. A. L., Viaud, M., Benito, E. P., Couloux, A., Coutinho, P. M., de Vries, R. P., Dyer, P. S., Fillinger, S., Fournier, E., Gout, L., Hahn, M., Kohn, L., Lapalu, N., Plummer, K. M., Pradier, J. M., Quévillon, E., Sharon, A., … Dickman, M. (2011). Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics, 7(8). Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Aragona, M., Haegi, A., Valente, M. T., Riccioni, L., Orzali, L., Vitale, S., Luongo, L., & Infantino, A. (2022). New-generation sequencing technology in diagnosis of fungal plant pathogens: a dream comes true? In Journal of Fungi (Vol. 8, Issue 7). MDPI. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene Ontology: tool for the unification of biology The Gene Ontology Consortium. http://www.flybase.bio.indiana.edu Atkinson, N. J., & Urwin, P. E. (2012). The interaction of plant biotic and abiotic stresses: from genes to the field. Journal of Experimental Botany, 63(10), 3523–3543. Avraham, R., Haseley, N., Fan, A., Bloom-Ackermann, Z., Livny, J., & Hung, D. T. (2016). A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes. Nature Protocols, 11(8), 1477–1491. Bailey, T. L., Williams, N., Misleh, C., & Li, W. W. (2006). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 34(Web Server), W369–W373. Baillo, Kimotho, Zhang, & Xu. (2019). Transcription factors associated with abiotic and biotic stress tolerance and their potential for crops improvement. Genes, 10(10), 771. Bai, Y., Sunarti, S., Kissoudis, C., Visser, R. G. F., & van der Linden, C. G. (2018). The role of tomato WRKY genes in plant responses to combined abiotic and biotic stresses. Frontiers in Plant Science, 9. Bari, R., & Jones, J. D. G. (2009). Role of plant hormones in plant defence responses. Plant Molecular Biology, 69(4), 473–488. Bateman, A., Martin, M. J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bursteinas, B., Bye-A-Jee, H., Coetzee, R., Cukura, A., da Silva, A., Denny, P., Dogan, T., Ebenezer, T. G., Fan, J., Castro, L. G., … Teodoro, D. (2021). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. Baulcombe, D. C., & Dean, C. (2014). Epigenetic regulation in plant responses to the environment. Cold Spring Harbor Perspectives in Biology, 6(9), a019471–a019471. Bernard, V., Brunaud, V., & Lecharny, A. (2010). TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. BMC Genomics, 11(1), 166. Bhattarai, K. K., Atamian, H. S., Kaloshian, I., & Eulgem, T. (2010). WRKY72‐type transcription factors contribute to basal immunity in tomato and Arabidopsis as well as gene‐for‐gene resistance mediated by the tomato R gene Mi‐1. The Plant Journal, 63(2), 229–240. Bilgin, D. D., Zavala, J. A., Zhu, J., Clough, S. J., Ort, D. R., & Delucia, E. H. (2010). Biotic stress globally downregulates photosynthesis genes. Plant, Cell & Environment, 33(10), 1597–1613. Blanco-Ulate, B., Vincenti, E., Powell, A. L. T., & Cantu, D. (2013). Tomato transcriptome and mutant analyses suggest a role for plant stress hormones in the interaction between fruit and Botrytis cinerea. Frontiers in Plant Science, 4. Boddy, L. (2016). Pathogens of Autotrophs. In The Fungi: Third Edition (pp. 245–292). Elsevier Böhnert, H. U., Fudal, I., Dioh, W., Tharreau, D., Notteghem, J.-L., & Lebrun, M.-H. (2004). A putative polyketide synthase/peptide synthetase from Magnaporthe grisea signals pathogen attack to resistant rice. The Plant Cell, 16(9), 2499–2513. Boller, T., & Felix, G. (2009). A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annual Review of Plant Biology, 60(1), 379–406. Bolwell, G. P., Bindschedler, L. V., Blee, K. A., Butt, V. S., Davies, D. R., Gardner, S. L., Gerrish, C., & Minibayeva, F. (2002). The apoplastic oxidative burst in response to biotic stress in plants: a three‐component system. Journal of Experimental Botany, 53(372), 1367–1376. Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology, 34(5), 525–527. Brown, R. L., Kazan, K., McGrath, K. C., Maclean, D. J., & Manners, J. M. (2003). A role for the GCC-Box in jasmonate-mediated activation of the PDF1.2 gene of Arabidopsis. Plant Physiology, 132(2), 1020–1032. Brown, T., Mann, B., Ryder, N., Subbiah, M., Kaplan, J., Dhariwal, P., Neelakantan, A., Shyam, P., Sastry, G., & Askell, A. (2020). Language models are few-shot learners. Adv Neural Inf Process Syst , 33, 1877–1901. Brutus, A., Sicilia, F., Macone, A., Cervone, F., & De Lorenzo, G. (2010). A domain swap approach reveals a role of the plant wall-associated kinase 1 (WAK1) as a receptor of oligogalacturonides. Proceedings of the National Academy of Sciences, 107(20), 9452–9457. Bryne, J. C., Valen, E., Tang, M.-H. E., Marstrand, T., Winther, O., da Piedade, I., Krogh, A., Lenhard, B., & Sandelin, A. (2007). JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Research, 36(Database), D102–D106. Campos, M. D., Félix, M. do R., Patanita, M., Materatski, P., Albuquerque, A., Ribeiro, J. A., & Varanda, C. (2022). Defense Strategies: The role of transcription factors in tomato–pathogen interaction. Biology, 11(2), 235. Casañal, A., Zander, U., Muñoz, C., Dupeux, F., Luque, I., Botella, M. A., Schwab, W., Valpuesta, V., & Marquez, J. A. (2013). The strawberry pathogenesis-related 10 (PR-10) Fra a proteins control flavonoid biosynthesis by binding to metabolic intermediates. Journal of Biological Chemistry, 288(49), 35322–35332. Cesarino, I., Eudes, A., Urbanowicz, B., & Xie, M. (2022). Editorial: Phenylpropanoid systems biology and biotechnology. Frontiers in Plant Science, 13. Chen, L.-H., Tsai, H.-C., Yu, P.-L., & Chung, K.-R. (2017). A major facilitator superfamily transporter-mediated resistance to oxidative stress and fungicides requires Yap1, Skn7, and MAP kinases in the citrus fungal pathogen Alternaria alternata. PLOS ONE, 12(1) Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. Chen, X., Li, C., Wang, H., & Guo, Z. (2019). WRKY transcription factors: evolution, binding, and action. Phytopathology Research, 1(1), 13. Chen, X., Sun, M., Chong, S., Si, J., & Wu, L. (2022). Transcriptomic and metabolomic approaches deepen our knowledge of plant–endophyte interactions. Frontiers in Plant Science, 12. Choquer, M., Fournier, E., Kunz, C., Levis, C., Pradier, J.-M., Simon, A., & Viaud, M. (2007). Botrytis cinerea virulence factors: new insights into a necrotrophic and polyphageous pathogen. FEMS Microbiology Letters, 277(1), 1–10. Chowdhary, A. A., Mishra, S., Mehrotra, S., Upadhyay, S. K., Bagal, D., & Srivastava, V. (2023). Plant transcription factors: an overview of their role in plant life. In Plant Transcription Factors (pp. 3–20). Elsevier. Colmenares, A. J., Aleu, J., Durán-Patrón, R., Collado, I. G., & Hernández-Galán, R. (2002). The putative role of botrydial and related metabolites in the infection mechanism of Botrytis cinerea. Journal of Chemical Ecology, 28(5), 997–1005. Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., & Mortazavi, A. (2016). A survey of best practices for RNA-seq data analysis. Genome Biology, 17(1), 13. https://doi.org/10.1186/s13059-016-0881-8 Cope, K. R., Prates, E. T., Miller, J. I., Demerdash, O. N. A., Shah, M., Kainer, D., Cliff, A., Sullivan, K. A., Cashman, M., Lane, M., Matthiadis, A., Labbé, J., Tschaplinski, T. J., Jacobson, D. A., & Kalluri, U. C. (2023). Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus. Computational and Structural Biotechnology Journal, 21, 1122–1139. Corchete, L. A., Rojas, E. A., Alonso-López, D., De Las Rivas, J., Gutiérrez, N. C., & Burguillo, F. J. (2020). Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis. Scientific Reports, 10(1), 19737. Couch, B. C., & Kohn, L. M. (2002). A multilocus gene genealogy concordant with host preference indicates segregation of a new species, Magnaporthe oryzae, from M. grisea. Mycologia, 94(4), 683–693. Cui, H., Tsuda, K., & Parker, J. E. (2015). Effector-triggered immunity: from pathogen perception to robust defense. Annual Review of Plant Biology, 66(1), 487–511. Cutler, H. G., Jacyno, J. M., Harwood, J. S., Dulik, D., Goodrich, P. D., & Roberts, R. G. (1993). Botcinolide: a biologically active natural product from Botrytis cinerea. Bioscience, Biotechnology, and Biochemistry, 57(11), 1980–1982 Dalmais, B., Schumacher, J., Moraga, J., Le Pêcheur, P., Tudzynski, B., Collado, I. G., & Viaud, M. (2011). The Botrytis cinerea phytotoxin botcinic acid requires two polyketide synthases for production and has a redundant role in virulence with botrydial. Molecular Plant Pathology, 12(6), 564–579. Deal, R. B., & Henikoff, S. (2011). Histone variants and modifications in plant gene regulation. Current Opinion in Plant Biology, 14(2), 116–122. Dean, R. A., Talbot, N. J., Ebbole, D. J., Farman, M. L., Mitchell, T. K., Orbach, M. J., Thon, M., Kulkarni, R., Xu, J.-R., Pan, H., Read, N. D., Lee, Y.-H., Carbone, I., Brown, D., Oh, Y. Y., Donofrio, N., Jeong, J. S., Soanes, D. M., Djonovic, S., … Birren, B. W. (2005). The genome sequence of the rice blast fungus Magnaporthe grisea. http://www.broad.mit.edu/annota- De Cremer, K., Mathys, J., Vos, C., Froenicke, L., Michelmore, R. W., Cammue, B. P. A., & De Coninck, B. (2013). RNAseq-based transcriptome analysis of Lactuca sativa infected by the fungal necrotroph Botrytis cinerea. Plant, Cell & Environment, n/a-n/a. Deighton, N., Muckenschnabel, I., Colmenares, A. J., Collado, I. G., & Williamson, B. (2001). Botrydial is produced in plant tissues infected by Botrytis cinerea. Phytochemistry, 57(5), 689–692. De Jesús-Pires, C., Ferreira-Neto, J. R. C., Pacifico Bezerra-Neto, J., Kido, E. A., de Oliveira Silva, R. L., Pandolfi, V., Wanderley-Nogueira, A. C., Binneck, E., da Costa, A. F., Pio-Ribeiro, G., Pereira-Andrade, G., Sittolin, I. M., Freire-Filho, F., & Benko-Iseppon, A. M. (2020). Plant thaumatin-like proteins: function, evolution and biotechnological applications. Current Protein & Peptide Science, 21(1), 36–51. Deng, R., Tao, M., Xing, H., Yang, X., Liu, C., Liao, K., & Qi, L. (2021). Automatic diagnosis of rice diseases using deep learning. Frontiers in Plant Science, 12. Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, C., & Lempicki, R. A. (2003). DAVID: database for annotation, visualization, and integrated discovery. In Genome Biology (Vol. 4, Issue 9). http://dot.ped.med.umich.edu:2000/ De Wit, P. J. G. M., Mehrabi, R., Van Den Burg, H. A., & Stergiopoulos, I. (2009). Fungal effector proteins: past, present and future. Molecular Plant Pathology, 10(6), 735–747. DeYoung, B. J., & Innes, R. W. (2006). Plant NBS-LRR proteins in pathogen sensing and host defense. Nature Immunology, 7(12), 1243–1249. Dixon, R. A., Achnine, L., Kota, P., Liu, C.-J., Reddy, M. S. S., & Wang, L. (2002). The phenylpropanoid pathway and plant defence-a genomics perspective. Molecular Plant Pathology, 3(5), 371–390. Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15–21. https://doi.org/10.1093/bioinformatics/bts635 Duan, L., Liu, H., Li, X., Xiao, J., & Wang, S. (2014). Multiple phytohormones and phytoalexins are involved in disease resistance to Magnaporthe oryzae invaded from roots in rice. Physiologia Plantarum, 152(3), 486–500. Ebbole, D. J. (2008). Magnaporthe as a model for understanding host-pathogen interactions. In Annual Review of Phytopathology (Vol. 45, pp. 437–456). Egan, M. J., Wang, Z.-Y., Jones, M. A., Smirnoff, N., & Talbot, N. J. (2007). Generation of reactive oxygen species by fungal NADPH oxidases is required for rice blast disease. Proceedings of the National Academy of Sciences, 104(28), 11772–11777. Emms, D. M., & Kelly, S. (2019). OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology, 20(1), 238. Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048. Falak, N., Imran, Q. M., Hussain, A., & Yun, B.-W. (2021). Transcription factors as the “blitzkrieg” of plant defense: a pragmatic view of nitric oxide’s role in gene regulation. International Journal of Molecular Sciences, 22(2), 522. Faris, JD., Zhang, Z., Lu, H., Lu, S., Reddy, L., Cloutier, S., Fellers, JP., Meinhardt, SW., Rasmussen, JB., Xu, SS., Oliver, RP., Simons, KJ., Friesen, TL. (2010). A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens. Proc Natl Acad Sci U S A, 27;107(30):13544-9. Feller, A., Machemer, K., Braun, E. L., & Grotewold, E. (2011). Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. The Plant Journal, 66(1), 94–116. Fernandez, J., & Orth, K. (2018). Rise of a Cereal Killer: The biology of Magnaporthe oryzae biotrophic growth. Trends in Microbiology, 26(7), 582–597. Flor, H. (1971). Current status of the gene-for-gene concept. Annual Review of Phytopathology 9(1), 275–296. Frazee, A. C., Pertea, G., Jaffe, A. E., Langmead, B., Salzberg, S. L., & Leek, J. T. (2015). Ballgown bridges the gap between transcriptome assembly and expression analysis. In Nature Biotechnology (Vol. 33, Issue 3, pp. 243–246). Nature Publishing Group. Frías, M., González, M., González, C., & Brito, N. (2019). A 25-residue peptide from Botrytis cinerea Xylanase BcXyn11A elicits plant defenses. Frontiers in Plant Science, 10. Fujimori, S., Washio, T., & Tomita, M. (2005). GC-compositional strand bias around transcription start sites in plants and fungi. BMC Genomics, 6(1), 26. Gao, P., Zhang, H., Yan, H., Wang, Q., Yan, B., Jian, H., Tang, K., & Qiu, X. (2021). RcTGA1 and glucosinolate biosynthesis pathway involvement in the defence of rose against the necrotrophic fungus Botrytis cinerea. BMC Plant Biology, 21(1), 223. Gao, X., Chen, X., Lin, W., Chen, S., Lu, D., Niu, Y., Li, L., Cheng, C., McCormack, M., Sheen, J., Shan, L., & He, P. (2013). Bifurcation of Arabidopsis NLR immune signaling via Ca2+-dependent protein kinases. PLoS Pathogens, 9(1), e1003127. Gonzalez, C., Brito, N., & Sharon, A. (2016). Botrytis - the Fungus, the Pathogen and its Management in Agricultural Systems (S. Fillinger & Y. Elad, Eds.). Springer. González-Rodríguez, V. E., Liñeiro, E., Colby, T., Harzen, A., Garrido, C., Cantoral, J. M., Schmidt, J., & Fernández-Acero, F. J. (2015). Proteomic profiling of Botrytis cinerea conidial germination. Archives of Microbiology, 197(2), 117–133. Govrin, E. M., & Levine, A. (2000). The hypersensitive response facilitates plant infection by the necrotrophic pathogen Botrytis cinerea. Current Biology, 10(13), 751–757. Grant, C. E., Bailey, T. L., & Noble, W. S. (2011). FIMO: scanning for occurrences of a given motif. Bioinformatics, 27(7), 1017–1018. Gui, Y.-J., Zhang, W.-Q., Zhang, D.-D., Zhou, L., Short, D. P. G., Wang, J., Ma, X.-F., Li, T.-G., Kong, Z.-Q., Wang, B.-L., Wang, D., Li, N.-Y., Subbarao, K. V., Chen, J.-Y., & Dai, X.-F. (2018). A Verticillium dahliae extracellular cutinase modulates plant immune responses. Molecular Plant-Microbe Interactions®, 31(2), 260–273. Gupta, R., Lee, S. E., Agrawal, G. K., Rakwal, R., Park, S., Wang, Y., & Kim, S. T. (2015). Understanding the plant-pathogen interactions in the context of proteomics-generated apoplastic proteins inventory. Frontiers in Plant Science, 6(June). Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L., & Noble, W. (2007). Quantifying similarity between motifs. Genome Biology, 8(2), R24. Haile, Z. M., Malacarne, G., Pilati, S., Sonego, P., Moretto, M., Masuero, D., Vrhovsek, U., Engelen, K., Baraldi, E., & Moser, C. (2020). Dual transcriptome and metabolic analysis of vitis vinifera cv. pinot noir berry and botrytis cinerea during quiescence and egressed infection. Frontiers in Plant Science, 10. Haile, Z. M., Nagpala-De Guzman, E. G., Moretto, M., Sonego, P., Engelen, K., Zoli, L., Moser, C., & Baraldi, E. (2019). Transcriptome profiles of strawberry (Fragaria vesca) fruit interacting with Botrytis cinerea at different ripening stages. Frontiers in Plant Science, 10. Han, X., & Kahmann, R. (2019). Manipulation of phytohormone pathways by effectors of filamentous plant pathogens. Frontiers in Plant Science, 10. Harel, Y. M., Mehari, Z. H., Rav-David, D., & Elad, Y. (2014). Systemic resistance to gray mold induced in tomato by benzothiadiazole and Trichoderma harzianum T39. Phytopathology®, 104(2), 150–157. Hartmann, A., Berkowitz, O., Whelan, J., & Narsai, R. (2022). Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment. BMC Plant Biology, 22(1), 62. 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), 169. Heller, J., & Tudzynski, P. (2011). Reactive oxygen species in phytopathogenic fungi: signaling, development, and disease. Annual Review of Phytopathology, 49(1), 369–390. He, Q., Liu, Y., Liang, P., Liao, X., Li, X., Li, X., Shi, D., Liu, W., Lin, C., Zheng, F., & Miao, W. (2021). A novel chorismate mutase from Erysiphe quercicola performs dual functions of synthesizing amino acids and inhibiting plant salicylic acid synthesis. Microbiological Research, 242, 126599. Hosmani, P. S., Flores-Gonzalez, M., van de Geest, H., Maumus, F., Bakker, L. v, Schijlen, E., van Haarst, J., Cordewener, J., Sanchez-Perez, G., Peters, S., Fei, Z., Giovannoni, J. J., Mueller, L. A., & Saha, S. (2019). An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. Huang, H., Ullah, F., Zhou, D.-X., Yi, M., & Zhao, Y. (2019). Mechanisms of ROS regulation of plant development and stress responses. Frontiers in Plant Science, 10. Huang, S., Gao, Y., Liu, J., Peng, X., Niu, X., Fei, Z., Cao, S., & Liu, Y. (2012). Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Molecular Genetics and Genomics, 287(6), 495–513. Huang, Y., Chen, H., Reinfelder, J. R., Liang, X., Sun, C., Liu, C., Li, F., & Yi, J. (2019). A transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root. Science of The Total Environment, 666, 445–460. Hubert, B. (2022). SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids. Scientific Data, 9(1), 92. Inoue, H., Hayashi, N., Matsushita, A., Xinqiong, L., Nakayama, A., Sugano, S., Jiang, C.-J., & Takatsuji, H. (2013). Blast resistance of CC-NB-LRR protein Pb1 is mediated by WRKY45 through protein–protein interaction. Proceedings of the National Academy of Sciences, 110(23), 9577–9582. Jeon, J., Lee, G. W., Kim, K. T., Park, S. Y., Kim, S., Kwon, S., Huh, A., Chung, H., Lee, D. Y., Kim, C. Y., & Lee, Y. H. (2020). Transcriptome profiling of the rice blast fungus Magnaporthe oryzae and its host Oryza sativa during infection. Molecular Plant-Microbe Interactions, 33(2), 141–144. Jia, Y., McAdams, S. A., Bryan, G. T., Hershey, H. P., & Valent, B. (2000). Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. The EMBO Journal, 19(15), 4004–4014. Joesch-Cohen, L. M., Robinson, M., Jabbari, N., Lausted, C. G., & Glusman, G. (2018). Novel metrics for quantifying bacterial genome composition skews. BMC Genomics, 19(1), 528. Kakei, Y., Masuda, H., Nishizawa, N. K., Hattori, H., & Aung, M. S. (2021). Elucidation of novel cis-regulatory elements and promoter structures involved in iron excess response mechanisms in rice using a bioinformatics approach. Frontiers in Plant Science, 12. Kaneda, T., Taga, Y., Takai, R., Iwano, M., Matsui, H., Takayama, S., Isogai, A., & Che, F.-S. (2009). The transcription factor OsNAC4 is a key positive regulator of plant hypersensitive cell death. The EMBO Journal, 28(7), 926–936. Kanehisa, M., & Goto, S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. In Nucleic Acids Research (Vol. 28, Issue 1). http://www.genome.ad.jp/kegg/ Kars, I., Krooshof, G. H., Wagemakers, L., Joosten, R., Benen, J. A. E., & Van Kan, J. A. L. (2005). Necrotizing activity of five Botrytis cinerea endopolygalacturonases produced in Pichia pastoris. The Plant Journal, 43(2), 213–225. Kashif, T., & Qasim, A. (2020). Handbook of Bioremediation. Elsevier. Kasprzewska A. (2003). Plant chitinases--regulation and function. Cell Mol Biol Lett., 8(3), 809–824. Kaur, A., Pati, P. K., Pati, A. M., & Nagpal, A. K. (2017). In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PLOS ONE, 12(9), e0184523. Kawahara, Y., Oono, Y., Kanamori, H., Matsumoto, T., Itoh, T., & Minami, E. (2012). Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PloS One, 7(11). K. Berwal, M., & Ram, C. (2019). Superoxide Dismutase: A stable biochemical marker for abiotic stress tolerance in higher plants. In Abiotic and Biotic Stress in Plants. IntechOpen. Kim, D., Langmead, B., & Salzberg, S. L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12(4), 357–360. Kim, D. S., & Hwang, B. K. (2014). An important role of the pepper phenylalanine ammonia-lyase gene (PAL1) in salicylic acid-dependent signalling of the defence response to microbial pathogens. Journal of Experimental Botany, 65(9), 2295–2306. Kim, S. G., Kim, S. T., Wang, Y., Yu, S., Choi, I. S., Kim, Y. C., Kim, W. T., Agrawal, G. K., Rakwal, R., & Kang, K. Y. (2011). The RNase activity of rice probenazole-induced protein1 (PBZ1) plays a key role in cell death in plants. Molecules and Cells, 31(1), 25–31. Klepikova, A. V., Logacheva, M. D., Dmitriev, S. E., & Penin, A. A. (2015). RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation. BMC Genomics, 16(1), 466. Kumar, V., Jain, P., Venkadesan, S., Karkute, S. G., Bhati, J., Abdin, M. Z., Sevanthi, A. M., Mishra, D. C., Chaturvedi, K. K., Rai, A., Sharma, T. R., & Solanke, A. U. (2021). Understanding rice-Magnaporthe oryzae interaction in resistant and susceptible cultivars of rice under panicle blast infection using a time-course transcriptome analysis. Genes, 12(2), 301. Leinonen, R., Sugawara, H., & Shumway, M. (2011). The sequence read archive. Nucleic Acids Research, 39(SUPPL. 1). Leroch, M., Kleber, A., Silva, E., Coenen, T., Koppenhöfer, D., Shmaryahu, A., Valenzuela, P. D. T., & Hahn, M. (2013). Transcriptome profiling of Botrytis cinerea conidial germination reveals upregulation of infection-related genes during the pre-penetration stage. Eukaryotic Cell, 12(4), 614–626. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078–2079. Lin, Z.-J. D., Liebrand, T. W. H., Yadeta, K. A., & Coaker, G. L. (2015). PBL13 is a serine/threonine protein kinase that negatively regulates Arabidopsis immune responses. Plant Physiology, pp.01391.2015. Liu, C., Chen, L., Zhao, R., Li, R., Zhang, S., Yu, W., Sheng, J., & Shen, L. (2019). Melatonin induces disease resistance to Botrytis cinerea in tomato fruit by activating jasmonic acid signaling pathway. Journal of Agricultural and Food Chemistry, 67(22), 6116–6124. Liu, M., Zong, Z., Fang, X., Liu, R., Mu, H., Chen, H., Niu, B., & Gao, H. (2023). Purification and characterization of cutinase from Botrytis cinerea and effect on blueberry cuticle. Journal of Agriculture and Food Research, 12, 100599. Liu, T., Chen, Y., Tian, S., & Li, B. (2023). Crucial roles of effectors in interactions between horticultural crops and pathogens. Horticulturae, 9(2), 250. Liu, T., Hou, J., Wang, Y., Jin, Y., Borth, W., Zhao, F., Liu, Z., Hu, J., & Zuo, Y. (2016). Genome-wide identification, classification and expression analysis in fungal–plant interactions of cutinase gene family and functional analysis of a putative ClCUT7 in Curvularia lunata. Molecular Genetics and Genomics, 291(3), 1105–1115. Liu, W., Liu, J., Triplett, L., Leach, J. E., & Wang, G.-L. (2014). Novel insights into rice innate immunity against bacterial and fungal pathogens. Annual Review of Phytopathology, 52(1), 213–241. Liu, X., Cao, X., Shi, S., Zhao, N., Li, D., Fang, P., Chen, X., Qi, W., & Zhang, Z. (2018). Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection. BMC Genetics, 19(1), 62. Li, Y., & Loake, G. J. (2016). Redox-regulated plant transcription factors. In Plant Transcription Factors (pp. 373–384). Elsevier. Lorenzo, O., Piqueras, R., Sánchez-Serrano, J. J., & Solano, R. (2003). Ethylene response factor1 integrates signals from ethylene and jasmonate pathways in plant defense. The Plant Cell, 15(1), 165–178. Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. Lu, L., Rong, W., Massart, S., & Zhang, Z. (2018). Genome-wide identification and expression analysis of cutinase gene family in Rhizoctonia cerealis and functional study of an active cutinase rccut1 in the fungal–wheat interaction. Frontiers in Microbiology, 9. Ma, L. J., Van Der Does, H. C., Borkovich, K. A., Coleman, J. J., Daboussi, M. J., Di Pietro, A., Dufresne, M., Freitag, M., Grabherr, M., Henrissat, B., Houterman, P. M., Kang, S., Shim, W. B., Woloshuk, C., Xie, X., Xu, J. R., Antoniw, J., Baker, S. E., Bluhm, B. H., … Rep, M. (2010). Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature, 464(7287), 367–373. Marschall, R., & Tudzynski, P. (2016). Reactive oxygen species in development and infection processes. Seminars in Cell & Developmental Biology, 57, 138–146. McIntyre, L. M., Lopiano, K. K., Morse, A. M., Amin, V., Oberg, A. L., Young, L. J., & Nuzhdin, S. V. (2011). RNA-seq: technical variability and sampling. BMC Genomics, 12(1), 293. Meena, M. (2019). Tomato: a model plant to study plant-pathogen interactions. Food Science & Nutrition Technology, 4(1), 1–6. Meng, H., Sun, M., Jiang, Z., Liu, Y., Sun, Y., Liu, D., Jiang, C., Ren, M., Yuan, G., Yu, W., Feng, Q., Yang, A., Cheng, L., & Wang, Y. (2021). Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae. Scientific Reports, 11(1), 809. Mengiste, T., Chen, X., Salmeron, J., & Dietrich, R. (2003). The BOTRYTIS SUSCEPTIBLE1 gene encodes an R2R3MYB transcription factor protein that is required for biotic and abiotic stress responses in Arabidopsis. The Plant Cell, 15(11), 2551–2565. Meng, Q., Gupta, R., Min, C. W., Kwon, S. W., Wang, Y., Je, B. il, Kim, Y. J., Jeon, J. S., Agrawal, G. K., Rakwal, R., & Kim, S. T. (2019). Proteomics of rice-Magnaporthe oryzae interaction: what have we learned so far? In Frontiers in Plant Science (Vol. 10). Frontiers Media S.A. Mentlak, T. A., Kombrink, A., Shinya, T., Ryder, L. S., Otomo, I., Saitoh, H., Terauchi, R., Nishizawa, Y., Shibuya, N., Thomma, B. P. H. J., & Talbot, N. J. (2012). Effector-mediated suppression of chitin-triggered immunity by Magnaporthe oryzae is necessary for rice blast disease. The Plant Cell, 24(1), 322–335. Mérillon, J. M., & Ramawat, K. G. (2012). Plant Defence: Biological Control (J. M. Mérillon & K. G. Ramawat, Eds.). Springer Netherlands. Mishra, S., Jha, A. B., & Dubey, R. S. (2011). Arsenite treatment induces oxidative stress, upregulates antioxidant system, and causes phytochelatin synthesis in rice seedlings. Protoplasma, 248(3), 565–577. Mittler, R., Vanderauwera, S., Suzuki, N., Miller, G., Tognetti, V. B., Vandepoele, K., Gollery, M., Shulaev, V., & Van Breusegem, F. (2011). ROS signaling: the new wave? Trends in Plant Science, 16(6), 300–309. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5(7), 621–628. Morton, T., Petricka, J., Corcoran, D. L., Li, S., Winter, C. M., Carda, A., Benfey, P. N., Ohler, U., & Megraw, M. (2014). Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. The Plant Cell, 26(7), 2746–2760. Mosquera, G., Giraldo, M. C., Khang, C. H., Coughlan, S., & Valent, B. (2009). Interaction transcriptome analysis identifies Magnaporthe oryzae BAS1-4 as biotrophy-associated secreted proteins in rice blast disease. The Plant Cell, 21(4), 1273–1290. Naveed, Z.A., Wei, X., Chen, J., Mubeen, H., Ali, G.S. (2020). The PTI to ETI continuum in phytophthora-plant interactions. Front. Plant Sci. 11, 593905. Newman, M.-A., Sundelin, T., Nielsen, J. T., & Erbs, G. (2013). MAMP (microbe-associated molecular pattern) triggered immunity in plants. Frontiers in Plant Science, 4. Ng, D., Abeysinghe, J., & Kamali, M. (2018). Regulating the regulators: the control of transcription factors in plant defense signaling. International Journal of Molecular Sciences, 19(12), 3737. Nguyen, Q., Iswanto, A., Son G., Kim S. (2021). Recent advances in effector-triggered immunity in plants: New pieces in the puzzle create a different paradigm. International Journal of Molecular Sciences. 22(9):4709. Ong, C.-T., & Corces, V. G. (2011). Enhancer function: new insights into the regulation of tissue-specific gene expression. Nature Reviews Genetics, 12(4), 283–293. Park, C.-H., Chen, S., Shirsekar, G., Zhou, B., Khang, C. H., Songkumarn, P., Afzal, A. J., Ning, Y., Wang, R., Bellizzi, M., Valent, B., & Wang, G.-L. (2012). The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern–triggered immunity in rice. The Plant Cell, 24(11), 4748–4762. Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods, 14(4), 417–419. Pavitra, K., Vinod, J., & Ravishankar, K. (2019). What is host-pathogen initial interaction telling us? an essential component of biotic stress response mechanism! Advances in Biotechnology & Microbiology, 12(4). Pedras, M. S. C., Hossain, S., & Snitynsky, R. B. (2011). Detoxification of cruciferous phytoalexins in Botrytis cinerea: Spontaneous dimerization of a camalexin metabolite. Phytochemistry, 72(2–3), 199–206. Peng, J., Aluthmuhandiram, J. V. S., Chethana, K. W. T., Zhang, Q., Xing, Q., Wang, H., Liu, M., Zhang, W., Li, X., & Yan, J. (2022). An NmrA-Like protein, Lws1, is important for pathogenesis in the woody plant pathogen Lasiodiplodia theobromae. Plants, 11(17), 2197. Pennisi, E. (2010). Armed and dangerous. Science, 327(5967), 804–805. Pertea, G., & Pertea, M. (2020). GFF utilities: GffRead and GffCompare. F1000Research, 9, 304. Pertea, M., Kim, D., Pertea, G. M., Leek, J. T., & Salzberg, S. L. (2016). Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols, 11(9), 1650–1667. Pertea, M., Pertea, G. M., Antonescu, C. M., Chang, T. C., Mendell, J. T., & Salzberg, S. L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33(3), 290–295. Phukan, U. J., Jeena, G. S., Tripathi, V., & Shukla, R. K. (2017). Regulation of apetala2/ethylene response factors in plants. Frontiers in Plant Science, 8. Pinedo, C., Wang, C.-M., Pradier, J.-M., Dalmais, B., Choquer, M., Le Pêcheur, P., Morgant, G., Collado, I. G., Cane, D. E., & Viaud, M. (2008). Sesquiterpene synthase from the botrydial biosynthetic gene cluster of the phytopathogen Botrytis cinerea. ACS Chemical Biology, 3(12), 791–801. Pitsili, E., Phukan, U. J., & Coll, N. S. (2020). Cell death in plant immunity. Cold Spring Harbor Perspectives in Biology, 12(6), a036483. Quinet, M., Angosto, T., Yuste-Lisbona, F. J., Blanchard-Gros, R., Bigot, S., Martinez, J.-P., & Lutts, S. (2019). Tomato fruit development and metabolism. Frontiers in Plant Science, 10. Rafiei, V., Vélëz, H., & Tzelepis, G. (2021). The role of glycoside hydrolases in phytopathogenic fungi and oomycetes virulence. International Journal of Molecular Sciences, 22(17), 9359. Ramos, R. N., Martin, G. B., Pombo, M. A., & Rosli, H. G. (2021). WRKY22 and WRKY25 transcription factors are positive regulators of defense responses in Nicotiana benthamiana. Plant Molecular Biology, 105(1–2), 65–82. R Core Team. (2021). R: A language and environment for statistical computing (4.1.2). R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Reboledo, G., Agorio, A., Vignale, L., Batista-García, R. A., & Ponce De León, I. (2020). Botrytis cinerea transcriptome during the infection process of the Bryophyte Physcomitrium patens and angiosperms. Journal of Fungi, 7(1), 11. Reignault, Ph., Valette-Collet, O., & Boccara, M. (2007). The importance of fungal pectinolytic enzymes in plant invasion, host adaptability and symptom type. European Journal of Plant Pathology, 120(1), 1–11. Reim, S., Rohr, A.-D., Winkelmann, T., Weiß, S., Liu, B., Beerhues, L., Schmitz, M., Hanke, M.-V., & Flachowsky, H. (2020). Genes involved in stress response and especially in phytoalexin biosynthesis are upregulated in four malus genotypes in response to apple replant disease. Frontiers in Plant Science, 10. Romani, F., & Moreno, J. E. (2021). Molecular mechanisms involved in functional macroevolution of plant transcription factors. New Phytologist, 230(4), 1345–1353. Ron, M., & Avni, A. (2004). The receptor for the fungal elicitor ethylene-inducing xylanase is a member of a resistance-like gene family in tomato. The Plant Cell, 16(6), 1604–1615. Saijo, Y., Loo, E. P., & Yasuda, S. (2018). Pattern recognition receptors and signaling in plant-microbe interactions. The Plant Journal, 93(4), 592–613. Sakai, H., Lee, S. S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y., Wakimoto, H., Yang, C. C., Iwamoto, M., Abe, T., Yamada, Y., Muto, A., Inokuchi, H., Ikemura, T., Matsumoto, T., Sasaki, T., & Itoh, T. (2013). Rice annotation project database (RAP-DB): An integrative and interactive database for rice genomics. Plant and Cell Physiology, 54(2). Sakuno, E., Tani, H., & Nakajima, H. (2007). 2- epi -Botcinin A and 3- O -Acetylbotcineric Acid from Botrytis cinerea. Bioscience, Biotechnology, and Biochemistry, 71(10), 2592–2595. Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., Madej, T., Marchler-Bauer, A., Lanczycki, C., Lathrop, S., Lu, Z., Thibaud-Nissen, F., Murphy, T., Phan, L., Skripchenko, Y., … Sherry, S. T. (2022). Database resources of the national center for biotechnology information. Nucleic Acids Research, 50(D1), D20–D26. Schulz, P., Herde, M., & Romeis, T. (2013). Calcium-dependent protein kinases: hubs in plant stress signaling and development. Plant Physiology, 163(2), 523–530. Selvaraju, R., Cogswell, M., Das, A., Vedantam, R., Parikh, D., & Batra, D. (2017). Grad-CAM: visual explanations from deep networks via gradient-based localization. Proceedings of the IEEE International Conference on Computer Vision (ICCV), 618–626. Sesma, A., & Osbourn, A. E. (2004). The rice leaf blast pathogen undergoes developmental processes typical of root-infecting fungi. Nature, 431(7008), 582–586. Shine, M. B., Yang, J., El‐Habbak, M., Nagyabhyru, P., Fu, D., Navarre, D., Ghabrial, S., Kachroo, P., & Kachroo, A. (2016). Cooperative functioning between phenylalanine ammonia lyase and isochorismate synthase activities contributes to salicylic acid biosynthesis in soybean. New Phytologist, 212(3), 627–636. https://doi.org/10.1111/nph.14078 Siegmund, U., & Viefhues, A. (2016). Reactive oxygen species in the Botrytis – host interaction. In Botrytis – the Fungus, the Pathogen and its Management in Agricultural Systems (pp. 269–289). Springer International Publishing. Siewers, V., Viaud, M., Jimenez-Teja, D., Collado, I. G., Gronover, C. S., Pradier, J.-M., Tudzynsk, B., & Tudzynski, P. (2005). Functional analysis of the cytochrome p450 monooxygenase gene bcbot1 of Botrytis cinerea indicates that botrydial is a strain-specific virulence factor. Molecular Plant-Microbe Interactions®, 18(6), 602–612. Singh, K. (2002). Transcription factors in plant defense and stress responses. Current Opinion in Plant Biology, 5(5), 430–436. Singh, N., Ujinwal, M., & Singh, A. (2022). Advances in agricultural bioinformatics: an outlook of multi “omics” approaches. In Bioinformatics in Agriculture (pp. 3–21). Elsevier. Singh, P., Verma, R. L., Singh, R. S., Singh, R. P., Singh, H. B., Arsode, P., Kumar, M., & Singh, P. K. (2020). Biotic stress management in rice (Oryza sativa L.) through conventional and molecular approaches. In New Frontiers in Stress Management for Durable Agriculture (pp. 609–644). Springer Singapore. Skamnioti, P., & Gurr, S. J. (2007). Magnaporthe grisea cutinase2 mediates appressorium differentiation and host penetration and is required for full virulence. The Plant Cell, 19(8), 2674–2689. Southwood, D., & Ranganathan, S. (2019). Host-pathogen interactions. In Encyclopedia of Bioinformatics and Computational Biology (pp. 103–112). Elsevier. Srivastava, D. A., Arya, G. C., Pandaranayaka, E. P. J., Manasherova, E., Prusky, D. B., Elad, Y., Frenkel, O., & Harel, A. (2020). Transcriptome profiling data of Botrytis cinerea infection on whole plant Solanum lycopersicum. Molecular Plant-Microbe Interactions, 33(9), 1103–1107. Suzuki, N. (2016). Hormone signaling pathways under stress combinations. Plant Signaling & Behavior, 11(11), e1247139. Tanaka, T., Koyanagi, K. O., & Itoh, T. (2009). Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis. Plant Physiology, 149(3), 1316–1324. Tang, Q., Zheng, X., Gou, J., & Yu, T. (2022). Tomato SlPti5 plays a regulative role in the plant immune response against Botrytis cinerea through modulation of ROS system and hormone pathways. Journal of Integrative Agriculture, 21(3), 697–709. Tatarinova, T., Brover, V., Troukhan, M., & Alexandrov, N. (2003). Skew in CG content near the transcription start site in Arabidopsis thaliana. Bioinformatics, 19(suppl_1), i313–i314. Tian, F., Yang, D.-C., Meng, Y.-Q., Jin, J., & Gao, G. (2019). PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Research. Tian, L., Shi, S., Nasir, F., Chang, C., Li, W., Tran, L.-S. P., & Tian, C. (2018). Comparative analysis of the root transcriptomes of cultivated and wild rice varieties in response to Magnaporthe oryzae infection revealed both common and species-specific pathogen responses. Rice, 11(1), 26. Tobias, T., Tonnies, J., Wrightsman, T., Buckler, E. S., Cuperus, J. T., Fields, S., & Queitsch, C. (2021). Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. Nature Plants, 7(6), 842–855. Touchman, J. (2010). Comparative genomics. Nature Education Knowledge, 3, 10–13. Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25(9), 1105–1111. Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28(5), 511–515. Turck, F., Zhou, A., & Somssich, I. E. (2004). Stimulus-dependent, promoter-specific binding of transcription factor WRKY1 to its native promoter and the defense-related gene PcPR1-1 in parsley. The Plant Cell, 16(10), 2573–2585. Ülker, B., & Somssich, I. E. (2004). WRKY transcription factors: from DNA binding towards biological function. Current Opinion in Plant Biology, 7(5), 491–498. Usadel, B., Poree, F., Nagel, A., Lohse, M., Czedik-Eysenberg, A., & Stitt, M. (2009). A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant, Cell & Environment, 32(9), 1211–1229. Van De Mortel, J. E., & Aarts, M. G. M. (2006). Comparative transcriptomics – model species lead the way. New Phytologist, 170(2), 199–201. Van Kan, J. A. L., Stassen, J. H. M., Mosbach, A., Van Der Lee, T. A. J., Faino, L., Farmer, A. D., Papasotiriou, D. G., Zhou, S., Seidl, M. F., Cottam, E., Edel, D., Hahn, M., Schwartz, D. C., Dietrich, R. A., Widdison, S., & Scalliet, G. (2017). A gapless genome sequence of the fungus Botrytis cinerea. Molecular Plant Pathology, 18(1), 75–89. van Kan, J. A. L., Van’t Klooster, J. W., Wagemakers, C. A. M., Dees, D. C. T., & van der Vlugt-Bergmans, C. J. B. (1997). Cutinase A of Botrytis cinerea is expressed, but not essential, during penetration of gerbera and tomato. In Molecular Plant-Microbe Interactions MPMI (Vol. 10, Issue 1). van Verk, M. C., Pappaioannou, D., Neeleman, L., Bol, J. F., & Linthorst, H. J. M. (2008). A Novel WRKY Transcription Factor Is Required for Induction of PR-1a Gene Expression by Salicylic Acid and Bacterial Elicitors . Plant Physiology, 146(4), 1983–1995. Vega, A., Canessa, P., Hoppe, G., Retamal, I., Moyano, T. C., Canales, J., Gutiérrez, R. A., & Rubilar, J. (2015). Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum. Frontiers in Plant Science, 6. Wang, H.-C., & Hickey, D. A. (2007). Rapid divergence of codon usage patterns within the rice genome. BMC Evolutionary Biology, 7(Suppl 1), S6. Wang, W., Feng, B., Zhou, J., & Tang, D. (2020). Plant immune signaling: advancing on two frontiers. Journal of Integrative Plant Biology, 62(1), 2–24. Wang, X., Xue, B., Dai, J., Qin, X., Liu, L., Chi, Y., Jones, J. T., & Li, H. (2018). A novel Meloidogyne incognita chorismate mutase effector suppresses plant immunity by manipulating the salicylic acid pathway and functions mainly during the early stages of nematode parasitism. Plant Pathology, 67(6), 1436–1448. Wang, Y., Huan, Q., Li, K., & Qian, W. (2021). Single-cell transcriptome atlas of the leaf and root of rice seedlings. Journal of Genetics and Genomics, 48(10), 881–898. Wang, Y., Kwon, S. J., Wu, J., Choi, J., Lee, Y. H., Agrawal, G. K., Tamogami, S., Rakwal, R., Park, S. R., Kim, B. G., Jung, K. H., Kang, K. Y., Kim, S. G., & Kim, S. T. (2014). Transcriptome analysis of early responsive genes in rice during Magnaporthe oryzae infection. Plant Pathology Journal, 30(4), 343–354. Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10(1), 57–63. Wani, S. H., Anand, S., Singh, B., Bohra, A., & Joshi, R. (2021). WRKY transcription factors and plant defense responses: latest discoveries and future prospects. Plant Cell Reports, 40(7), 1071–1085. Wan, J., Stacey, G., Stacey, M., & Zhang, X. (2013). LysM receptor-like kinases to improve plant defense response against fungal pathogens. United States. Weiberg, A., Wang, M., Lin, F.-M., Zhao, H., Zhang, Z., Kaloshian, I., Huang, H.-D., & Jin, H. (2013). Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science, 342(6154), 118–123. Wickham H. (2016). Elegant graphics for data analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, Https://Ggplot2.Tidyverse.Org. Williamson, B., Tudzynski, B., Tudzynski, P., & Van Kan, J. A. L. (2007). Botrytis cinerea: the cause of grey mould disease. Molecular Plant Pathology, 8(5), 561–580. Windram, O., Madhou, P., McHattie, S., Hill, C., Hickman, R., Cooke, E., Jenkins, D. J., Penfold, C. A., Baxter, L., Breeze, E., Kiddle, S. J., Rhodes, J., Atwell, S., Kliebenstein, D. J., Kim, Y., Stegle, O., Borgwardt, K., Zhang, C., Tabrett, A. Denby, K. J. (2012). Arabidopsis defense against Botrytis cinerea : chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. The Plant Cell, 24(9), 3530–3557. Wittkopp, P. J., & Kalay, G. (2012). Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nature Reviews Genetics, 13(1), 59–69. Wu, L., Zhang, X., Xu, B., Li, Y., Jia, L., Wang, R., Ren, X., Wang, G., & Xia, Q. (2018). Identification and expression analysis of EDR1 -like genes in tobacco (Nicotiana tabacum) in response to Golovinomyces orontii. PeerJ, 6, e5244. Wu, W., Wu, Y., Gao, Y., Li, M., Yin, H., Lv, M., Zhao, J., Li, J., & He, K. (2015). Somatic embryogenesis receptor-like kinase 5 in the ecotype Landsberg erecta of Arabidopsis is a functional RD LRR-RLK in regulating brassinosteroid signaling and cell death control. Frontiers in Plant Science, 6. Xiao, G., Zhang, Q., Zeng, X., Chen, X., Liu, S., & Han, Y. (2022). Deciphering the molecular signatures associated with resistance to Botrytis cinerea in strawberry flower by comparative and dynamic transcriptome analysis. Frontiers in Plant Science, 13. Xiao, S., Hu, Q., Shen, J., Liu, S., Yang, Z., Chen, K., Klosterman, S. J., Javornik, B., Zhang, X., & Zhu, L. (2021). GhMYB4 downregulates lignin biosynthesis and enhances cotton resistance to Verticillium dahliae. Plant Cell Reports, 40(4), 735–751. Xiong, J.-S., Zhu, H.-Y., Bai, Y.-B., Liu, H., & Cheng, Z.-M. (2018). RNA sequencing-based transcriptome analysis of mature strawberry fruit infected by necrotrophic fungal pathogen Botrytis cinerea. Physiological and Molecular Plant Pathology, 104, 77–85. Yadav, V., Wang, Z., Wei, C., Amo, A., Ahmed, B., Yang, X., & Zhang, X. (2020). Phenylpropanoid pathway engineering: an emerging approach towards plant defense. Pathogens, 9(4), 312. Yang, F., Abdelnabby, H., & Xiao, Y. (2015). The Zn(II)2Cys6 putative transcription factor is involved in the regulation of leucinostatin production and pathogenicity of the nematophagous fungus Paecilomyces lilacinus. Canadian Journal of Plant Pathology, 37(3), 342–352. Yang, H., Sun, Y., Wang, H., Zhao, T., Xu, X., Jiang, J., & Li, J. (2021). Genome-wide identification and functional analysis of the ERF2 gene family in response to disease resistance against Stemphylium lycopersici in tomato. BMC Plant Biology, 21(1), 72. Yang, Y., Saand, M. A., Huang, L., Abdelaal, W. B., Zhang, J., Wu, Y., Li, J., Sirohi, M. H., & Wang, F. (2021). Applications of multi-omics technologies for crop improvement. In Frontiers in Plant Science (Vol. 12). Frontiers Media S.A. Yang, Y., Yang, X., Dong, Y., & Qiu, D. (2018). The Botrytis cinerea xylanase BcXyl1 modulates plant immunity. Frontiers in Microbiology, 9. Yano, R., Ariizumi, T., Nonaka, S., Kawazu, Y., Zhong, S., Mueller, L., Giovannoni, J. J., Rose, J. K. C., & Ezura, H. (2020). Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. Communications Biology, 3(1). Yates, A. D., Allen, J., Amode, R. M., Azov, A. G., Barba, M., Becerra, A., Bhai, J., Campbell, L. I., Carbajo Martinez, M., Chakiachvili, M., Chougule, K., Christensen, M., Contreras-Moreira, B., Cuzick, A., Da Rin Fioretto, L., Davis, P., De Silva, N. H., Diamantakis, S., Dyer, S., … Flicek, P. (2022). Ensembl genomes 2022: An expanding genome resource for non-vertebrates. Nucleic Acids Research, 50(D1), D996–D1003. Yuan, X., Wang, H., Cai, J., Li, D., & Song, F. (2019). NAC transcription factors in plant immunity. Phytopathology Research, 1(1), 3. Zambounis, A., Ganopoulos, I., Valasiadis, D., Karapetsi, L., & Madesis, P. (2020). RNA sequencing-based transcriptome analysis of kiwifruit infected by Botrytis cinerea. Physiological and Molecular Plant Pathology, 111, 101514. Zang, Z., Lv, Y., Liu, S., Yang, W., Ci, J., Ren, X., Wang, Z., Wu, H., Ma, W., Jiang, L., & Yang, W. (2020). A novel ERF transcription factor, ZmERF105, positively regulates maize resistance to Exserohilum turcicum. Frontiers in Plant Science, 11. Zaynab, M., Fatima, M., Abbas, S., Sharif, Y., Umair, M., Zafar, M. H., & Bahadar, K. (2018). Role of secondary metabolites in plant defense against pathogens. Microbial Pathogenesis, 124, 198–202. Zhai, K., Liang, D., Li, H., Jiao, F., Yan, B., Liu, J., Lei, Z., Huang, L., Gong, X., Wang, X., Miao, J., Wang, Y., Liu, J.-Y., Zhang, L., Wang, E., Deng, Y., Wen, C.-K., Guo, H., Han, B., & He, Z. (2022). NLRs guard metabolism to coordinate pattern- and effector-triggered immunity. Nature, 601(7892), 245–251. Zhang, L., Zhang, F., Melotto, M., Yao, J., & He, S. Y. (2017). Jasmonate signaling and manipulation by pathogens and insects. Journal of Experimental Botany, erw478. Zhang, S., & Xu, J.-R. (2014). Effectors and Effector Delivery in Magnaporthe oryzae. PLoS Pathogens, 10(1), e1003826. Zhou, J., Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., & Troyanskaya, O. G. (2018). Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nature Genetics, 50(8), 1171–1179. Zhou, M., & Memelink, J. (2016). Jasmonate-responsive transcription factors regulating plant secondary metabolism. Biotechnology Advances, 34(4), 441–449. Zhou, P., Enders, T. A., Myers, Z. A., Magnusson, E., Crisp, P. A., Noshay, J. M., Gomez-Cano, F., Liang, Z., Grotewold, E., Greenham, K., & Springer, N. M. (2022). Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information. The Plant Cell, 34(1), 514–534. Zhu, G., Gao, C., Wu, C., Li, M., Xu, J. R., Liu, H., & Wang, Q. (2021). Comparative transcriptome analysis reveals distinct gene expression profiles in Brachypodium distachyon infected by two fungal pathogens. BMC Plant Biology, 21(1). | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/88733 | - |
| dc.description.abstract | 真菌病原体持续发展不同的策略来规避植物防御，以便攻击并进入宿主。灰葡萄孢 (Botrytis cinerea) 是番茄的一种毁灭性坏死营养型病原体。然而，之前的大多数研究只探索了有限的感染阶段，并且病原体末端的反应仍然很大程度上未经调查。因此，本研究旨在分析番茄叶片五个感染阶段的高质量病原体富集混合转录组。还进行了番茄和水稻之间的直系同源分析，以确定当宿主植物感染真菌病原体时保守和非保守的植物-宿主反应。结果，在感染后23小时、40小时和47小时（hpi）观察到与番茄病原体反应相关的几个差异表达基因（DEG）；发现了 144 个 DEG，其中 2.6% 在三个时间点上持续表达。虽然番茄 DEG 编码抗病蛋白、受体样激酶以及与茉莉酸 (JA) 和乙烯 (ET) 介导的反应相关的发病机制相关蛋白，但也表达了一些毒力和生长相关基因以及候选效应子灰霉病菌。有趣的是，这种真菌表达了一些与氧化还原反应和解毒有关的防御相关基因。因此，表明病原体反应并非完全被动，而是表现出主动防御策略，可能涉及宿主防御反应的调节或抵消效应子的分泌。此外，比较转录组分析显示，84%的直系同源DEG在番茄和水稻之间高度保守，其中10.23%显示出与病原体防御反应相关的功能重要性。此外，利用 1DCNN 模型和引导反向传播进行顺式调控元件富集和深度学习分析，确定 WRKY 和 ERF 是与番茄生物胁迫响应表达模式相关的相关调控基序。此外，对番茄和水稻转录起始位点（TSS）的大规模比较分析揭示了有趣的模式。发现基因表达水平与GC-skew和AT-skew呈正相关，表明TSS周围的核苷酸组成可能对基因表达产生影响。虽然这两个物种都表现出保守的调控元件，例如上游 TSS 中的 TATA 盒，但在下游区域观察到了变化。具体来说，水稻显示出番茄中不存在的 Y 补丁信号。这些发现表明下游转录调控中有专门的系统和独特的调控元件参与，有助于植物基因组中 TSS 的多样性。 | zh_TW |
| dc.description.abstract | Fungal pathogens persistently develop different strategies to circumvent plant defenses so that they can attack and enter their host. Botrytis cinerea is a devastating necrotrophic pathogen of tomato. However, most previous studies have explored limited infection stages, and the response at the pathogen end still remains largely uninvestigated. Therefore, this study aimed to analyze high-quality pathogen-enriched mixed-transcriptome at five infection stages of tomato leaves. Ortholog analysis between tomato and rice was also carried out to identify the conserved and non-conserved plant-host responses when host plants were infected with a fungal pathogen. As a result, several differentially expressed genes (DEGs) related to pathogen response in tomato were observed at 23, 40, and 47 hours post-infection (hpi); 144 DEG’s were found, and 2.6% were constantly expressed across three time points. While tomato DEGs encoding disease-resistance proteins, receptor-like kinases, and pathogenesis-related proteins associated to jasmonic acid (JA) and ethylene (ET)-mediated responses, some virulence- and growth-related genes as well as candidate effectors were expressed in B. cinerea. Interestingly, the fungus expressed some defense-related genes for redox reaction and detoxification. Thus, it is suggested that the pathogen response is not completely passive, but rather exhibits an active defense strategy, potentially involving modulation of host defense responses or secretion of counteracting effectors. In addition, comparative transcriptome analysis revealed that 84% of the orthologous DEGs were highly conserved between tomato and rice, and 10.23% of which showed functional importance related to pathogen defense response. Moreover, cis-regulatory elements enrichment and deep learning analysis with the 1DCNN model and guided-backpropagation identified WRKY and ERF as relevant regulatory motifs associated with biotic stress-responsive expression patterns in tomato. Furthermore, the large-scale comparative analysis of transcription start sites (TSS) in tomato and rice revealed intriguing patterns. A positive correlation was found between gene expression levels and both GC-skew and AT-skew, indicating that the nucleotide composition around the TSS may exert influence on gene expression. While both species exhibited conserved regulatory elements, such as the TATA box in the upstream TSS, variations were observed in the downstream regions. Specifically, rice displayed Y-patch signals that were absent in tomato. These findings suggest the involvement of specialized systems and distinct regulatory elements in the downstream transcriptional regulation, contributing to the diversity of TSS in plant genomes. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2023-08-15T17:33:54Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2023-08-15T17:33:54Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | Acknowledgments i
ABSTRACT ii Table of Contents iv List of Tables viii List of Figures viii Abbreviation xi Chapter 1. Introduction 1 Host-Pathogen Interactions 1 Tomato - Botrytis cinerea Interaction 3 Rice - Magnaporthe oryzae Interaction 5 Mixed transcriptome to study plant-pathogen interactions 9 Data analysis of mixed transcriptome 11 Transcription start sites analysis 12 Objectives of this study 15 Chapter 2. Materials and Methods 16 2.1 Mixed transcriptome data 16 2.2 RNA-Seq data analysis 16 2.2.1 Preprocessing of RNA-Seq data 16 2.2.2 RNA-Seq read mapping 17 2.2.3 Transcript assembly and quantify differentially expressed genes 18 2.3 Functional classification based on gene ontology and Mapman terms 19 2.4 KEGG pathway analysis 20 2.5 Comparative analysis based on orthology 20 2.6 Transcription start site analysis 21 2.6.1 Identification of transcription start sites and extraction of upstream and downstream regions 21 2.6.2 Calculation of GC and AT skew 21 2.6.3 Calculation of relative entropy 22 2.6.4 Motif enrichment analysis on the stress-responsive genes of tomato 22 2.6.5 1DCNN deep learning model to predict tomato defense response genes based on cis-regulatory motifs (CREs) 23 2.6.6 Identification of relevant CREs responsible for gene expression of stress-responsive genes in tomato 24 2.6.7 Statistical analysis 25 Chapter 3. Results 26 RNA-seq Analysis Pipeline 26 Quality assessment and mapping of tomato - B. cinerea mixed transcriptome 27 Overview of tomato expression patterns in response to B. cinerea infection 29 Functional annotations and classifications of differentially expressed genes (DEGs) in tomato infected with B. cinerea 31 Differential expression of PRRs and hormonal signaling pathways in response to B. cinerea infection in tomato 35 Transcriptional regulators involved in defense response of tomato 38 Defense response genes and secondary metabolites of tomato 40 Overview of B. cinerea DEGs during infection 43 Gene ontology and KEGG pathway enrichment in B. cinerea DEGs 45 Functional characterization of B. cinerea DEGs and prediction of candidate effectors during tomato infection 48 Re-analysis of rice and Magnaphore oryzae mixed transcriptome using HISAT2 pipeline 52 Comparative transcriptomics between two crop species during fungal infection 55 Transcription start site (TSS) analysis in the promoter regions of rice and tomato DEGs 63 Identification and functional analysis of enriched cis-regulatory elements (CRE) in tomato defense response genes to B. cinerea infection 66 Deep learning model for prediction of tomato stress responsive genes 69 Chapter 4. Discussion 72 Tomato showed a dynamic and complex transcriptional response to B. cinerea infection at different time points 72 Botrytis cinerea genes encoding virulence factors, cell wall degrading enzymes, and predicted effectors are induced during tomato infection 77 The comparative analysis of transcriptomes in tomato and rice infected with fungal pathogens unveiled shared as well as distinct pathogen responses in each species. 81 The transcription start sites (TSS) in tomato and rice exhibit diversification. 85 Regulatory motifs associated with defense response to fungal infection 88 Chapter 5. Conclusions and Perspectives 92 References 95 Supplementary Data 116 | - |
| dc.language.iso | en | - |
| dc.title | Comparative Analysis of Mixed-Transcriptomes between Tomato and Rice Infected with the Plant Pathogenic Fungi Botrytis cinerea and Magnaporthe oryzae | zh_TW |
| dc.title | Comparative Analysis of Mixed-Transcriptomes between Tomato and Rice Infected with the Plant Pathogenic Fungi Botrytis cinerea and Magnaporthe oryzae | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 111-2 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 鄭秋萍;花田 耕介 | zh_TW |
| dc.contributor.oralexamcommittee | CHIU-PING CHENG;Kousuke Hanada | en |
| dc.subject.keyword | 混合轉錄組,灰葡萄孢,植物-病原體相互作用,直系學,RNA測序,稻瘟病菌, | zh_TW |
| dc.subject.keyword | Mixed Transcriptome,Botrytis cinerea,Plant-Pathogen Interaction,Orthology,RNA-seq,Magnaporthe oryzae, | en |
| dc.relation.page | 119 | - |
| dc.identifier.doi | 10.6342/NTU202302136 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2023-08-09 | - |
| dc.contributor.author-college | 國際學院 | - |
| dc.contributor.author-dept | 全球農業科技與基因體科學碩士學位學程 | - |
| Appears in Collections: | 全球農業科技與基因體科學碩士學位學程 | |
Files in This Item:
| File | Size | Format | |
|---|---|---|---|
| ntu-111-2.pdf Access limited in NTU ip range | 4.69 MB | Adobe PDF | View/Open |
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.