Antony G, Zhou J, Huang S, Li T, Liu B, White F, Yang B. 2010. Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3. Plant Cell 22: 3864–3876.
Bi G, Su M, Li N, Liang Y, Dang S, Xu J, Hu M, Wang J, Zou M, Deng Y et al. 2021. The ZAR1 resistosome is a calcium-permeable channel triggering plant immune signaling. Cell 184: 3528–3541.
Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326: 1509–1512.
Chen L, Hamada S, Fujiwara M, Zhu T, Thao NP, Wong HL, Krishna P, Ueda T, Kaku H, Shibuya N et al. 2010. The Hop/Sti1-Hsp90 chaperone complex facilitates the maturation and transport of a PAMP receptor in rice innate immunity. Cell Host & Microbe 7: 185–196.
Dangl JL, Horvath DM, Staskawicz BJ. 2013. Pivoting the plant immune system from dissection to deployment. Science 341: 746–751.
Dou D, Zhou JM. 2012. Phytopathogen effectors subverting host immunity: different foes, similar battleground. Cell Host & Microbe 12: 484–495.
Hiei Y, Ohta S, Komari T, Kumashiro T. 1994. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. The Plant Journal 6: 271–282.
van der Hoorn RA, Kamoun S. 2008. From guard to decoy: a new model for perception of plant pathogen effectors. Plant Cell 20: 2009–2017.
Horsefield S, Burdett H, Zhang X, Manik MK, Shi Y, Chen J, Qi T, Gilley J, Lai JS, Rank MX et al. 2019. NAD+ cleavage activity by animal and plant TIR domains in cell death pathways. Science 365: 793–799.
Ishikawa K, Yamaguchi K, Sakamoto K, Yoshimura S, Inoue K, Tsuge S, Kojima C, Kawasaki T. 2014. Bacterial effector modulation of host E3 ligase activity suppresses PAMP-triggered immunity in rice. Nature Communications 5: 5430. Jacob P, Kim NH, Wu F, El-Kasmi F, Chi Y, Walton WG, Furzer OJ, Lietzan AD, Sunil S, Kempthorn K et al. 2021. Plant “helper” immune receptors are
Ca2+-permeable nonselective cation channels. Science 373: 420–425.
Ji C, Ji Z, Liu B, Cheng H, Liu B, Liu S, Yang B, Chen G. 2020. Xa1 allelic R genes activate rice blight resistance suppressed by interfering TAL effectors. Plant Communications 1: 100087.
Ji Z, Ji C, Liu B, Zou L, Chen G, Yang B. 2016. Interfering TAL effectors of Xanthomonas oryzae neutralize R-gene-mediated plant disease resistance. Nature Communications 7: 13435.
Jin Y, Pan W, Zheng X, Cheng X, Liu M, Ma H, Ge X. 2018. OsERF101, an ERF family transcription factor, regulates drought stress response in reproductive tissues. Plant Molecular Biology 98: 51–65.
Jones JD, Vance RE, Dangl JL. 2016. Intracellular innate immune surveillance devices in plants and animals. Science 354: aaf6395.
Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12: 357–360.
Liao Y, Smyth GK, Shi W. 2014. FEATURECOUNTS: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30: 923–930.
Lim C, Kang K, Shim Y, Sakuraba Y, An G, Paek NC. 2020. Rice ETHYLENE RESPONSE FACTOR 101 promotes leaf senescence through Jasmonic acid-ediated regulation of OsNAP and OsMYC2. Frontiers in Plant Science 11: 1096.
Lo CC, Chain PS. 2014. Rapid evaluation and quality control of next generation sequencing data with FAQCS. BMC Bioinformatics 15: 366.
Ma S, Lapin D, Liu L, Sun Y, Song W, Zhang X, Logemann E, Yu D, Wang J, Jirschitzka J et al. 2020. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science 370: eable3069.
Martin R, Qi T, Zhang H, Liu F, King M, Toth C, Nogales E, Staskawicz BJ. 2020. Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ. Science 370: eabd9993.
Mikami M, Toki S, Endo M. 2015. Comparison of CRISPR/Cas9 expression constructs for efficient targeted mutagenesis in rice. Plant Molecular Biology 88: 561–572.
Moscou MJ, Bogdanove AJ. 2009. A simple cipher governs DNA recognition by TAL effectors. Science 326: 1501.
Nakagawa T, Kurose T, Hino T, Tanaka K, Kawamukai M, Niwa Y, Toyooka K, Matsuoka K, Jinbo T, Kimura T. 2007. Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. Journal of Bioscience and Bioengineering 104: 34–41.
Naseem M, Kunz M, Dandekar T. 2017. Plant–pathogen maneuvering over apoplastic sugars. Trends in Plant Science 22: 740–743.
Ochiai H, Inoue Y, Takeya M, Sasaki A, Kaku H. 2005. Genome sequence of Xanthomonas oryzae pv oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. Japan Agricultural Research Quarterly 39: 275–287.
Ogawa T, Morinaka T, Fujii K, Kimura T. 1978. Inheritance of resistance of rice varieties Kogyoku and Java 14 to bacterial group V of Xanthomonas oryzae. Annals of the Phytopathological Society of Japan 44: 137–141.
Oliva R, Ji C, Atienza-Grande G, Huguet-Tapia JC, Perez-Quintero A, Li T, Eom JS, Li C, Nguyen H, Liu B et al. 2019. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nature Biotechnology 37: 1344– 1350.
Paulus JK, van der Hoorn RAL. 2018. Tricked or trapped-two decoy mechanisms in host–pathogen interactions. PLoS Pathogens 14: e1006761.
Read AC, Moscou MJ, Zimin AV, Pertea G, Meyer RS, Purugganan MD, Leach JE, Triplett LR, Salzberg SL, Bogdanove AJ. 2020. Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing. PLoS Genetics 16: e1008571.
Read AC, Rinaldi FC, Hutin M, He YQ, Triplett LR, Bogdanove AJ. 2016. Suppression of Xo1-mediated disease resistance in rice by a truncated, non- DNA-binding TAL effector of Xanthomonas oryzae. Frontiers in Plant Science 7: 1516.
Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T, Choi IR, Omura T, Kikuchi S. 2011. Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant and Cell Physiology 52: 344–360.
Sun J, Nishiyama T, Shimizu K, Kadota K. 2013. TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics 14: 219.
Taoka KI, Shimatani Z, Yamaguchi K, Ogawa M, Saitoh H, Ikeda Y, Akashi H, Terada R, Kawasaki T, Tsuji H. 2021. Novel assays to monitor gene expression and protein–protein interactions in rice using the bioluminescent protein, NanoLuc. Plant Biotechnology 38: 89–99.
Tian D, Wang J, Zeng X, Gu K, Qiu C, Yang X, Zhou Z, Goh M, Luo Y, Murata-Hori M et al. 2014. The rice TAL effector-dependent resistance protein XA10 triggers cell death and calcium depletion in the endoplasmic reticulum. Plant Cell 26: 497–515.
Uji Y, Taniguchi S, Tamaoki D, Shishido H, Akimitsu K, Gomi K. 2016. Overexpression of OsMYC2 results in the up-regulation of early JA-responsive genes and bacterial blight resistance in rice. Plant and Cell Physiology 57: 1814– 1827.
Wamaitha MJ, Yamamoto R, Wong HL, Kawasaki T, Kawano Y, Shimamoto
K. 2012. OsRap2.6 transcription factor contributes to rice innate immunity through its interaction with receptor for activated kinase-C 1 (RACK1). Rice 5: 35.
Wan L, Essuman K, Anderson RG, Sasaki Y, Monteiro F, Chung EH, Osborne Nishimura E, DiAntonio A, Milbrandt J, Dangl JL et al. 2019. TIR domains of plant immune receptors are NAD+-cleaving enzymes that promote cell death. Science 365: 799–803.
Wang J, Hu M, Wang J, Qi J, Han Z, Wang G, Qi Y, Wang HW, Zhou JM, Chai J. 2019. Reconstitution and structure of a plant NLR resistosome conferring immunity. Science 364: eaav5870.
Xie Z, Nolan TM, Jiang H, Yin Y. 2019. AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in Arabidopsis. Frontiers in Plant Science 10: 228.
Xu X, Xu Z, Ma W, Haq F, Li Y, Shah SMA, Zhu B, Zhu C, Zou L, Chen G. 2021. TALE-triggered and iTALE-suppressed Xa1 resistance to bacterial blight is independent of OsTFIIAc1 or OsTFIIAc5 in rice. Journal of Experimental Botany 72: 3249–3262.
Yamaguchi K, Yamada K, Ishikawa K, Yoshimura S, Hayashi N, Uchihashi K, Ishihama N, Kishi-Kaboshi M, Takahashi A, Tsuge S et al. 2013. A receptor- like cytoplasmic kinase targeted by a plant pathogen effector is directly phosphorylated by the chitin receptor and mediates rice immunity. Cell Host & Microbe 13: 347–357.
Yoshihisa A, Yoshimura S, Shimizu M, Yamaguchi K, Kawasaki T. 2021. Identification of TAL and iTAL effectors in the Japanese strain T7133 of Xanthomonas oryzae pv oryzae. Journal of General Plant Pathology 87: 354–360.
Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang ZX, Kono I, Kurata N, Yano M, Iwata N, Sasaki T. 1998. Expression of Xa1, a bacterial blight- resistance gene in rice, is induced by bacterial inoculation. Proceedings of the National Academy of Sciences, USA 95: 1663–1668.
Yu D, Song W, Tan EYJ, Liu L, Cao Y, Jirschitzka J, Li E, Logemann E, Xu C, Huang S et al. 2022. TIR domains of plant immune receptors are 2',3'-cAMP/ cGMP synthetases mediating cell death. Cell 185: 2370–2386.
Zhang B, Zhang H, Li F, Quyang Y, Yuan M, Li X, Xiao J, Wang S. 2020. Multiple alleles encoding atypical NLRs with unique central tandem repeats in rice confer resistance to Xanthomonas oryzae pv oryzae. Plant Communications 1: 100088.
Zuluaga P, Szurek B, Koebnik R, Kroj T, Morel JB. 2017. Effector mimics and integrated decoys, the never-ending arms race between Rice and Xanthomonas oryzae. Frontiers in Plant Science 8: 431.