Agrawal GK, Rakwal R, Jwa N-S, Agrawal VP (2001) Signalling molecules and blast pathogen attack activates rice OsPR1a and OsPR1b genes: A model illustrating components participating during defence/stress response. Plant Physiology and Biochemistry 39:1095-1103
Baldrich P, San Segundo B (2016) MicroRNAs in rice innate immunity. Rice (N Y) 9:6
Bohman S, Wang M, Dixelius C (2002) Arabidopsis thaliana-derived resistance against Leptosphaeria maculans in a Brassica napus genomic background. Theor Appl Genet 105:498-504
Chen LL, Yang L (2015) Regulation of circRNA biogenesis. RNA Biol 12:381-388
Chu Q, Bai P, Zhu X, Zhang X, Mao L, Zhu QH, Fan L, Ye CY (2018) Characteristics of plant circular RNAs. Brief Bioinform 21:135-143
Cocquerelle C, Mascrez B, Hétuin D, Bailleul B (1993) Mis-splicing yields circular RNA molecules. Faseb j 7:155-160
Conn VM, Hugouvieux V, Nayak A, Conos SA, Capovilla G, Cildir G, Jourdain A, Tergaonkar V, Schmid M, Zubieta C, Conn SJ (2017) A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants 3:17053
Daudi A, Cheng Z, O'Brien JA, Mammarella N, Khan S, Ausubel FM, Bolwell GP (2012) The apoplastic oxidative burst peroxidase in Arabidopsis is a major component of pattern-triggered immunity. Plant Cell 24:275-287
Ebbesen KK, Kjems J, Hansen TB (2016) Circular RNAs: Identification, biogenesis and function. Biochim Biophys Acta 1859:163-168
Fan J, Quan W, Li GB, Hu XH, Wang Q, Wang H, Li XP, Luo X, Feng Q, Hu ZJ, Feng H, Pu M, Zhao JQ, Huang YY, Li Y, Zhang Y, Wang WM (2020) circRNAs are involved in the rice-Magnaporthe oryzae interaction. Plant Physiol 182:272-286
Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150-3152
Gao Y, Zhang J, Zhao F (2018) Circular RNA identification based on multiple seed matching. Brief Bioinform 19:803-810
Gao Y, Zhao F (2018) Computational strategies for exploring circular RNAs. Trends Genet 34:389-400
Gao Z, Li J, Luo M, Li H, Chen Q, Wang L, Song S, Zhao L, Xu W, Zhang C, Wang S, Ma C (2019) Characterization and cloning of grape circular RNAs identified the cold resistance-related Vv-circATS1. Plant Physiol 180:966-985
Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495:384-388
Hansen TB, Venø MT, Damgaard CK, Kjems J (2016) Comparison of circular RNA prediction tools. Nucleic Acids Res 44:e58
Hofius D, Li L, Hafrén A, Coll NS (2017) Autophagy as an emerging arena for plant-pathogen interactions. Curr Opin Plant Biol 38:117-123
Ivashuta S, Banks IR, Wiggins BE, Zhang Y, Ziegler TE, Roberts JK, Heck GR (2011) Regulation of gene expression in plants through miRNA inactivation. PLoS One 6:e21330
Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, Marzluff WF, Sharpless NE (2013) Circular RNAs are abundant, conserved, and associated with ALU repeats. Rna 19:141-157
Jia Y, Li C, Li Q, Liu P, Liu D, Liu Z, Wang Y, Jiang G, Zhai W (2020) Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice. Int J Mol Sci 21:785
Kangasjärvi S, Neukermans J, Li S, Aro EM, Noctor G (2012) Photosynthesis, photorespiration, and light signalling in defence responses. J Exp Bot 63:1619-1636
Kansal S, Mutum RD, Balyan SC, Arora MK, Singh AK, Mathur S, Raghuvanshi S (2015) Unique miRNome during anthesis in drought-tolerant indica rice var. Nagina 22. Planta 241:1543-1559
Kauffman H (1973) An improved technique for evaluat-ing resistance of rice varieties to Xanthomonas oryzae. Plant Dis. Rep 57:537-541
Kawano Y, Shimamoto K (2013) Early signaling network in rice PRR-mediated and R-mediated immunity. Curr Opin Plant Biol 16:496-504
Ke Y, Deng H, Wang S (2017) Advances in understanding broad-spectrum resistance to pathogens in rice. Plant J 90:738-748
Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) miRBase: from microRNA sequences to function. Nucleic Acids Research 47:D155-D162
Kristensen LS, Andersen MS, Stagsted LVW, Ebbesen KK, Hansen TB, Kjems J (2019) The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet 20:675-691
Kruszka K, Pieczynski M, Windels D, Bielewicz D, Jarmolowski A, Szweykowska-Kulinska Z, Vazquez F (2012) Role of microRNAs and other sRNAs of plants in their changing environments. J Plant Physiol 169:1664-1672
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754-1760
Li QF, Zhang YC, Chen YQ, Yu Y (2017) Circular RNAs roll into the regulatory network of plants. Biochem Biophys Res Commun 488:382-386
Li Y, Lu YG, Shi Y, Wu L, Xu YJ, Huang F, Guo XY, Zhang Y, Fan J, Zhao JQ, Zhang HY, Xu PZ, Zhou JM, Wu XJ, Wang PR, Wang WM (2014) Multiple rice microRNAs are involved in immunity against the blast fungus Magnaporthe oryzae. Plant Physiol 164:1077-1092
Litholdo CG, Jr., da Fonseca GC (2018) Circular RNAs and plant stress responses. Adv Exp Med Biol 1087:345-353
Lu T, Cui L, Zhou Y, Zhu C, Fan D, Gong H, Zhao Q, Zhou C, Zhao Y, Lu D, Luo J, Wang Y, Tian Q, Feng Q, Huang T, Han B (2015) Transcriptome-wide investigation of circular RNAs in rice. Rna 21:2076-2087
Lu X, Zhang J, Brown B, Li R, Rodríguez-Romero J, Berasategui A, Liu B, Xu M, Luo D, Pan Z, Baerson SR, Gershenzon J, Li Z, Sesma A, Yang B, Peters RJ (2018) Inferring roles in defense from metabolic allocation of rice diterpenoids. Plant Cell 30:1119-1131
Mammarella ND, Cheng Z, Fu ZQ, Daudi A, Bolwell GP, Dong X, Ausubel FM (2015) Apoplastic peroxidases are required for salicylic acid-mediated defense against Pseudomonas syringae. Phytochemistry 112:110-121
Mateo A, Mühlenbock P, Rustérucci C, Chang CC, Miszalski Z, Karpinska B, Parker JE, Mullineaux PM, Karpinski S (2004) LESION SIMULATING DISEASE 1 is required for acclimation to conditions that promote excess excitation energy. Plant Physiol 136:2818-2830
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333-338
Moffat AS (2001) Finding new ways to fight plant diseases. Science 292:2270-2273
Morris KV, Mattick JS (2014) The rise of regulatory RNA. Nat Rev Genet 15:423-437
Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136:629-641
Qu S, Yang X, Li X, Wang J, Gao Y, Shang R, Sun W, Dou K, Li H (2015) Circular RNA: a new star of noncoding RNAs. Cancer Lett 365:141-148
Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, Okunishi R, Fukuda S, Ru K, Frith MC, Gongora MM, Grimmond SM, Hume DA, Hayashizaki Y, Mattick JS (2006) Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res 16:11-19
Rojas CM, Senthil-Kumar M, Tzin V, Mysore K (2014) Regulation of primary plant metabolism during plant-pathogen interactions and its contribution to plant defense. Frontiers in plant science 5:17
Rojas CM, Senthil-Kumar M, Wang K, Ryu CM, Kaundal A, Mysore KS (2012) Glycolate oxidase modulates reactive oxygen species-mediated signal transduction during nonhost resistance in Nicotiana benthamiana and Arabidopsis. Plant Cell 24:336-352
Sablok G, Zhao H, Sun X (2016) Plant Circular RNAs (circRNAs): Transcriptional Regulation Beyond miRNAs in Plants. Mol Plant 9:192-194
Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7:e30733
Schäfer P, Hückelhoven R, Kogel KH (2004) The white barley mutant albostrians shows a supersusceptible but symptomless interaction phenotype with the hemibiotrophic fungus Bipolaris sorokiniana. Mol Plant Microbe Interact 17:366-373
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504
Sun X, Wang L, Ding J, Wang Y, Wang J, Zhang X, Che Y, Liu Z, Zhang X, Ye J, Wang J, Sablok G, Deng Z, Zhao H (2016) Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA. FEBS Lett 590:3510-3516
Tang B, Hao Z, Zhu Y, Zhang H, Li G (2018) Genome-wide identification and functional analysis of circRNAs in Zea mays. PLoS One 13:e0202375
Tong W, Yu J, Hou Y, Li F, Zhou Q, Wei C, Bennetzen JL (2018) Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis). Planta 248:1417-1429
Wang H, Jiao X, Kong X, Hamera S, Wu Y, Chen X, Fang R, Yan Y (2016) A signaling cascade from miR444 to RDR1 in rice antiviral RNA silencing pathway. Plant Physiol 170:2365-2377
Wang Y, Xiong Z, Li Q, Sun Y, Jin J, Chen H, Zou Y, Huang X, Ding Y (2019) Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition. BMC Plant Biol 19:340
Wang Z, Liu Y, Li D, Li L, Zhang Q, Wang S, Huang H (2017) Identification of circular RNAs in kiwifruit and their species-specific response to bacterial canker pathogen invasion. Front Plant Sci 8:413
Ye CY, Chen L, Liu C, Zhu QH, Fan L (2015) Widespread noncoding circular RNAs in plants. New Phytol 208:88-95
Yu G, Wang L-G, Han Y, He Q-Y (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. Omics: a journal of integrative biology 16:284-287
Yu Y, Zhou YF, Feng YZ, He H, Lian JP, Yang YW, Lei MQ, Zhang YC, Chen YQ (2020) Transcriptional landscape of pathogen-responsive lncRNAs in rice unveils the role of ALEX1 in jasmonate pathway and disease resistance. Plant Biotechnol J 18:679-690
Zeng Y, Du WW, Wu Y, Yang Z, Awan FM, Li X, Yang W, Zhang C, Yang Q, Yee A, Chen Y, Yang F, Sun H, Huang R, Yee AJ, Li RK, Wu Z, Backx PH, Yang BB (2017) A circular RNA binds to and activates AKT phosphorylation and nuclear localization reducing apoptosis and enhancing cardiac repair. Theranostics 7:3842-3855
Zhang H, Wang S (2013) Rice versus Xanthomonas oryzae pv. oryzae: a unique pathosystem. Curr Opin Plant Biol 16:188-195
Zhang J, Chen S, Yang J, Zhao F (2020a) Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun 11:90
Zhang J, Liu R, Zhu Y, Gong J, Yin S, Sun P, Feng H, Wang Q, Zhao S, Wang Z, Li G (2020b) Identification and characterization of circRNAs responsive to methyl jasmonate in Arabidopsis thaliana. Int J Mol Sci 21:792
Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L (2016) Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res 26:1277-1287
Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z (2010) PMRD: plant microRNA database. Nucleic Acids Research 38:D806-D813
Zhao T, Wang L, Li S, Xu M, Guan X, Zhou B (2017) Characterization of conserved circular RNA in polyploid Gossypium species and their ancestors. FEBS Lett 591:3660-3669
Zhao W, Cheng Y, Zhang C, You Q, Shen X, Guo W, Jiao Y (2017) Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean. Sci Rep 7:5636
Zhao W, Chu S, Jiao Y (2019) Present scenario of circular RNAs (circRNAs) in plants. Front Plant Sci 10:379
Zhou R, Xu L, Zhao L, Wang Y, Zhao T (2018) Genome-wide identification of circRNAs involved in tomato fruit coloration. Biochem Biophys Res Commun 499:466-469
Zhou R, Zhu Y, Zhao J, Fang Z, Wang S, Yin J, Chu Z, Ma D (2017) Transcriptome-wide identification and characterization of potato circular RNAs in response to Pectobacterium carotovorum subspecies brasiliense infection. Int J Mol Sci 19:71
Zhu YX, Jia JH, Yang L, Xia YC, Zhang HL, Jia JB, Zhou R, Nie PY, Yin JL, Ma DF, Liu LC (2019) Identification of cucumber circular RNAs responsive to salt stress. BMC Plant Biol 19:164
Zuo J, Wang Q, Zhu B, Luo Y, Gao L (2016) Deciphering the roles of circRNAs on chilling injury in tomato. Biochem Biophys Res Commun 479:132-138