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Hehong Zhang, Xiaoxiang Tan, Lulu Li, Yuqing He, G. Hong, Junmin Li, Lin Lin, Ye Cheng, Fei Yan, Jianping Chen, Zongtao Sun (2019)
Suppression of auxin signalling promotes rice susceptibility to Rice black streaked dwarf virus infectionMolecular Plant Pathology, 20
Aiqin Li, Guanghui Li, Yuhan Zhao, Zhaodong Meng, Meng Zhao, Changsheng Li, Ye Zhang, Pengcheng Li, Chang-Le Ma, H. Xia, Shuzhen Zhao, L. Hou, Chuanzhi Zhao, Xingjun Wang (2018)
Combined small RNA and gene expression analysis revealed roles of miRNAs in maize response to rice black-streaked dwarf virus infectionScientific Reports, 8
Qianhao Zhu, S. Stephen, Jennifer Taylor, C. Helliwell, Ming-Bo Wang (2014)
Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana.The New phytologist, 201 2
J. Cui, Yushi Luan, Ning Jiang, Hang Bao, Jun Meng (2017)
Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co‐expressing glutaredoxinThe Plant Journal, 89
H. Rahim, M. Bhuiyan, L. Lim, K. Sabu, A. Saad, M. Azhar, R. Wickneswari (2012)
Identification of quantitative trait loci for blast resistance in BC₂F₃ and BC₂F5 advanced backcross families of rice.Genetics and molecular research : GMR, 11 3
Zhao-hui Wang, S. Fang, Zhi-yan Zhang, Cheng-gui Han, Da-wei Li, Jialin Yu (2006)
Development of an ID-ELISA for the detection of Rice black-streaked dwarf virus in plants.Journal of virological methods, 134 1-2
Xi Huang, Jiejie Feng, Rui Wang, Hongsheng Zhang, Ji Huang (2018)
Comparative analysis of microRNAs and their targets in the roots of two cultivars with contrasting salt tolerance in rice (Oryza sativa L.)Plant Growth Regulation, 87
Rémi Peyraud, Ullrich Dubiella, Adelin Barbacci, S. Genin, S. Raffaele, D. Roby (2017)
Advances on plant–pathogen interactions from molecular toward systems biology perspectivesThe Plant Journal, 90
V. Huynh-Thu, P. Geurts (2018)
dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression dataScientific Reports, 8
Robert Patro, Geet Duggal, M. Love, R. Irizarry, Carl Kingsford (2017)
Salmon: fast and bias-aware quantification of transcript expression using dual-phase inferenceNature methods, 14
Pingchuan Deng, Shu Liu, Xiaojun Nie, S. Weining, Liang Wu (2018)
Conservation analysis of long non-coding RNAs in plantsScience China Life Sciences, 61
Xinyue Zhao, Jingrui Li, B. Lian, Hanqing Gu, Yan Li, Y. Qi (2018)
Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNANature Communications, 9
Binghua Chen, Lin Lin, Yuwen Lu, Jiejun Peng, Hongying Zheng, Qiankun Yang, Shaofei Rao, Guanwei Wu, Junmin Li, Zhuo Chen, Baoan Song, Jianping Chen, Fei Yan (2020)
Ubiquitin-Like protein 5 interacts with the silencing suppressor p3 of rice stripe virus and mediates its degradation through the 26S proteasome pathwayPLoS Pathogens, 16
M. Wheeler (1996)
Measuring mercury.Environmental Health Perspectives, 104
Mengdi Li, Aqin Cao, Ruihua Wang, Zeyu Li, Shaoqing Li, Jianbo Wang (2020)
Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)BMC Plant Biology, 20
F. Bai, Qu Zc, J. Yan, Hongwei Zhang, J. Xu, Ye Mm, Wu Hl, Liao Xg, Shen Dl (2001)
Identification of rice black streaked dwarf virus in different cereal crops with dwarfing symptoms in China.Acta virologica, 45 5-6
Guojie Zhang, Guangwu Guo, Xueda Hu, Yong Zhang, Qiye Li, Ruiqiang Li, Ruhong Zhuang, Zhike Lu, Zengquan He, X. Fang, Li Chen, W. Tian, Y. Tao, K. Kristiansen, Xiuqing Zhang, Songgang Li, Huanming Yang, J. Wang, Jun Wang (2010)
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.Genome research, 20 5
Xiaobo Zhao, Liming Gan, Caixia Yan, Chunjuan Li, Quanxi Sun, Juan Wang, C. Yuan, Hao Zhang, S. Shan, Jian Liu (2019)
Genome-Wide Identification and Characterization of Long Non-Coding RNAs in PeanutGenes, 10
Tianzuo Wang, Min Liu, Mingui Zhao, Rujin Chen, Wen‐Hao Zhang (2015)
Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencingBMC Plant Biology, 15
Wei Wu, Haoqiu Liu, Yan Dong, Yun Zhang, Sek-Man Wong, Changchun Wang, Yi-jun Zhou, Qiufang Xu (2019)
Determination of Suitable RT-qPCR Reference Genes for Studies of Gene Functions in Laodelphax striatellus (Fallén)Genes, 10
Lanlan Wang, Jingjing Jin, Lihua Li, Shaohong Qu (2020)
Long Non-coding RNAs Responsive to Blast Fungus Infection in RiceRice, 13
Shouli Feng, Min Xu, Fujie Liu, Changjiang Cui, Baoliang Zhou (2019)
Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australeBMC Plant Biology, 19
Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang, Ming Chen (2018)
Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf developmentBMC Genomics, 19
S. Fang, J. Yu, J. Feng, C. Han, D. Li, Y. Liu (2001)
Identification of rice black-streaked dwarf fijivirus in maize with rough dwarf disease in ChinaArchives of Virology, 146
Bingbing Xu, Y. Meng, Yongfeng Jin (2020)
RNA structures in alternative splicing and back‐splicingWiley Interdisciplinary Reviews: RNA, 12
Jianmin Zhang, Zhen Yang, Pei Feng, Xiao Zhong, Q. Ma, Q. Su, Xiangping Wang, Chuanren Li, Yazhen Yang (2019)
Identification and the potential roles of long non-coding RNAs in cotton leaves damaged by Aphis gossypiiPlant Growth Regulation, 88
E. Shikata, Yoshichika Kitagawa (1977)
Rice black-streaked dwarf virus: its properties, morphology and intracellular localization.Virology, 77 2
Y. Kawahara, M. Bastide, J. Hamilton, H. Kanamori, W. McCombie, Ouyang Shu, D. Schwartz, Tsuyoshi Tanaka, Jianzhon Wu, Shiguo Zhou, K. Childs, R. Davidson, Haining Lin, Haining Lin, L. Quesada-Ocampo, Brieanne Vaillancourt, H. Sakai, S. Lee, Jungsok Kim, H. Numa, T. Itoh, C. Buell, T. Matsumoto (2013)
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map dataRice, 6
Jun-Bo Luan, Fei Wang, Yujie Li, Bin Zhang, Juren Zhang (2012)
Mapping quantitative trait loci conferring resistance to rice black-streaked virus in maize (Zea mays L.)Theoretical and Applied Genetics, 125
X. Mao, Tao Cai, John Olyarchuk, Liping Wei (2005)
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabularyBioinformatics, 21 19
T. Zhou, L. Du, Lijiao Wang, Ying Wang, Cunyi Gao, Y. Lan, Feng Sun, Yongjian Fan, Guoliang Wang, Yi-jun Zhou (2015)
Genetic analysis and molecular mapping of QTLs for resistance to rice black-streaked dwarf disease in riceScientific Reports, 5
S Foissac (2007)
297Nucleic Acids Res, 35
Matthias Berens, Hannah Berry, A. Mine, Cristiana Argueso, K. Tsuda (2017)
Evolution of Hormone Signaling Networks in Plant Defense.Annual review of phytopathology, 55
Tao Qin, Huayan Zhao, P. Cui, Nour Albesher, L. Xiong (2017)
A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance[OPEN]Plant Physiology, 175
Tong Yu, David Tzeng, Ran Li, Jian-ye Chen, S. Zhong, D. Fu, B. Zhu, Yunbo Luo, Hongliang Zhu (2018)
Genome-wide identification of long non-coding RNA targets of the tomato MADS box transcription factor RIN and function analysisAnnals of Botany, 123
M. Perțea, Daehwan Kim, G. Pertea, J. Leek, S. Salzberg (2016)
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and BallgownNature Protocols, 11
Yang Yu, Yan-Fei Zhou, Yan-Zhao Feng, Huang He, Jian-Ping Lian, Yu-Wei Yang, Meng-Qi Lei, Yu-Chan Zhang, Yue‐Qin Chen (2019)
Transcriptional landscape of pathogen‐responsive lncRNAs in rice unveils the role of ALEX1 in jasmonate pathway and disease resistancePlant Biotechnology Journal, 18
Kaili Xie, Lulu Li, Hehong Zhang, Rong Wang, Xiaoxiang Tan, Yuqing He, G. Hong, Junmin Li, F. Ming, Xuefeng Yao, Fei Yan, Zongtao Sun, Jianping Chen (2018)
Abscisic acid negatively modulates plant defence against rice black-streaked dwarf virus infection by suppressing the jasmonate pathway and regulating reactive oxygen species levels in rice.Plant, cell & environment, 41 10
Rajiv Parvathaneni, Edoardo Bertolini, M. Shamimuzzaman, Daniel Vera, Pei-Yau Lung, Brian Rice, Jinfeng Zhang, P. Brown, A. Lipka, H. Bass, A. Eveland (2019)
The regulatory landscape of early maize inflorescence developmentGenome Biology, 21
Julia Chekanova (2015)
Long non-coding RNAs and their functions in plants.Current opinion in plant biology, 27
Zhiyang Liu, Xuejuan Li, Feng Sun, T. Zhou, Yi-jun Zhou (2017)
Overexpression of OsCIPK30 Enhances Plant Tolerance to Rice stripe virusFrontiers in Microbiology, 8
D. Riaño-Pachón, S. Ruzicic, I. Dreyer, B. Mueller‐Roeber (2007)
PlnTFDB: an integrative plant transcription factor databaseBMC Bioinformatics, 8
Jianchao Ma, Xiaotao Bai, Wenchun Luo, Yannan Feng, Xuemin Shao, Qiuxian Bai, Shujiao Sun, Qiming Long, Dongshi Wan (2019)
Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related PoplarsFrontiers in Genetics, 10
Ying Wang, Xiaojin Luo, Fan Sun, Jianhua Hu, X. Zha, W. Su, Jinshui Yang (2018)
Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in riceNature Communications, 9
Jian-xiang Wu, Yuequn Ni, Huan‐Wun Liu, Li-xia Rao, Yi-jun Zhou, Xue-ping Zhou (2013)
Development and use of three monoclonal antibodies for the detection of rice black-streaked dwarf virus in field plants and planthopper vectorsVirology Journal, 10
Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shuqi Zhao, Liping Wei, Ge Gao (2007)
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machineNucleic Acids Research, 35
G. Pertea, M. Perțea (2020)
GFF Utilities: GffRead and GffCompareF1000Research, 9
Valentin Wucher, F. Legeai, B. Hédan, Guillaume Rizk, L. Lagoutte, T. Leeb, V. Jagannathan, É. Cadieu, Audrey David, H. Lohi, S. Cirera, M. Fredholm, Nadine Botherel, P. Leegwater, C. Béguec, H. Fieten, Jeremy Johnson, Jessica Alföldi, C. André, K. Lindblad-Toh, C. Hitte, T. Derrien (2017)
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptomeNucleic Acids Research, 45
Paul Shannon, Andrew Markiel, Owen Ozier, N. Baliga, Jonathan Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, T. Ideker (2003)
Cytoscape: a software environment for integrated models of biomolecular interaction networks.Genome research, 13 11
Eun-Deok Kim, Yuqing Xiong, B. Kang, Sibum Sung (2019)
Identification of Long Noncoding RNAs in the Developing Endosperm of Maize.Methods in molecular biology, 1933
Chaozheng Zhang, Yueyong Liu, Liyue Liu, Z. Lou, Hongyan Zhang, H. Miao, Xuebo Hu, Ya-min Pang, B. Qiu (2008)
Rice black streaked dwarf virus P 9-1 , an a-helical protein , self-interacts and forms viroplasms in vivo
Jingjing Wang, Qi Chen, Wenyi Wu, Yujie Chen, Yincong Zhou, Guoji Guo, Ming Chen (2020)
Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thalianaFunctional & Integrative Genomics, 21
MI Love (2014)
550Genome Biol, 15
JH Zhang, Y Dong, W Wu, DS Yi, M Wang, HT Wang, QF Xu (2020)
Comprehensive identification and characterization of long non-coding RNAs associated with rice black-streaked dwarf virus infection in Laodelphax striatellus (Fallén) midgutFront Physiol, 11
Tianze Zhang, Qian Liang, Chenyang Li, Shuai Fu, J. Kundu, Xue-ping Zhou, Jian-xiang Wu (2020)
Transcriptome Analysis of Rice Reveals the lncRNA–mRNA Regulatory Network in Response to Rice Black-Streaked Dwarf Virus InfectionViruses, 12
Lin Zhang, Maojun Wang, Nannan Li, Honglei Wang, P. Qiu, Liuling Pei, Zheng Xu, Tianyi Wang, Erlin Gao, Junxia Liu, Shiming Liu, Qin Hu, Y. Miao, K. Lindsey, Lili Tu, Longfu Zhu, Xianlong Zhang (2017)
Long noncoding RNAs involve in resistance to Verticillium dahliae, a fungal disease in cottonPlant Biotechnology Journal, 16
Tianzuo Wang, Mingui Zhao, Xiuxiu Zhang, Min Liu, C. Yang, Yuhui Chen, Rujin Chen, J. Wen, K. Mysore, Wen‐Hao Zhang (2017)
Novel phosphate deficiency-responsive long non-coding RNAs in the legume model plant Medicago truncatulaJournal of Experimental Botany, 68
Daehwan Kim, Ben Langmead, S. Salzberg (2015)
HISAT: a fast spliced aligner with low memory requirementsNature Methods, 12
Yanting Shen, Zhengkui Zhou, Zheng Wang, Weiyu Li, Chao Fang, Mian Wu, Yanming Ma, Tengfei Liu, Lingping Kong, D. Peng, Zhixi Tian (2014)
Global Dissection of Alternative Splicing in Paleopolyploid Soybean[W]Plant Cell, 26
Yu-Chan Zhang, Jian-You Liao, Ze-Yuan Li, Yang Yu, Jin-Ping Zhang, Quan-Feng Li, L. Qu, W. Shu, Yue‐Qin Chen (2014)
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of riceGenome Biology, 15
(2016)
F1000Research. https:// doi
S. Üstün, Arsheed Sheikh, Selena Gimenez-Ibanez, Alexandra Jones, V. Ntoukakis, F. Börnke (2016)
The Proteasome Acts as a Hub for Plant Immunity and Is Targeted by Pseudomonas Type III Effectors1[OPEN]Plant Physiology, 172
Hu Xiaoqing, Li Dandan, Wu Juan (2015)
[Long non-coding RNAs in plants].Yi chuan = Hereditas, 37 4
Anthony Bolger, M. Lohse, B. Usadel (2014)
Trimmomatic: a flexible trimmer for Illumina sequence dataBioinformatics, 30
E. Boutet, D. Lieberherr, M. Tognolli, Michel Schneider, A. Bairoch (2007)
UniProtKB/Swiss-Prot.Methods in molecular biology, 406
Yingbo Liang, Ze Li, Yi Zhang, Fanlu Meng, D. Qiu, H. Zeng, Guangyue Li, Xiufen Yang (2020)
Nbnrp1 Mediates Verticillium dahliae Effector PevD1-Triggered Defense Responses by Regulating Sesquiterpenoid Phytoalexins Biosynthesis Pathway in Nicotiana benthamiana.Gene
Jianhua Zhang, Yan Dong, Wei Wu, Dianshan Yi, Man Wang, Haitao Wang, Qiu-fang Xu (2020)
Comprehensive Identification and Characterization of Long Non-coding RNAs Associated With Rice Black-Streaked Dwarf Virus Infection in Laodelphax striatellus (Fallén) MidgutFrontiers in Physiology, 11
Haiying Tian, F. Guo, Zhimeng Zhang, H. Ding, J. Meng, Xinguo Li, Zhenying Peng, S. Wan (2020)
Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.BMC Plant Biology, 20
Chengjie Chen, Hao Chen, Yi Zhang, Hannah Thomas, Margaret Frank, Yehua He, Rui Xia (2020)
TBtools - an integrative toolkit developed for interactive analyses of big biological data.Molecular plant
R. Ramírez-González, P. Borrill, D. Lang, S. Harrington, J. Brinton, Luca Venturini, M. Davey, J. Jacobs, F. Ex, A. Pasha, Y. Khedikar, S. Robinson, A. Cory, T. Florio, L. Concia, C. Juery, H. Schoonbeek, B. Steuernagel, D. Xiang, C. Ridout, B. Chalhoub, K. Mayer, M. Benhamed, D. Latrasse, A. Bendahmane, B. Wulff, R. Appels, V. Tiwari, R. Datla, F. Choulet, C. Pozniak, N. Provart, A. Sharpe, E. Paux, M. Spannagl, A. Bräutigam, C. Uauy (2018)
The transcriptional landscape of polyploid wheatScience, 361
Bin Zhu, Manyu Xu, Haiyan Shi, Xiwu Gao, P. Liang (2017)
Genome-wide identification of lncRNAs associated with chlorantraniliprole resistance in diamondback moth Plutella xylostella (L.)BMC Genomics, 18
Thomas Chaloner, J. Kan, R. Grant-Downton (2016)
RNA 'Information Warfare' in Pathogenic and Mutualistic Interactions.Trends in plant science, 21 9
Yamile Marquez, John Brown, C. Simpson, A. Barta, M. Kalyna (2012)
Transcriptome survey reveals increased complexity of the alternative splicing landscape in ArabidopsisGenome Research, 22
D. Pastrana, W. Vass, D. Lowy, J. Schiller (2001)
NHPV16 VLP vaccine induces human antibodies that neutralize divergent variants of HPV16.Virology, 279 1
J. Cui, Ning Jiang, Xinxin Hou, Sihan Wu, Qiang Zhang, Jun Meng, Yushi Luan (2020)
Genome-wide Identification of LncRNAs and Analysis of CeRNA Networks during Tomato Resistance to Phytophthora infestans.Phytopathology
I. Ulitsky (2016)
Evolution to the rescue: using comparative genomics to understand long non-coding RNAsNature Reviews Genetics, 17
Mingxia Ran, Yuan Li, Yan Zhang, Kai Liang, Ying-Nan Ren, Ming Zhang, G. Zhou, Yingmin Zhou, K. Wu, Chengdong Wang, Y. Huang, B. Luo, I. Qazi, He-min Zhang, C. Zeng (2018)
Transcriptome Sequencing Reveals the Differentially Expressed lncRNAs and mRNAs Involved in Cryoinjuries in Frozen-Thawed Giant Panda (Ailuropoda melanoleuca) SpermInternational Journal of Molecular Sciences, 19
V. Tran, S. Moretti, A. Coste, Sara Amorim-Vaz, D. Sanglard, M. Pagni (2017)
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysisBioinformatics, 35
Xi Sun, Hong-xiang Zheng, N. Sui (2018)
Regulation mechanism of long non-coding RNA in plant response to stress.Biochemical and biophysical research communications, 503 2
Mingming Xin, Yu Wang, Yingyin Yao, Na Song, Zhaorong Hu, D. Qin, C. Xie, Huiru Peng, Z. Ni, Qixin Sun (2011)
Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencingBMC Plant Biology, 11
(2020)
2020b) Long non-coding RNAs
Long non-coding RNAs (lncRNAs) produced by the plant genome are essential regulators of diverse biological processes. Despite increasing knowledge on the role of lncRNAs in plant development, their action in response to plant disease, especially in rice, is poorly understood. In this study, the comprehensive disease-responding lncRNA profile in rice response to rice black-streaked dwarf virus (RBSDV) and rice stripe virus (RSV) was investigated for the first time. Transcriptomic analysis of rice leaves infected with these two pathogens had identified 1925 lncRNAs, of which 724 were derived from alternative splicing (AS) events. Differentially expression analysis identified 344 and 176 differentially expression lncRNAs (DELs) in RBSDV vs CK and RSV vs CK, respectively. The targets of these DELs mainly associated with multiple immune-related pathways, such as “plant hormone signal transduction,” and “phenylpropanoid biosynthesis”, and ‘plant-pathogen interaction’. For further analyzing the regulatory relationship among transcription factors, lncRNAs, and mRNAs, the gene regulatory network was constructed by performing GENIE3. Finally, a total of 2484 TF-lncRNA-target pairs, including 60 TFs (as regulatory factors), 21 lncRNAs regulated by TFs and targeting mRNAs (as regulatory factors and targets), and 1064 mRNAs (as targets) were obtained, and all transcripts from TF-lncRNA-target pairs were up-regulated in both comparisons. In these transcripts, each lncRNA regulated by corresponding TF can regulate the TF-targeted mRNA, suggesting that TF may regulate the mRNA via the corresponding lncRNA. This study identified lncRNAs related to multiple viruses infection in rice, which provides another layer of candidates that regulate rice and virus interactions.
Plant Growth Regulation – Springer Journals
Published: Sep 1, 2022
Keywords: Long non-coding RNAs; Rice black-streaked dwarf virus; Rice stripe virus; Alternative splicing; Transcription factor
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