LncRNA33732‐respiratory burst oxidase module associated with WRKY1 in tomato‐ <i>Phytophthora infestans</i> interactions

Cui, Jun; Jiang, Ning; Meng, Jun; Yang, Guanglei; Liu, Weiwei; Zhou, Xiaoxu; Ma, Ning; Hou, Xinxin; Luan, Yushi

doi:10.1111/tpj.14173

Cited by 124 publications

(78 citation statements)

References 89 publications

(101 reference statements)

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“…Thus, a gene suppression assay of MSTRG.139242.1 and TEA027212.1 (Ca 2+ -transporting ATPase 13) using AsODNs was conducted and suggested that lncRNA MSTRG.139242.1 may be regulated by its nearby coding gene, TEA027212.1. In a previous study, the tomato lncRNA lncRNA33732 activated by WRKY1 induces RBOH expression and conferred resistance to Phytophthora infestans infection (Cui et al, 2018). In this study, we can speculate that lncRNA MSTRG.139242.1 may interact with its nearby mRNA TEA027212.1 in response to salt stress.…”

Section: Discussionmentioning

confidence: 56%

“…Recent studies in plants have found that lncRNAs may co-express with nearby coding genes, thereby regulating the downstream targets of the coding genes and exerting biological functions (Cui et al, 2017(Cui et al, , 2018. Interestingly, in this study, 42 differentially expressed coding genes spaced less than 100 kb away from 35 DE-lncRNAs were identified ( Figure 6 and Supplementary Data Sheet S1: Table S3).…”

Section: Interactions Of De-lncrnas With Mrnasmentioning

confidence: 66%

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Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis

et al. 2020

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Tea plant (Camellia sinensis), an important economic crop, is seriously affected by various abiotic stresses, including salt stress, which severely diminishes its widespread planting. However, little is known about the roles of long non-coding RNAs (lncRNAs) in transcriptional regulation under salt stress. In this study, high-throughput sequencing of tea shoots under salt-stress and control conditions was performed. Through sequencing analysis, 16,452 unique lncRNAs were identified, including 172 differentially expressed lncRNAs (DE-lncRNAs). The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of their cis-and trans-target genes showed that these DE-lncRNAs play important roles in many pathways such as the galactinol synthase (GOLS), calcium signaling pathway, and interact with transcription factors (TFs) under salt stress. The data from the gene-specific antisense oligodeoxynucleotide-mediated reduction in the lncRNA MSTRG.139242.1 and its predicted interacting gene, TEA027212.1 (Ca 2+-ATPase 13), in tea leaves revealed that MSTRG.139242.1 may function in the response of tea plants to high salinity. In addition, 12 lncRNAs were predicted to be target mimics of 17 known mature miRNAs, such as miR156, that are related to the salt-stress response in C. sinensis. Our results provide new insights into lncRNAs as ubiquitous regulators in response to salt stress in tea plants.

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Section: Discussionmentioning

confidence: 56%

Section: Interactions Of De-lncrnas With Mrnasmentioning

confidence: 66%

Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis

et al. 2020

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“…Wang [41] reported the expression and evolution of lncRNAs in Solanaceae. Cui's [42] results provided insights into the WRKY1 − lncRNA33732 − RBOH module involved in the regulation of H 2 O 2 accumulation and resistance to pathogens in tomato. Wang [43] identified several lnRNAs that are involved in TYLCV infection by virus-induced gene silencing (VIGS) and genome-wide analysis.…”

Section: Introductionmentioning

confidence: 99%

LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network

Xue

Sun

et al. 2020

BMC Plant Biol

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Background: Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results: Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, 'LA1698' (cracking-resistant, CR) and 'LA2683' (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the 'hormone metabolic process', 'cell wall organization', 'oxidoreductase activity' and 'catalytic activity' categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 (Peroxide, POD), Solyc01g008710.3 (Mannan endo-1,4-beta-mannosidase, MAN), Solyc08g077910.3 (Expanded, EXP), Solyc09g075330.3 (Pectinesterase, PE), Solyc07g055990.3 (Xyloglucan endotransglucosylase-hydrolase 7, XTH7), Solyc12g011030.2 (Xyloglucan endotransglucosylase-hydrolase 9, XTH9), Solyc10g080210.2 (Polygalacturonase-2, PG2), Solyc08g081010.2 (Gamma-glutamylcysteine synthetase, gamma-GCS), Solyc09g008720.2 (Ethylene receptor, ER), Solyc11g042560.2 (Ethylene-responsive transcription factor 4, ERF4) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions:This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs (XLOC_ 16662 and XLOC_033910, etc.).

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“…LncRNAs can execute their biological functions in various ways, e.g., they can regulate the expression of genes either in cis-or trans-acting through sequence complementarity with DNAs or RNAs, epigenetic modification, and promoter activity regulation [1,4]. In cisregulation, a flowering time associated lncRNA (MAS) positively regulated the transcription of MAF4 by interacting with WDR5a, a key element of COMPASS-like complexes [5]; lncRNA33732, which was activated by WRKY1 and located 1.8 kb downstream of RBOH, prompted the transcription of RBOH to increase H 2 O 2 content in tomato defense responses [6]. In transregulation, nitrogen-responsive lncRNA TAS3 regulated the expression of NRT2.4 to affect root development under low-nitrogen condition [7].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed

Ding

et al. 2020

BMC Genomics

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Background: Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown. Results: In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the transacting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell-and cell wallrelated metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_ 00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interactions in the regulation of salt stress responses. Finally, a representative network of lncRNA-miRNA-mRNA was proposed and discussed to participate in duckweed salt stress via auxin signaling. Conclusions: This study is the first report on salt-responsive lncRNAs in duckweed, and the findings will provide a solid foundation for in-depth functional characterization of duckweed lncRNAs in response to salt stress.

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LncRNA33732‐respiratory burst oxidase module associated with WRKY1 in tomato‐ Phytophthora infestans interactions

Cited by 124 publications

References 89 publications

Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis

Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis

LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network

Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed

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