Dataset Information

Genome-wide identification and characterization of long non-coding RNAs responsive to Dickeya zeae in rice.

ABSTRACT: Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses. However, it is unknown whether lncRNAs are involved in resistance responses between rice and Dickeya zeae, a bacterial agent causing rice foot rot disease. In this study, RNA-seq was performed to uncover the co-expression regulating networks mediated by D. zeae responsive lncRNAs and their candidate target genes. Of the 4709 lncRNAs identified, 2518 and 2191 were up- and down-regulated in response to D. zeae infection, respectively. Expression changes of 17 selected lncRNAs and their predicted targets with a potential role in defense response were investigated by qPCR. The expression levels of five lncRNAs were up-regulated while their cognate candidate target genes were down-regulated upon D. zeae infection. In addition, several lncRNAs were predicted to be target mimics of osa-miR396 and osa-miR156. These results suggest that lncRNAs might play a role in response to D. zeae infection by regulating the transcript levels of their targets and miRNAs in rice.

SUBMITTER: Li WQ

PROVIDER: S-EPMC9087051 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Genome-wide identification and characterization of long non-coding RNAs responsive to Dickeya zeae in rice.

Li Wen Qi WQ Jia Yu Lin YL Liu Feng Quan FQ Wang Fang Quan FQ Fan Fang Jun FJ Wang Jun J Zhu Jin Yan JY Xu Yang Y Zhong Wei Gong WG Yang Jie J

RSC advances 20181008 60

Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses. However, it is unknown whether lncRNAs are involved in resistance responses between rice and Dickeya zeae, a bacterial agent causing rice foot rot disease. In this study, RNA-seq was performed to uncover the co-expression regulating networks mediated by D. zeae responsive lncRNAs and their candidate target genes. Of t ...[more]

PMID: 35548658

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Project description:Key messageThis study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation-reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

Dataset Information

Genome-wide identification and characterization of long non-coding RNAs responsive to Dickeya zeae in rice.

Publications

Genome-wide identification and characterization of long non-coding RNAs responsive to <i>Dickeya zeae</i> in rice.

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