Identification and Differential Analysis of Noncoding RNAs in Response to Drought in F.

Overview

Journal Front Plant Sci

Date 2022 Nov 28

PMID 36438105

Authors

Yang Yang

Yuanmeng Gao

Yiqian Li

Xueping Li

Affiliations

Soon will be listed here.

Abstract

The role of noncoding RNAs (ncRNAs) in plant resistance to abiotic stresses is increasingly being discovered. Drought stress is one of the most common stresses that affecting plant growth, and high intensity drought has a significant impact on the normal growth of plants. In this study, a high-throughput sequencing was performed on plant tissue samples of f. C. D. Chu et C. S. Chao by drought treatment for 0, 2, 4 and 6 days. The sequencing results were analysed bioinformatically. We detected 336,946 RNAs among all 12 samples, including 192,098 message RNAs (mRNAs), 142,761 long noncoding RNAs (lncRNAs), 1,670 circular RNAs (circRNAs), and 417 microRNAs (miRNAs). We detected 2,419 differentially expressed (DE) ncRNAs, including 213 DE circRNAs, 2,088 DE lncRNAs and 118 DE miRNAs. Then, we used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to functionally predict DE ncRNAs. The results showed that most DE ncRNAs are involved in the response to drought stress, mainly in biochemical reactions involved in some metabolites, as well as in organelle activities. In addition, we validated two random circRNAs and demonstrated their circularity. We also found a stable internal reference gene available for f. and validated the accuracy of this experiment by quantitative real-time polymerase chain reaction (qRT-PCR).

Citing Articles

Whole-Transcriptome Sequencing Reveals the Global Molecular Responses and NAC Transcription Factors Involved in Drought Stress in .

Zhang S, Han Y, Zeng Q, Wang C, Wang H, Zhang J Antioxidants (Basel). 2024; 13(1).

PMID: 38247518 PMC: 10812421. DOI: 10.3390/antiox13010094.

References

Andersen C, Jensen J, Orntoft T . Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004; 64(15):5245-50. DOI: 10.1158/0008-5472.CAN-04-0496. View

Kumar M, Patel M, Kumar N, Bajpai A, Siddique K . Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants. Int J Mol Sci. 2021; 22(17). PMC: 8431676. DOI: 10.3390/ijms22179108. View

Nakashima K, Yamaguchi-Shinozaki K, Shinozaki K . The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat. Front Plant Sci. 2014; 5:170. PMC: 4032904. DOI: 10.3389/fpls.2014.00170. View

Li C, Jiang D, Wollenweber B, Li Y, Dai T, Cao W . Waterlogging pretreatment during vegetative growth improves tolerance to waterlogging after anthesis in wheat. Plant Sci. 2011; 180(5):672-8. DOI: 10.1016/j.plantsci.2011.01.009. View

Mercer T, Dinger M, Mattick J . Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009; 10(3):155-9. DOI: 10.1038/nrg2521. View

Cheng Z, Hou D, Ge W, Li X, Xie L, Zheng H . Integrated mRNA, MicroRNA Transcriptome and Degradome Analyses Provide Insights into Stamen Development in Moso Bamboo. Plant Cell Physiol. 2019; 61(1):76-87. DOI: 10.1093/pcp/pcz179. View

Qin T, Zhao H, Cui P, Albesher N, Xiong L . A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance. Plant Physiol. 2017; 175(3):1321-1336. PMC: 5664461. DOI: 10.1104/pp.17.00574. View

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

Zhong S, Fei Z, Chen Y, Zheng Y, Huang M, Vrebalov J . Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol. 2013; 31(2):154-9. DOI: 10.1038/nbt.2462. View

10.

Mutum R, Kumar S, Balyan S, Kansal S, Mathur S, Raghuvanshi S . Identification of novel miRNAs from drought tolerant rice variety Nagina 22. Sci Rep. 2016; 6:30786. PMC: 4976344. DOI: 10.1038/srep30786. View

11.

Li Z, Tian P, Huang T, Huang J . Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants. Int J Mol Sci. 2021; 22(20). PMC: 8539900. DOI: 10.3390/ijms222011205. View

12.

Song L, Fang Y, Chen L, Wang J, Chen X . Role of non-coding RNAs in plant immunity. Plant Commun. 2021; 2(3):100180. PMC: 8132121. DOI: 10.1016/j.xplc.2021.100180. View

13.

Li J, Ma W, Zeng P, Wang J, Geng B, Yang J . LncTar: a tool for predicting the RNA targets of long noncoding RNAs. Brief Bioinform. 2014; 16(5):806-12. DOI: 10.1093/bib/bbu048. View

14.

Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L . Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. Plant J. 2017; 93(5):814-827. DOI: 10.1111/tpj.13804. View

15.

Wang L, Zhao H, Chen D, Li L, Sun H, Lou Y . Characterization and primary functional analysis of a bamboo NAC gene targeted by miR164b. Plant Cell Rep. 2016; 35(6):1371-83. DOI: 10.1007/s00299-016-1970-6. View

16.

Deng F, Zhang X, Wang W, Yuan R, Shen F . Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress. BMC Plant Biol. 2018; 18(1):23. PMC: 5785843. DOI: 10.1186/s12870-018-1238-0. View

17.

Jogawat A, Yadav B, Chhaya , Lakra N, Singh A, Narayan O . Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review. Physiol Plant. 2021; 172(2):1106-1132. DOI: 10.1111/ppl.13328. View

18.

Friedlander M, Mackowiak S, Li N, Chen W, Rajewsky N . miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2011; 40(1):37-52. PMC: 3245920. DOI: 10.1093/nar/gkr688. View

19.

Di C, Yuan J, Wu Y, Li J, Lin H, Hu L . Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J. 2014; 80(5):848-61. DOI: 10.1111/tpj.12679. View

20.

Ding Z, Wu C, Tie W, Yan Y, He G, Hu W . Strand-specific RNA-seq based identification and functional prediction of lncRNAs in response to melatonin and simulated drought stresses in cassava. Plant Physiol Biochem. 2019; 140:96-104. DOI: 10.1016/j.plaphy.2019.05.008. View