Abstract
Nutrient stress is the most important environmental stress that limits plant growth and development. Although recent evidence highlights the vital functions of long non-coding RNAs (lncRNA) in response to single nutrient stress in some model plants, a comprehensive investigation of the effect of lncRNAs in response to nutrient stress has not been performed in Arabidopsis thaliana. Here, we presented the identification and characterization of lncRNAs under seven nutrient stress conditions. The expression pattern analysis revealed that aberrant expression of lncRNAs is a stress-specific manner under nutrient stress conditions and that lncRNAs are more sensitive to nutrient stress than protein-coding genes (PCGs). Moreover, competing endogenous RNA (ceRNA) network and lncRNA-mRNA co-expression network (CEN) were constructed to explore the potential function of these lncRNAs under nutrient stress conditions. We further combined different expressed lncRNAs with ceRNA network and CEN to select key lncRNAs in response to nutrient stress. Together, our study provides important information for further insights into the role of lncRNAs in response to stress in plants.
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Acknowledgements
We are grateful to the other members of Ming Chen’s laboratory for helpful discussions and helpful comments. The authors are also grateful for the critical comments of anonymous reviewers.
Funding
This work was supported by the National Natural Sciences Foundation of China (No. 31771477).
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J.W. and Q.C. designed the study. W.W., Y.C., and Y. Z. collected the data and performed the analysis. J.W. drafted the manuscript. G.G. and M. C. completed the final version of the manuscript. All co-authors read and approved the final manuscript.
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Supporting Information
Supplementary Fig. S1
Heat map of differentially expressed lncRNAs fold change value pattern in different nutrient stress conditions. (PNG 2098 kb)
Supplementary Fig. S2
The ceRNA network under nutrient stress conditions. Blue nodes denote mRNAs, red nodes denote lncRNAs and orange nodes denote miRNAs that are represented as circles. (PNG 4901 kb)
Supplementary Fig. S3
Visualization of genome region for four isoforms of XLOC_014118. Blue bars refer to protein coding genes on the forward strand (Gene (+)) and reverse strand (Gene (-)). Red bars refer to lncRNA isoforms. Green bars refer to A. thaliana lncRNAs stored in NONCODE database. (PNG 2842 kb)
Supplementary Fig. S4
The DNA methylation pattern of XLOC_014118 and XLOC_001771. Red box presents the DNA methylation in 5kb upstream of TSS regions. (PNG 5069 kb)
ESM 1
Supplementary Table S1. The gff file of identified lncRNAs. Supplementary Table S2. Nutrient-responsive miRNAs in A. thaliana. Supplementary Table S3. List of 360 key lncRNAs in this study. (XLSX 282 kb)
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Wang, J., Chen, Q., Wu, W. et al. Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana. Funct Integr Genomics 21, 17–30 (2021). https://doi.org/10.1007/s10142-020-00758-5
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DOI: https://doi.org/10.1007/s10142-020-00758-5