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. 2021 Apr 28;11(1):9211.
doi: 10.1038/s41598-021-88709-3.

Regulatory role of non-coding RNA in ginseng rusty root symptom tissue

Xingbo Bian  1   2 , Pengcheng Yu  2 , Ling Dong  1   2 , Yan Zhao  2 , He Yang  1   2 , Yongzhong Han  3 , Lianxue Zhang  4   5
Affiliations

Regulatory role of non-coding RNA in ginseng rusty root symptom tissue

Xingbo Bian et al. Sci Rep. .

Abstract

Ginseng rusty root symptom (GRS) is one of the primary diseases of ginseng. It leads to a severe decline in the quality of ginseng and significantly affects the ginseng industry. The regulatory mechanism of non-coding RNA (ncRNA) remains unclear in the course of disease. This study explored the long ncRNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) in GRS tissues and healthy ginseng (HG) tissues and performed functional enrichment analysis of the screened differentially expressed ncRNAs. Considering the predictive and regulatory effects of ncRNAs on mRNAs, we integrated ncRNA and mRNA data to analyze and construct relevant regulatory networks. A total of 17,645 lncRNAs, 245 circRNAs, and 299 miRNAs were obtained from HG and GRS samples, and the obtained ncRNAs were characterized, including the classification of lncRNAs, length and distribution of circRNA, and the length and family affiliations of miRNAs. In the analysis of differentially expressed ncRNA target genes, we found that lncRNAs may be involved in the homeostatic process of ginseng tissues and that lncRNAs, circRNAs, and miRNAs are involved in fatty acid-related regulation, suggesting that alterations in fatty acid-related pathways may play a key role in GRS. Besides, differentially expressed ncRNAs play an essential role in regulating transcriptional translation processes, primary metabolism such as starch and sucrose, and secondary metabolism such as alkaloids in ginseng tissues. Finally, we integrated the correlations between ncRNAs and mRNAs, constructed corresponding interaction networks, and identified ncRNAs that may play critical roles in GRS. These results provide a basis for revealing GRS's molecular mechanism and enrich our understanding of ncRNAs in ginseng.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Prediction results and characteristics of lncRNAs. (A) lncRNAs classification; (B) comparison of length, number of exons and open reading frame between novel lncRNAs and mRNAs. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 2
Figure 2
Identification results and characteristics of circRNA. (A) Length distribution of circRNAs; (B) circRNAs classification. Image generated with Microsoft Office Excel and R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 3
Figure 3
Identification results and characteristics of miRNA. (A) Statistics of length distribution of sRNA fragments obtained; (B) miRNA family statistics of miRNAs in ginseng tissue; (C) statistics of miRNA in ginseng tissue in other species. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 4
Figure 4
Expression profiling changes of ncRNAs in diseased tissues (the data used in heatmaps are Z-score of expressions). (A) Volcano plot indicating upregulated and downregulated; (B) heatmap of lncRNAs; (C) Volcano plot indicating upregulated and downregulated circRNAs; (D) heatmap of circRNAs; (E) Volcano plot indicating upregulated and downregulated miRNAs; (F) heatmap of miRNAs. GRS: ginseng rusty root symptom; HG healthy ginseng. Image generated with R 3.6.3 (https://www.R-project.org) pheatmap package (https://cran.r-project.org/web/packages/pheatmap/) and ggplot2 package (https://ggplot2.tidyverse.org).
Figure 5
Figure 5
Differentially expressed lncRNAs in ginseng tissues predicted the GO enrichment analysis of target genes according to the co-location. (A) The directed acyclic graph of the BP part; (B) the directed acyclic graph of the CC part; (C) the directed acyclic graph of the MF part; (D) statistical histogram. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 5
Figure 5
Differentially expressed lncRNAs in ginseng tissues predicted the GO enrichment analysis of target genes according to the co-location. (A) The directed acyclic graph of the BP part; (B) the directed acyclic graph of the CC part; (C) the directed acyclic graph of the MF part; (D) statistical histogram. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 6
Figure 6
Differentially expressed lncRNAs in ginseng tissues predicted the GO enrichment analysis of target genes according to the expression correlation. (A) The directed acyclic graph of the BP part; (B) the directed acyclic graph of the CC part; (C) the directed acyclic graph of the MF part; (D) statistical histogram. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 6
Figure 6
Differentially expressed lncRNAs in ginseng tissues predicted the GO enrichment analysis of target genes according to the expression correlation. (A) The directed acyclic graph of the BP part; (B) the directed acyclic graph of the CC part; (C) the directed acyclic graph of the MF part; (D) statistical histogram. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 7
Figure 7
Differentially expressed circRNAs in ginseng tissues predicted the GO enrichment analysis of target genes. (A) The directed acyclic graph of the BP part; (B) the directed acyclic graph of the CC part; (C) the directed acyclic graph of the MF part; (D) statistical histogram. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 7
Figure 7
Differentially expressed circRNAs in ginseng tissues predicted the GO enrichment analysis of target genes. (A) The directed acyclic graph of the BP part; (B) the directed acyclic graph of the CC part; (C) the directed acyclic graph of the MF part; (D) statistical histogram. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 8
Figure 8
Differentially expressed miRNAs in ginseng tissues predicted the GO enrichment analysis of target genes. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 8
Figure 8
Differentially expressed miRNAs in ginseng tissues predicted the GO enrichment analysis of target genes. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 9
Figure 9
Scatter plot of KEGG pathway enrichment results for differentially expressed ncRNAs target genes. (A) Co-location of lncRNA; (B) expression correlation of lncRNA; (C) circRNA; (D) miRNA. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org).
Figure 10
Figure 10
qRT-PCR validation of significant differentially expressed genes. (A) qRT-PCR, the data were presented as the mean ± SEM (n = 3); **p < 0.05; (B) RNA-seq. The figure was created by using GraphPad Prism 7 (https://www.graphpad.com/).
Figure 11
Figure 11
Association analysis of mRNA and ncRNA in the diseased tissues. (A) Venn diagram showing the overlap number of targeted mRNA of up regulated lncRNAs and differentially expressed mRNAs; (B) Venn diagram showing the overlap number of targeted mRNA of down regulated lncRNAs and differentially expressed mRNAs; (C) Interaction network of miRNA-mRNA in ginseng tissues. Image generated with R 3.6.3 (https://www.R-project.org) ggplot2 package (https://ggplot2.tidyverse.org) and network diagram made by Cytoscape sofware 3.8.2 (https://cytoscape.org/).
Figure 12
Figure 12
Interaction network of miRNA-lncRNA in ginseng tissues. Network diagram made by Cytoscape sofware 3.8.2 (https://cytoscape.org/).
Figure 13
Figure 13
Interaction network of lncRNA-miRNA-mRNA in ginseng tissues. Network diagram made by Cytoscape sofware 3.8.2 (https://cytoscape.org/).
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