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. 2023 Dec 18:11:e16658.
doi: 10.7717/peerj.16658. eCollection 2023.

Integrated transcriptome and metabolome revealed the drought responsive metabolic pathways in Oriental Lily (Lilium L.)

Zhenkui Cui  1 , Huaming Huang  1 , Tianqing Du  2 , Jianfeng Chen  1 , Shuyan Huang  1 , Qushun Dai  1
Affiliations

Integrated transcriptome and metabolome revealed the drought responsive metabolic pathways in Oriental Lily (Lilium L.)

Zhenkui Cui et al. PeerJ. .

Abstract

Objective: Lily is an essential ornamental flowering species worldwide. Drought stress is a major constraint affecting the morphology and physiology and lily leaves and flowers. Therefore, understanding the molecular mechanism underlying lily response to drought stress is important.

Method: Transcriptome and metabolome analysis were performed on Oriental Lily subjected to drought stress.

Result: Most transcription factors and metabolites yielded by the conjoint analysis displayed a downregulated expression pattern. Differential genes and metabolites mainly co-enriched in glycolic pathways related to sugars, such as galactose, and sucrose, glycolysis and gluconeogenesis, indicating that drought stress reduced the sugar metabolism level of Oriental Lily. Combined with transcriptome and metabolome data, nine pairs of differentially expressed metabolites and the genes (p < 0.05) were obtained. Interestingly, a gene named TRINITY_DN2608 (encoding a type of alpha-D-glucose) cloned and its overexpression lines in Arabidopsis thaliana was generated. Overexpression of TRINITY_DN2608 gene elevated the susceptibility to drought stress possibly by suppressing the glucose level.

Conclusion: The enrichment of sugar-related pathways advocates the potential role of glucose metabolism in drought stress. Our study provides theoretical information related to the glucose-mediated drought response and would be fruitful in future lily breeding programs.

Keywords: Drought; Lily; Metabolome; TRINITY_DN2608 gene; Transcriptome.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Phenotypic analysis of lily under drought stress.
(A) Represents the phenotype of lily under normal, (B) after drought stress, (C) leaf length before and after drought stress, (D) leaf width before and after drought stress, (E) ratio of length/width of lily before and after drought stress, (F) area of lily leaves before and after drought stress, (G) 100x mirror leaf anatomical structure under normal, (H) 100x mirror leaf anatomical structure after drought stress, (I) 200x mirror leaf anatomical structure under normal, (J) 200x mirror leaf anatomical structure after drought stress. The asterisk (*) in the figure is on the normal plant line, indicating a significant difference at the 0.01 level.
Figure 2
Figure 2. Metabolomic analysis of Oriental Lily under drought stress.
(A) Statistical analysis of differential metabolites. The X axis represents the number of differential metabolites, and the Y axis represents the group comparison conditions. (B) Volcanic map of differential metabolites. Each point in the figure represents a metabolite, and the X-axis represents the logarithm value of Log2 of the multiple of quantitative difference of a metabolite in two samples. Y-axis represents the logarithm of −log10 for P. (C) Scatter plot of charge ratio and p value of differentially expressed metabolites. The Y-axis is the log−10. Red dots represent up-regulated differentially expressed metabolites, blue dots represent down-regulated differentially expressed metabolites, and gray dots represent metabolites that were detected but not expressed.
Figure 3
Figure 3. Hierarchical clustering heat map of differential metabolites in Oriental Lily under drought stress.
(A) Hierarchical clustering heat map of differential metabolites. The relative content in the figure is shown by the color difference. Red color represents the higher expression level and blue color represents lower expression level. (B) Volcanic map of differentially expressed metabolites. Each point represents a metabolite, and the X-axis represents the mass/charge ratio of a metabolite. The Y-axis is the log−10. (C) The association heat map of differentially expressed metabolites. Both ordinate and oblique ordinate represent the names of differential metabolites, color represents correlation, red is positively correlated, blue is negatively correlated, and the darker the color, the greater the correlation.
Figure 4
Figure 4. Analysis of differentially expressed genes in Oriental Lily.
(A) Number of differentially expressed genes in lily, (B) correlation analysis of different samples. The different colored squares represent the high and low correlation of the two samples, (C) MA map of differentially expressed genes, (D) KEGG enrichment analysis of up-regulated genes, (E) and down-regulated genes.
Figure 5
Figure 5. Integrated transcriptome and metabolome analysis of Oriental Lily.
(A) Correlation analysis between mRNAs and metabolites. (B) Enriched P Value bar chart by KEGG, the horizontal axis represents the name of the metabolic pathway, and the vertical axis represents the p-values of two omics enrichment analyses. The color represents different omics. (C) Nine pairs of differentially expressed metabolites and the corresponding differential transcripts. The horizontal axis represents the names of related metabolites and transcripts, while the vertical axis represents differential expression multiples.
Figure 6
Figure 6. Functional verification of TRINITY_DN2608 under drought stress.
(A) Identification of the transgenic strain, (B) transgenic strain was screened on a resistant plate containing kanamycin, (C) relative expression levels of drought-related genes in transgenic and wild-type plants under drought conditions, (D) normal management of wild-type and transgenic plant phenotypes, (E) after drought treatment, wild-type and transgenic plant phenotypes, (F) statistics of in vitro leaf water loss rate of wild-type and transgenic plant lines. Two asterisks (**) in the figure is on the overexpression plant line, indicating a significant difference with wild-type Arabidopsis at the 0.01 level.
See this image and copyright information in PMC

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