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. 2025 Nov 5;14(11):1554.
doi: 10.3390/biology14111554.

Transcriptomics and Metabolomics Reveal Mechanisms Underlying the Adaptation of Lamiophlomis rotata to High Altitudes

Yunzhang Xu  1 , Sangjie Jiancuo  2 , Xiao Luo  3 , Yu-E Ma  4 , Xin Wu  2 , Zhenzhong Wu  1 , Hengxia Yin  1 , Shaoshan Zhang  4   5 , Wenbing Li  5   6 , Huachun Sheng  5   6
Affiliations

Transcriptomics and Metabolomics Reveal Mechanisms Underlying the Adaptation of Lamiophlomis rotata to High Altitudes

Yunzhang Xu et al. Biology (Basel). .

Abstract

Lamiophlomis rotata (Benth.) Kudo is a typical alpine medicinal plant. However, the mechanism underlying its adaptation to high altitudes remains incompletely understood. In this study, we integrated transcriptome and metabolome analyses. Specifically, we used third-generation sequencing for building a reference transcriptome and second-generation sequencing for differential gene expression analysis. Our findings revealed that the activation of the hydrogen sulfide signaling pathway and the reprogramming of amino acid metabolism are probable adaptation mechanisms. Different from previous reports, the hydrogen sulfide signaling may regulate the activity of cellulose synthase in addition to enhancement of antioxidant capacity and accumulation of osmolytes. By altering the agronomic traits of plants in a cell wall remodeling-dependent manner, it enables L. rotata to adapt to alpine stress. The accumulated amino acids not only store energy-efficient organic nitrogen as precursors for the synthesis of secondary metabolites but also act as signaling molecules to activate defense responses. Additionally, we propose a potential link between the hydrogen sulfide signaling pathway and amino acid metabolism. Overall, this study systematically explores the adaptation mechanism of L. rotata to high-altitude environments, offering a novel perspective for understanding the growth, development, stress responses, and secondary metabolic processes of alpine plants.

Keywords: Lamiophlomis rotata; amino acid metabolism; cell wall remodeling; high altitude; hydrogen sulfide.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Figure 1
Figure 1
Habitat of L. rotata (A) and sampling parts (B). The yellow arrow indicates the sampling location.
Figure 2
Figure 2
Summary of full-length transcriptome sequences. (A) Length distribution of CCS reads. (B) Distribution of high-quality isoform lengths. (C) Venn diagram of annotation results from four major databases. (D) Homologous species distribution of L. rotata based on the NR database. (E) Statistics of KOG annotation information.
Figure 3
Figure 3
Quality control analysis of RNA-Seq data and differentially expressed genes (DEGs) in comparison group. (A) Principal component analysis (PCA) of all the samples. (B) The heatmap of Pearson’s correlation of 12 samples. (C) The number of upregulated (purple) and downregulated (blue) DEGs. (D) The interrelationships of DEGs among different comparison groups.
Figure 4
Figure 4
Comparative analysis of GO enrichment. GO analysis of DEGs in 3500 m vs. 4000 m (A), 3500 m vs. 4600 m (B), and 4000 m vs. 4600 m (C).
Figure 5
Figure 5
Metabolomics analysis of differentially accumulated metabolites (DAMs). (A) The quantities of DAMs in three comparison groups. (B) The interrelationships of DAMs among three comparison groups. (C) Chemical classification of DAMs, along with the quantities and percentages of each type of differential metabolite.
Figure 6
Figure 6
Analysis and identification of important differential metabolites. (A) Volcano plot reveals potential important differential metabolites. (B) The top 20 identified important differential metabolites.
Figure 7
Figure 7
The relationship between the accumulation amounts of amino acids and their derivatives and altitude. The data indicate that the accumulation levels of the majority of amino acids and their derivatives exhibit an upward trend as altitude increases.
See this image and copyright information in PMC

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