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Background <p><i>Phyllanthus emblica L.</i> (Indian gooseberry, amla) is a dual-purpose plant valued for both nutritional and medicinal applications. In recent years, research on <i>P. emblica</i> has mainly concentrated on examining its chemical components and pharmacological effects. Metabolic diversity among different <i>P. emblica</i> varieties has attracted considerable research interest. However, the molecular mechanisms underlying this variation remain largely unexplored. The present study aimed to evaluate the multi-omics differences among varieties by conducting integrated metabolomic and transcriptomic analyses of three major varieties grown in Guangxi: Tianyougan, Pingdan No. 1, and Daguoyougan.</p> Results <p>The results showed that Tianyougan and Pingdan No. 1 had similar expression patterns, significantly differing from Daguoyougan. Tianyougan and Pingdan No. 1 exhibited rich flavor-related metabolite profiles, while Daguoyougan accumulated higher levels of metabolites associated with antioxidant properties and stress response. A total of 150 and 143 differentially accumulated metabolites (DAMs) were identified in fruits and leaves, respectively. These metabolites were predominantly enriched in pathways associated with organic acid metabolism. Specifically, 29 DAMs and 132 DEGs were mapped to the tricarboxylic acid (TCA) cycle, glycolysis/gluconeogenesis, pentose phosphate pathway, amino acid biosynthesis, D-amino acid metabolism, and phenylpropanoid biosynthesis. Among these, <i>PGAM</i>, <i>pfkA</i>, <i>ACO</i>, <i>HK</i>, <i>ilvH</i>, <i>PK</i>,<i> pckA</i>,<i> ALDO</i>, and <i>CS</i> were identified as key DEGs regulating organic acid metabolic divergence across the three varieties. In addition, two genes (<i>TRINITY_DN549104_c2_g2</i> and <i>TRINITY_DN567014_c3_g3</i>) were screened and showed strong correlations with various differential organic acids, which can serve as potential pleiotropic factors to regulate organic acid metabolism.</p> Conclusions <p>This work provides novel insights into the metabolic diversity and molecular regulation of Tianyougan, Pingdan No. 1, and Daguoyougan, offering a theoretical foundation for quality improvement and functional gene discovery in <i>P. emblica</i>.</p>

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Integrated transcriptomic and metabolomic analyses reveal distinct molecular and metabolic signatures in fruits and leaves of three Phyllanthus emblica cultivars

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月27日

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  • Xiaoling Hao,
  • Hui Wen,
  • Xiaohua Dai,
  • Junru Qu,
  • Liyan Lu,
  • Gao Li,
  • Yewei Tan,
  • Usman Rasheed,
  • Xinrong Li,
  • Kaikai Meng

摘要

Background

Phyllanthus emblica L. (Indian gooseberry, amla) is a dual-purpose plant valued for both nutritional and medicinal applications. In recent years, research on P. emblica has mainly concentrated on examining its chemical components and pharmacological effects. Metabolic diversity among different P. emblica varieties has attracted considerable research interest. However, the molecular mechanisms underlying this variation remain largely unexplored. The present study aimed to evaluate the multi-omics differences among varieties by conducting integrated metabolomic and transcriptomic analyses of three major varieties grown in Guangxi: Tianyougan, Pingdan No. 1, and Daguoyougan.

Results

The results showed that Tianyougan and Pingdan No. 1 had similar expression patterns, significantly differing from Daguoyougan. Tianyougan and Pingdan No. 1 exhibited rich flavor-related metabolite profiles, while Daguoyougan accumulated higher levels of metabolites associated with antioxidant properties and stress response. A total of 150 and 143 differentially accumulated metabolites (DAMs) were identified in fruits and leaves, respectively. These metabolites were predominantly enriched in pathways associated with organic acid metabolism. Specifically, 29 DAMs and 132 DEGs were mapped to the tricarboxylic acid (TCA) cycle, glycolysis/gluconeogenesis, pentose phosphate pathway, amino acid biosynthesis, D-amino acid metabolism, and phenylpropanoid biosynthesis. Among these, PGAM, pfkA, ACO, HK, ilvH, PK, pckA, ALDO, and CS were identified as key DEGs regulating organic acid metabolic divergence across the three varieties. In addition, two genes (TRINITY_DN549104_c2_g2 and TRINITY_DN567014_c3_g3) were screened and showed strong correlations with various differential organic acids, which can serve as potential pleiotropic factors to regulate organic acid metabolism.

Conclusions

This work provides novel insights into the metabolic diversity and molecular regulation of Tianyougan, Pingdan No. 1, and Daguoyougan, offering a theoretical foundation for quality improvement and functional gene discovery in P. emblica.