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<p><i>Pueraria montana</i> var. <i>thomsonii</i>, the botanical origin of the traditional Chinese herb Gegen, is now extensively utilized in both medicinal and food applications. In this study, we generated a high-quality chromosome-scale genome assembly for <i>P. thomsonii</i> by integrating high-throughput sequencing with Hi-C technology. The assembled genome spans 1,076.26&#xa0;Mb, with 94.4% of the sequences anchored onto 11 chromosomes. Annotation of the genome structure identified a repeat content of 48.54% and predicted 46,222 protein-coding genes. Among these, over 95% were functionally annotated in public databases, including NR, GO, and KEGG. Comparative genomic analysis revealed that <i>P. thomsonii</i> is not a variety of <i>Pueraria montana</i> var. <i>lobata</i> (hereinafter referred to as <i>P. lobata</i>), but rather a distinct variety that diverged during the same period, further demonstrating their phylogenetic relationship; To further elucidate the tuber expansion mechanism in <i>P. thomsonii</i>, we performed transcriptomic and untargeted metabolomic analyses on its tubers at one-, two-, and three-year growth stages. This approach identified 17,960 differentially expressed genes, which were enriched in pathways including glycolysis along with starch and sucrose metabolism. Concurrent metabolomic profiling revealed 2,236 differentially accumulated metabolites. Integrated analysis indicated that key metabolic pathways—including phenylpropanoid biosynthesis, flavonoid synthesis, and starch–sucrose metabolism—play significant roles in distinct stages of tuberous root expansion. By integrating habitat analysis with a stage-wise reconstruction of the <i>P. thomsonii</i> tuberous root expansion process, we elucidated the molecular developmental mechanism underlying “HYG” tuberous root growth. Furthermore, the phenylpropanoid and flavonoid biosynthesis pathways were shown to regulate tuberous root expansion. This finding provides a mechanistic basis for further research on <i>P. thomsonii</i> tuberous root development and facilitates its high-yield breeding.</p>

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Multi-omics Analysis Provide Insight Into the Mechanism of Pueraria montana var. thomsonii Tuberous Root Expansion

  • 期刊论文

  • 发表日期：

    2026年5月12日

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  • Hongxuan Wang,
  • Shuiqing Hu,
  • Mengting Yang,
  • Yuye Zhu,
  • Bo Wu

摘要

Pueraria montana var. thomsonii, the botanical origin of the traditional Chinese herb Gegen, is now extensively utilized in both medicinal and food applications. In this study, we generated a high-quality chromosome-scale genome assembly for P. thomsonii by integrating high-throughput sequencing with Hi-C technology. The assembled genome spans 1,076.26 Mb, with 94.4% of the sequences anchored onto 11 chromosomes. Annotation of the genome structure identified a repeat content of 48.54% and predicted 46,222 protein-coding genes. Among these, over 95% were functionally annotated in public databases, including NR, GO, and KEGG. Comparative genomic analysis revealed that P. thomsonii is not a variety of Pueraria montana var. lobata (hereinafter referred to as P. lobata), but rather a distinct variety that diverged during the same period, further demonstrating their phylogenetic relationship; To further elucidate the tuber expansion mechanism in P. thomsonii, we performed transcriptomic and untargeted metabolomic analyses on its tubers at one-, two-, and three-year growth stages. This approach identified 17,960 differentially expressed genes, which were enriched in pathways including glycolysis along with starch and sucrose metabolism. Concurrent metabolomic profiling revealed 2,236 differentially accumulated metabolites. Integrated analysis indicated that key metabolic pathways—including phenylpropanoid biosynthesis, flavonoid synthesis, and starch–sucrose metabolism—play significant roles in distinct stages of tuberous root expansion. By integrating habitat analysis with a stage-wise reconstruction of the P. thomsonii tuberous root expansion process, we elucidated the molecular developmental mechanism underlying “HYG” tuberous root growth. Furthermore, the phenylpropanoid and flavonoid biosynthesis pathways were shown to regulate tuberous root expansion. This finding provides a mechanistic basis for further research on P. thomsonii tuberous root development and facilitates its high-yield breeding.