Integrative transcriptomic and metabolomic analysis of Drynaria roosii reveals genes involved in the biosynthesis of medicinal compounds

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Integrative transcriptomic and metabolomic analysis of Drynaria roosii reveals genes involved in the biosynthesis of medicinal compounds

Scientific Reports , Article number:  (2026) Cite this article

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Abstract

The rhizome of Drynaria roosii (Drynariae Rhizoma) holds significant medicinal and economic value. It is traditionally used to promote blood circulation, remove blood stasis, and strengthen the kidneys and bones. However, the distribution and biosynthetic pathways of medicinal compounds in different tissues of D. roosii remain unclear. In this study, non-targeted metabolomics and transcriptomics analyses were conducted on leaves, stems, and tubers of D. roosii, and a high-quality reference transcriptome was obtained using Pacific BioSciences (PacBio) single-molecule real-time (SMRT) sequencing. A total of 1,151 metabolites were identified, including 203 flavonoid-related compounds. Among them, 31 flavonoids-such as quercetin 7-glucoside, tamarixetin, and naringenin 7-rutinoside—were found to be relatively abundant in the tuber. PacBio SMRT sequencing yielded 151,192 consensus reads. A total of 5,581 intron retention (IR) events were identified through alternative splicing analysis, and 56,773 non-redundant transcripts were obtained after transcript redundancy removal. Comparative transcriptome analysis revealed that metabolic pathways such as steroid biosynthesis (ko00100) and phenylpropanoid biosynthesis were enriched in the tuber and leaf. Correlation network analysis identified key genes, including Glycosyltransferase, 4CL, DELLA and others, to be significantly associated with the biosynthesis of naringin 6’’-rhamnoside and naringenin 7-rutinoside. This study provides a foundation for the resource utilization, medicinal compound biosynthesis, and molecular breeding of D. roosii.

Data availability

The raw bam file from PacBio SMRT sequencing has been deposited in the NCBI SRA database (BioProject acc. PRJNA1291835). The raw reads generated from Illumina sequencing have been deposited in the NCBI SRA database (BioProject acc. PRJNA1291623).

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Funding

This research was funded by Guizhou Provincial Science and Technology Plan Project (QKH Support [2023] General 003; Talent Base Project of Guizhou Provincial Committee Organization Department (RCJD2020-21); Guangzhou Science and Technology Plan Project (2023B03J1292); Bijie Science and Technology Innovation Platform and Talent Team (BKH [2023] No. 66); Scientific Research Team Project of Bijie Medical College (BJYZXT202401).

Author information

Authors and Affiliations

  1. Bijie Institute of Traditional Chinese Medicine, Bijie, 551700, Guizhou, China

    Xiangyu Zhang, Yong Wang, Min Liu & Caiyun Wang

  2. Guizhou Key Laboratory for Germplasm Innovation and Resource-Efficient Utilization of Dao-Di Herbs, Guiyang, 550025, China

    Xiangyu Zhang, Yong Wang, Min Liu, Caiyun Wang & Tao Zhou

  3. Bijie Medical College, Bijie, 551700, Guizhou, China

    Xiaofang Chen

  4. Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China

    Tao Zhou

Authors

  1. Xiangyu Zhang
  2. Xiaofang Chen
  3. Yong Wang
  4. Min Liu
  5. Caiyun Wang
  6. Tao Zhou

Contributions

Conceptualization, Z.X. and C.X.; methodology, Z.X. and C.X..; software, Z.X..; validation, W.Y, W.C. and Z.T.; formal analysis, Z.X. and C.X.; investigation, Z.X. and C.X.; resources, W.Y, L.M., W.C. and Z.T.; data curation, Z.X.; writing—original draft preparation, Z.X. and C.X.; writing—review and editing, Z.X. and C.X..; visualization, Z.X.; supervision, Z.X.; project administration, Z.X.; funding acquisition, Z.X. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Xiangyu Zhang or Xiaofang Chen.

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The authors declare no competing interests.

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Zhang, X., Chen, X., Wang, Y. et al. Integrative transcriptomic and metabolomic analysis of Drynaria roosii reveals genes involved in the biosynthesis of medicinal compounds. Sci Rep (2026). https://doi.org/10.1038/s41598-026-39037-x

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  • DOI: https://doi.org/10.1038/s41598-026-39037-x

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