Abstract
The genus Oldenlandia encompasses numerous medicinal plants with significant pharmacological potential, yet their tissue-specific metabolic pathways and transcriptional profiles remain understudied. This study combined transcriptomic and metabolomic analyses to compare the differences in five tissues (roots, stems, leaves, flowers, and fruits) between two closely related Oldenlandia species, Oldenlandia diffusa and Oldenlandia corymbosa. Using a widely targeted metabolomics approach based on UPLC-MS/MS, we monitored 1,343 metabolites across 60 samples from the two species. Transcriptome sequencing generated 272.12 Gb and 257.03 Gb of clean data for Oldenlandia diffusa and Oldenlandia corymbosa, respectively, along with 37,644 and 20,825 annotated genes. Comparative analysis revealed numerous differentially expressed genes, whose diverse functions were elucidated through GO enrichment. This comprehensive dataset provides a valuable resource for further investigating the phenotypic traits and metabolic mechanisms underlying the pharmacological activities of these medicinally important Oldenlandia species.
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Data availability
The original data of the present study cohort were deposited in the NCBI public repository (https://identifiers.org/ncbi/insdc.sra:SRP665145). Metabolomic raw data have been archived in MetaboLights (MTBLS13314, https://www.ebi.ac.uk/metabolights/MTBLS13314). Additionally, expression and quality control data for metabolome and transcriptome analyses have been uploaded to the figshare database for accessibility.
Code availability
The methods section details the software and R packages employed for metabolomic and transcriptomic analyses. The R scripts for the comparative transcriptome analysis of the two species have been stored in figshare.
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Acknowledgements
This work was supported by the Special Training Plan for Minority Science and Technology Talents, Chinese Medicine of Hubei University of Chinese Medicine (2023ZZXZ002), and Tianshan Innovation Team Program (2020D14030). We gratefully acknowledge Bioyi Biotechnology Co., Ltd., Wuhan, China for providing metabolomics and transcriptomics services.
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Pengyu Chen: Select topic, research proposal design, data analysis and paper writing. Zhuang Huang: Select topic and data analysis. Ping Huang: data analysis. Kaojiang Zhu, Benjiang Xiao and Meng Chen: data sorting. Yuxin Wen and Qi Jiang: Data organization and visualization. Rui Qian, Xing Hong, and Shihao Li: Data review and manuscript review. Fang Huang and Lintao Han: review and editing, experimental funding supporting.
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Chen, P., Huang, Z., Wen, Y. et al. Metabolomic and Transcriptomic Profiling of Two Closely Related Species within the Genus Oldenlandia. Sci Data (2026). https://doi.org/10.1038/s41597-026-06745-y
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DOI: https://doi.org/10.1038/s41597-026-06745-y
