Integrated study on the genome, transcriptome, and metabolome of Gelsemium elegans and mining of related enzyme genes involved in koumine biosynthesis

Yao Zhang; Li-Mei Pan; Yi-Song Liu; De-Tian Mu; Wen-Qiang Chen; Ying Lu; Iain W Wilson; Meng-Ting Zuo; Li-Ya Wang; Zhao-Ying Liu; De-You Qiu; Qi Tang

doi:10.1016/j.plaphy.2025.110069

Integrated study on the genome, transcriptome, and metabolome of Gelsemium elegans and mining of related enzyme genes involved in koumine biosynthesis

Plant Physiol Biochem. 2025 May 24:227:110069. doi: 10.1016/j.plaphy.2025.110069. Online ahead of print.

Authors

Yao Zhang¹, Li-Mei Pan², Yi-Song Liu³, De-Tian Mu¹, Wen-Qiang Chen¹, Ying Lu¹, Iain W Wilson⁴, Meng-Ting Zuo³, Li-Ya Wang¹, Zhao-Ying Liu⁵, De-You Qiu⁶, Qi Tang⁷

Affiliations

¹ College of Horticulture, Yuelushan Laboratory & National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China.
² Guangxi Key Laboratory of for High-Quality Formation and Utilization of Dao-Di Herbs, National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
³ College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China.
⁴ CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia.
⁵ College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China. Electronic address: liu_zhaoying@hunau.edu.cn.
⁶ State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
⁷ College of Horticulture, Yuelushan Laboratory & National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China. Electronic address: tangqi@hunau.edu.cn.

PMID: 40450816
DOI: 10.1016/j.plaphy.2025.110069

Abstract

Gelsemium elegans a plant of the Loganiaceae family, is highly toxic and contains many alkaloids of potential pharmacological value. Koumine, is the most abundant component of G. elegans, and belongs to monoterpene indole alkaloids and is valued in medical research as it has important anti-inflammatory and anxiolytic properties. The biosynthesis pathway of this compound has been little studied, and is poorly understood, limiting the ability to improve koumine production via breeding or synthetic biology. To investigate G. elegans biosynthesis of koumine, its genomes was sequenced and assembled (331.82 Mb) and a comprehensive transcriptome cDNA library from different tissues and hormone treatments constructed and sequenced using PacBio (10.9 Gb subreads). Using liquid chromatography-mass spectrometry techniques, we identified 29 alkaloids in extracts of G. elegans and analyzed their synthesis and accumulation in different tissues and this data was compared to the transcriptomic data to identify 20 candidate genes likely to be involved in the synthesis of koumine. Finally, a preliminary validation of the functions of two candidate genes GeLAMT and GeTDC were performed and found that both proteins catalyze the production of products in koumine biosynthesis. This data provides a rich molecular resource for the study of G. elegans, as well as the first functional validation of genes in G. elegans, that will help to inform further MIA biosynthetic pathway studies.

Keywords: Biosynthesis; Co-expression; Gelsemium elegans; Koumine; PacBio; RNA-Seq.