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

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.