Multiomics comparison among populations of three plant sources of Amomi Fructus

Abstract

Amomi Fructus (Sharen, AF) is a traditional Chinese medicine (TCM) from three source species (or varieties), including Wurfbainia villosa var. villosa (WVV), W. villosa var. xanthioides (WVX), or W. longiligularis (WL). Among them, WVV has been transplanted from its top-geoherb region, Guangdong, to its current main production area, Yunnan, for >50 years in China. However, the genetic and transcriptomic differentiation among multiple AF source species (or varieties) and between the origin and transplanted populations of WVV is unknown. In our study, the observed overall higher expression of terpenoid biosynthesis genes in WVV than in WVX provided possible evidence for the better pharmacological effect of WVV. We also screened six candidate borneol dehydrogenases (BDHs) that potentially catalyzed borneol into camphor in WVV and functionally verified them. Highly expressed genes at the P2 stage of WVV, Wv05G1424 and Wv05G1438, were capable of catalyzing the formation of camphor from (+)-borneol, (−)-borneol and DL-isoborneol. Moreover, the BDH genes may experience independent evolution after acquiring the ancestral copies, and the following tandem duplications might account for the abundant camphor content in WVV. Furthermore, four populations of WVV, WVX, and WL are genetically differentiated, and the gene flow from WVX to WVV in Yunnan contributed to the greater genetic diversity in the introduced population (WVV-JH) than in its top-geoherb region (WVV-YC), which showed the lowest genetic diversity and might undergo genetic degradation. In addition, terpene synthesis ( TPS) and BDH genes were selected among populations of multiple AF source species (or varieties) and between the top- and non-top-geoherb regions, which might explain the difference in metabolites between these populations. Our findings provide important guidance for the conservation, genetic improvement, and industrial development of the three source species (or varieties) and for identifying top-geoherbalism with molecular markers, and proper clinical application of AF.

Acknowledgements

This study was supported by Yunnan Science and Technology Talents and Platform Program (Academician and Expert Workstations, 202205AF150071), the National Key Research and Development Program of China (Nos. 2020YFA0907900, 2022YFD1600300, and 2017YFC1701100), Open Projects of Guangxi Key Laboratory of Medicinal Resources Conservation and Genetic Improvement (No. KL2022KF01), the Shenzhen Science and Technology Program (No. KQTD2016113010482651), special funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District (Nos. RC201901-05 and PT201901-19), the China Postdoctoral Science Foundation (No. 2020 M672904), the Basic and Applied Basic Research Fund of Guangdong (No. 2020A1515110912), National Natural Science Foundation of China (Nos. 32070242 and 82260736) and Science Technology and Innovation Commission of Shenzhen Municipality of China (ZDSYS 20200811142605017).

Authors contributions

LW, DY, XC, SS, and XH [2] conceived and designed the study. XC, DY, LW, GL, YW, CL [5], LZ and JY prepared the materials. JJ performed flow cytometry experiment. XC, SS, XH [2], CL [2], BN, and ZH performed data analysis. XC, FW, WL, SY did the enzyme activity assay in tobacco. XC, SS, XH [2] and LW wrote the manuscript. LW, SS, CL, XH [1, 2] and DY revised the manuscript. All authors read and approved the final draft.

Data availability statement

The data presented in the study were deposited in National Center for Biotechnology Information (NCBI), and BioProject accession number was PRJNA910288.

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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