Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla

Kun Pan; Shuiping Dai; Jianping Tian; Junqing Zhang; Jiaqi Liu; Ming Li; Shanshan Li; Shengkui Zhang; Bingmiao Gao

doi:10.3389/fpls.2023.1161257

Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla

Front Plant Sci. 2023 Jun 8:14:1161257. doi: 10.3389/fpls.2023.1161257. eCollection 2023.

Authors

Kun Pan¹, Shuiping Dai¹, Jianping Tian¹, Junqing Zhang^{1

2}, Jiaqi Liu¹, Ming Li¹, Shanshan Li¹, Shengkui Zhang³, Bingmiao Gao^{1

2}

Affiliations

¹ Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China.
² Academician Workstation of Hainan Province and The Specific Research Fund of The Innovation Platform for Academicians of Hainan Province, Haikou, Hainan, China.
³ School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China.

Abstract

Introduction: Alpinia oxyphylla Miquel (A. oxyphylla), one of the "Four Famous South Medicines" in China, is an essential understory cash crop that is planted widely in the Hainan, Guangdong, Guangxi, and Fujian provinces. Particularly, A. oxyphylla from Hainan province is highly valued as the best national product for geo-herbalism and is an important indicator of traditional Chinese medicine efficacy. However, the molecular mechanism underlying the formation of its quality remains unspecified.

Methods: To this end, we employed a multi-omics approach to investigate the authentic quality formation of A. oxyphylla.

Results: In this study, we present a high-quality chromosome-level genome assembly of A. oxyphylla, with contig N50 of 76.96 Mb and a size of approximately 2.08Gb. A total of 38,178 genes were annotated, and the long terminal repeats were found to have a high frequency of 61.70%. Phylogenetic analysis demonstrated a recent whole-genome duplication event (WGD), which occurred before A. oxyphylla's divergence from W. villosa (~14 Mya) and is shared by other species from the Zingiberaceae family (Ks, ~0.3; 4DTv, ~0.125). Further, 17 regions from four provinces were comprehensively assessed for their metabolite content, and the quality of these four regions varied significantly. Finally, genomic, metabolic, and transcriptomic analyses undertaken on these regions revealed that the content of nootkatone in Hainan was significantly different from that in other provinces.

Discussion: Overall, our findings provide novel insights into germplasm conservation, geo-herbalism evaluation, and functional genomic research for the medicinal plant A. oxyphylla.

Keywords: Alpinia oxyphylla; genome; geo-herbalism; metabolomics; nootkatone; transcriptomics; valenene synthase.

Grants and funding

This research was supported by the National Natural Science Foundation of China (No. 81660629) and the Hainan Province Science and Technology Special Fund (ZDYF2022XDNY170).