Pan Kun, Dai Shuiping, Tian Jianping, Zhang Junqing, Liu Jiaqi, Li Ming, Li Shanshan, Zhang Shengkui, Gao Bingmiao
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.
Academician Workstation of Hainan Province and The Specific Research Fund of The Innovation Platform for Academicians of Hainan Province, Haikou, Hainan, China.
Front Plant Sci. 2023 Jun 8;14:1161257. doi: 10.3389/fpls.2023.1161257. eCollection 2023.
Miquel (), 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, 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.
To this end, we employed a multi-omics approach to investigate the authentic quality formation of .
In this study, we present a high-quality chromosome-level genome assembly of , 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 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.
Overall, our findings provide novel insights into germplasm conservation, geo-herbalism evaluation, and functional genomic research for the medicinal plant .
益智是中国“四大南药”之一，是一种重要的林下经济作物，广泛种植于海南、广东、广西和福建等省份。特别是来自海南省的益智被高度评价为道地药材中的上品，是中药药效的重要指标。然而，其品质形成的分子机制仍不明确。
为此，我们采用多组学方法来研究益智的道地品质形成。
在本研究中，我们展示了高质量的益智染色体水平基因组组装，重叠群N50为76.96 Mb，大小约为2.08 Gb。共注释了38178个基因，发现长末端重复序列的频率很高，为61.70%。系统发育分析表明，最近发生了一次全基因组复制事件（WGD），该事件发生在益智与毛叶山姜分化之前（约1400万年前），并为姜科其他物种所共有（Ks约为0.3；4DTv约为0.125）。此外，对来自四个省份的17个区域的代谢物含量进行了综合评估，这四个区域的品质差异显著。最后，对这些区域进行的基因组、代谢组和转录组分析表明，海南益智中诺卡酮的含量与其他省份的有显著差异。
总体而言，我们的研究结果为这种药用植物的种质资源保护、道地性评价和功能基因组研究提供了新的见解。
