Pei Yifei, Leng Liang, Sun Wei, Liu Baocai, Feng Xue, Li Xiwen, Chen Shilin
Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
Sci China Life Sci. 2024 Feb;67(2):258-273. doi: 10.1007/s11427-022-2375-y. Epub 2023 Oct 12.
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
基因组学的进展极大地加速了药用植物的研究，草药基因组学的发展推动了“千种药用植物基因组计划”以破解其遗传密码。然而，由于多倍体普遍存在和/或基因组杂合度高，难以获得其高质量的全基因组。截至2022年9月，已公布了123种药用植物的全基因组。本综述对这些已公布的基因组序列进行了研究，涵盖了它们的分类、研究团队、倍性、药用功能和测序策略。全球有1000多个机构或大学以及50个国家正在开展药用植物基因组研究。二倍体物种在已测序的药用植物中占大多数。禾本科植物的全基因组研究得最多。近40%的已发表论文研究了具有滋补、补益和清热药用功效的物种。与作物相比，药用植物仍处于驯化过程中，因此遗传背景不明确且缺乏纯系，这使得它们的基因组更难完成。此外，目前仍没有一个清晰的常规框架来获得药用植物的高质量全基因组。在此，首次提出了一个清晰完整的策略来创建药用植物的高质量全基因组。此外，还综述了基于全基因组的药用植物生物学研究，包括育种和生物合成。我们还主张应建立一个模式药用植物研究平台，以促进药用植物的基因组学研究。
