The research team of this laboratory launched the "Yunnan Medicine Genomics Project" in 2014, successively decoding the genomes of medicinal plants including Panax notoginseng (Sanqi), Erigeron breviscapus (Dengzhanhua), Gastrodin elata (Tianma), Moringa oleifera (Moringa), Salvia miltiorrhiza (Danshen), and Lepidium meyenii (Maca). The team has published more than 50 scientific papers, decoded over 400 medicinal plant transcriptomes, accounting for more than 70% of the data volume in the field of medicinal plant genomics and transcriptomics. In 2018, the laboratory, in collaboration with the Guangxi Medicinal Botanical Garden, BGI (Beijing Genomics Institute), and the University of Macau, launched the "Medicinal Plant 4.0 Research Plan," decoding 100 medicinal plant genomes, 12,000 transcriptomes, conducting 600 medicinal plant efficacy analyses and fractionation analyses, and isolating more than 3,700 compounds. This has formed the largest and most comprehensive medicinal plant omics big-data system globally. Currently, the laboratory has completed genome decoding for more than 50 medicinal plants, is conducting genome decoding for more than 30 medical and edible plants, and has completed sampling, specimen preparation, and transcriptome sequencing for 13,022 medicinal plant species. Relevant data are currently under analysis, and an ultra-fine phylogenetic tree is also under construction to explore the genetic mechanisms underlying metabolite diversity formation and traces of artificial domestication in medicinal plants.
Leveraging the rich characteristic medicinal plant resources of the Yunnan Plateau, this laboratory has conducted genome sequencing of 26 medicinal plant species based on PacBio and Illumina sequencing platforms, including Andrographis paniculata (Chuanxinlian), Amomum villosum (Sharen), Glycyrrhiza uralensis (Gancao/licorice), Panax notoginseng (Sanqi), Davidia involucrata (Gongtong/dove tree), Eleutherococcus senticosus (Ciwujia/Siberian ginseng), Tamarix sp. (Duohua chengliu), Codonopsis pilosula (Dangshen), Lindenbergia sp. (Zhongecao), Gynostemma pentaphyllum (Jiaogulan), Tacca chantrieri (Laohuxu/black bat flower), Panax vietnamensis (Yuenan renshen/Vietnamese ginseng), Desmodium sp. (Shanmahuang), Cistanche tubulosa (Guanhua roucongrong), Luculia sp. (Diandingxiang), Synsepalum dulcificum (Shenmiguo/miracle fruit), Calotropis gigantea (Niujiaogua), Gentiana rigescens (Dianlongdan), Bougainvillea spectabilis (Sanjiaomei/bougainvillea), Platycodon grandiflorus (Jiegeng/balloon flower), Alpinia sp. (Mala liangjiang/Malaysian galangal), Amomum tsao-ko (Caoguo/Tsao-ko), Coptis teeta (Yunhuanglian/Yunnan goldthread), Lycium ruthenicum (Heigouqi/black goji), Ceratophyllum demersum (Jinyuzao/hornwort), and Euglena sp. (Luozao/euglenoids).
Based on high-quality sequencing data, the team completed fine genome assembly for 20 species and preliminary genome assembly for 3 species. Assembly results showed that the genome sizes of the sequenced species ranged from 282.99 Mb to 10.78 Gb, with Cistanche tubulosa having the largest genome at 10.78 Gb, and Tacca chantrieri having the smallest genome at 282.99 Mb.
Based on genome assembly and annotation results, the research team used bioinformatics to deeply mine and analyze the important active substances in these medicinal plants, decoded several important enzyme gene families, and achieved a series of influential scientific results. Currently, relying on this project, the research team has published 4 scientific papers in journals such as Plant Biotechnology Journal, Plant Communications, Molecular Ecology Resources, and Frontiers in Genetics, effectively advancing the project's work. In addition, work on biosynthesis, multi-omics regulation, and biological evolution of other medicinal plants is also progressing well.
Overall, relying on this project, this laboratory has conducted genome sequencing of 26 characteristic medicinal plant species in Yunnan Province. Combined with multi-omics analysis and deep bioinformatics mining, the team has decoded the biosynthetic pathways and biological evolutionary histories of a batch of important active components. Meanwhile, the research team has accumulated substantial omics data, core data processing technologies, and experience based on this project, becoming a leading team in medicinal plant research both domestically and internationally, laying a solid foundation for further promoting the development and utilization of medicinal plant resources in our province.
Finally, this laboratory has established a medicinal plant efficacy screening system based on transcriptome big data. Medicinal plant fractions were screened in tumor cell lines, and the results were compared with known chemotherapeutic drugs. Post-administration transcriptome analogical analysis was conducted. Screening of 117 medicinal plants against lung cancer, liver cancer, and breast cancer has been completed, identifying 3 anti-lung-cancer, 5 anti-liver-cancer, and 3 anti-breast-cancer medicinal plants. Related research has published 2 scientific papers and continues to generate research outputs.