Herbal genomics is an international scientific research project with the goal of determining the sequence of chemical base pairs which make up herb DNA, and with a series of post genomics study of medicinal plant with important economic value or typical secondary metabolic pathway.This project promotes the establishment of research platform of a batch of model plants with typical secondary metabolic pathway and drives the application of various genomics research methods to the areas of medicinal plant study, leading the study of traditional Chinese medicine to the frontiers of Life Sciences.The related results have been published in a series of internationally renowned academic journals, such as Nature Communication, Molecular Plant, New Phytologist, Biotech Adv, Plant Journal,PNAS, Nat Prod Rep, Biol Rev., Genetics, Sci Rep and JEP.Many genome maps of herbs, including medicinal plants and fungus, such as Ganoderma lucidum, Ganoderma sinense, Panax ginseng and Salvia miltiorrhiza, were obtained using next generation high-throughput sequencing technology,combined with genetic map and optical map.We firstly finished the whole genome sequencing of G.lucidum, a well-known medicinal fungus over the world.The whole genome sequence was published in Nature Communication and was specially recommended as Featured Image.US TODAY also reported the research with the title of Chinese "mushroom of immortality" genome mapped.The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism of Ganoderma triterpenoids.A lot of microRNA were identified through analysis of small RNA in S.miltiorrhiza, P.ginseng, P.quinquefolium, G.lucidum and Digitalis purpurea, which revealed the species-specific and tissue-specific expression patterns of the microRNA in these medicinal plants.It was found that microRNA regulated plant growth and development, involved in plant stress responses to adversity and had a close relationship with biosynthesis of active pharmaceutical ingredients and regulation of quality formation of materia medica.The whole genome sequence of Salvia miltiorrhiza helps us to localize the metabolism of the bioactive tanshinone diterpenoids from the medicine plant to the root periderm, and carry out tissue-differentiated transcriptome analysis of this plant organ using a combination with Illumina short-reads and SMRT long-reads sequencing approach.The development of Herbal genomics provides a rare opportunity for basic research of TCM to occupy scientific and technological commanding point.It will pose a profound impact on the research and development of natural drugs and agriculture of TCM by the analysis of biosynthetic pathway of medicinal plant effective ingredients and breeding of good varieties.