Whole-genome sequencing in medicinal plants: current progress and prospect.

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.

Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research.

Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin.

BACKGROUND: Viola philippica Cav. is the only original plant for Violae Herba, as described in the Chinese Pharmacopoeia. The quality of this crude drug is affected by several adulterants from congeneric Viola species, and the authentic plant origin of Violae Herba is still controversial. Genome-based identification offers abundant genetic information and potential molecular markers that can be used for the authentication of closely related species. This study aims to investigate the certified origin of Violae Herba and to develop more effective markers for these easily confused species at the genetic level. METHODS: We compared the morphology and chemical composition of 18 batches of commercial samples and six widespread medicinal Viola plants used as Violae Herba or its substitutes by TLC and HPLC-Triple-TOF-MS/MS analyses. The complete chloroplast genomes of these species were sequenced and analyzed, including the general features, repeat sequences, mutational hotspots and phylogeny. The complete chloroplast genomes used as superbarcodes and some specific barcodes screened from mutational hotspots were tested for their ability to distinguish Viola species. RESULTS: A comparative study showed that Violae Herba is a multi-origin traditional Chinese medicine. Commercial decoction pieces and the standard reference drug were mainly derived from V. prionantha, clashing with the record in the Chinese Pharmacopoeia. Chloroplast genome analyses of V. philippica and five adulterants indicated that sequence divergence was relatively low within Viola species. By tree-based approaches, the complete chloroplast genomes showed a better discrimination ability and phylogenetic resolution for each Viola species. These results indicate that the whole chloroplast genomes can be used as superbarcodes to differentiate Viola medicinal plants. More specific DNA barcodes could be further developed from the Viola chloroplast genomes for more efficient and rapid identification of commercial Violae Herba and its adulterants. CONCLUSIONS: This study has implications for chloroplast genome-based phylogenetic analysis and the authentication of multiple Viola species used as Violae Herba. The legal origin recorded in the Chinese Pharmacopoeia should be further revised to V. prionantha, in line with the commercial Violae Herba in the TCM markets.

Establishing a genomic database for the medicinal plants in the Brazilian Pharmacopoeia.

BACKGROUND: Brazil is exceptionally abundant in medicinal plant resources and has a rich ethnopharmacological history. Brazilian Pharmacopoeia (BP) acts as a national standard that regulates drug quality and has six published editions. Recent genomic approaches have led to a resurgence of interest in herbal drugs. The genomic data of plants has been used for pharmaceutical applications, protecting natural resources, and efficiently regulating the market. However, there are few genomic databases specifically for medicinal plants, and the establishment of a database that focuses on the herbs contained in the BP is urgently required. METHODS: The medicinal plant species included in each edition of the BP were analyzed to understand the evolution of the Brazilian herbal drugs. The data of 82 plants in the BP were collected and categorized into four sections: DNA barcodes, super-barcodes, genomes, and sequencing data. A typical web server architecture pattern was used to build the database and website. Furthermore, the cp-Gs of the Aloe genus in the database were analyzed as an illustration. RESULTS: A new database, the Brazilian Pharmacopoeia Genomic Database (BPGD) was constructed and is now publicly accessible. A BLAST server for species identification and sequence searching with the internal transcribed spacer 2 (ITS2), the intergenic region (psbA-trnH), and the chloroplast genome (cp-G) of Brazilian medicinal plants was also embedded in the BPGD. The database has 753 ITS2 of 76 species, 553 psbA-trnH and 190 genomes (whole genome and chloroplast genome) of 57 species. In addition, it contains 37 genome sequence data sets of 24 species and 616 transcriptome sequence data sets of 34 species and also includes 187 cp-Gs representing 57 medicinal species in the BP. Analyses of the six cp-Gs of three Aloe species identified the variable regions in the cp-Gs. These can be used to identify species and understand the intraspecific relationships. CONCLUSIONS: This study presents the first genomic database of medicinal plants listed in the latest BP. It serves as an efficient platform to obtain and analyze genomic data, accelerate studies regarding Brazilian medicinal plants and facilitate the rational development on their market regulation.

The characteristics of complete chloroplast genome sequence and phylogenetic analysis of Dendrobium moniliforme / 药学学报

italic>Dendrobium moniliforme is an important source of Dendrobii Caulis and one of the main sources of authentic Fengdou. The complete chloroplast genome of D. moniliforme was sequenced using Illumina Hiseq technology and its gene map and genomic structure were analyzed. Then comparative and phylogenetic analysis of the complete chloroplast genomes of D. moniliforme and its related species were conducted. The chloroplast genome of D. moniliforme was 150 754 bp in length and had a typical quadripartite structure with a large single copy (LSC, 84 818 bp), a small single copy (SSC, 14 124 bp) and two inverted repeats (IRs, 25 906 bp each). A total of 123 chloroplast genes were annotated, including 77 protein-coding genes, 38 tRNA genes and 8 rRNA genes, of which 17 genes contained introns. Bioinformatics analysis identified 53 SSR sites, most of which had A-T base preference. A phylogenetic tree was constructed using the chloroplast genome sequences of 33 Dendrobium species. The results showed that Dendrobium complex species were clustered in a single large branch, indicating that they were closely related. This study provides a scientific basis for the identification of D. moniliforme and the phylogenetic relationship of D. moniliforme complex species necessary for Herbgenomics research.

Chloroplast Genomic Analysis of Pyrrosia assimilis / 中国实验方剂学杂志

Objective::The complete chloroplast genome of Pyrrosia assimilis was sequenced, its sequence characteristics was analyzed and herbgenomics of P. assimilis was discussed. Method::Its complete chloroplast genome sequence was determined through high-throughput sequencing technology, and its structural characteristics and phylogenetic relationships were analyzed by bioinformatics. Result::The chloroplast genome of P. assimilis was a circular double-chain structure with a total length of 154 964 bp, and the total content of guanine and cytosine (GC) was 41.2%. A total of 131 genes were annotated, including 88 protein-coding genes, 35 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. A total of 43 dispersed repetitive sequences and 56 simple sequence repeats (SSRs) were detected. The frequency of codon encoding leucine was the highest, while the number of codon encoding tryptophan was the lowest. Five highly divergent regions (psbA, rrn16, petA-psbJ, ndhC-trnM, and psbM-petN) were screened, phylogenetic analysis showed that P. assimilis was closely related to P. bonii. Conclusion::Comparative analysis of the complete chloroplast genome of P. assimilis reveals that non-coding regions exhibited a higher divergence than the coding regions, the large single copy region (LSC) and small single copy region (SSC) are more divergent than the reverse repeat region (IR), the selected five highly variable regions can be used as specific DNA barcodes for identification of Pyrrosia species. Study on the chloroplast genome of P. assimilis can provide a reference for the molecular identification, genetic transformation, expression of resistance protein and secondary metabolism pathway analysis of other Pyrrosia medicinal plants.

[Application of phylogenomics in Chinese medicine resources].

China is rich in the diversified Chinese medicine resources and is notable for the wide and long-term applications of Chinese medicine. However,the lack of genomic information on medicinal taxa leads to problems in relation to resource conservation and the downstream application of traditional Chinese medicine resources,which restricts the modernization process of traditional Chinese medicine. Molecular phylogenetics is an important tool to understand the origin and evolution of the earth's biodiversity and promote the conservation and use of medicinal taxa. With the development of sequencing technology,the combination of genomic data extends the traditional molecular phylogenetics to the research level of phylogenomics,making it more powerfully applied to all aspects of biological research. Undoubtedly,carrying out phylogenomic research on Chinese medicine species will greatly promote their resources conservation,molecular evaluation and identification,and the exploration and utilization of natural pharmacodynamic components,promoting the modernization of traditional Chinese medicine. This article starts with a brief introduction of the developing history and basic research methods of phylogenomics,and then reviews the current research progress in phylogenomics related to traditional Chinese medicine resources. Finally,it discusses the problems existing in the current research and the next direction of phylogenomics research in medicinal taxa. The article will hopefully provide a reference for relevant researches in future.

Herbgenomics: A stepping stone for research into herbal medicine.

From the prehistoric era until the publishing of the Compendium of Materia Medica and the first scientific Nobel Prize in the Chinese mainland for Tu's discovery on anti-malarial tablets, each milestone and stepping stone in the developmental history of herbal medicine involved intrepid exploration, bold hypothesis formulation, and cautious verification. After thousands of years of discovery and development, herbal research has entered a new era-the era of herbgenomics. Herbgenomics combines herbal and genomic research, bridging the gap between traditional herbal medicine and cutting-edge omics studies. Therefore, it provides a general picture of the genetic background of traditional herbs, enabling researchers to investigate the mechanisms underlying the prevention and treatment of human diseases from an omics perspective.

The AP2/ERF transcription factor SmERF128 positively regulates diterpenoid biosynthesis in Salvia miltiorrhiza.

KEY MESSAGE: The novel AP2/ERF transcription factor SmERF128 positively regulates diterpenoid tanshinone biosynthesis by activating the expression of SmCPS1, SmKSL1, and SmCYP76AH1 in Salvia miltiorrhiza. Certain members of the APETALA2/ethylene-responsive factor (AP2/ERF) family regulate plant secondary metabolism. Although it is clearly documented that AP2/ERF transcription factors (TFs) are involved in sesquiterpenoid biosynthesis, the regulation of diterpenoid biosynthesis by AP2/ERF TFs remains elusive. Here, we report that the novel AP2/ERF TF SmERF128 positively regulates diterpenoid tanshinone biosynthesis in Salvia miltiorrhiza. Overexpression of SmERF128 increased the expression levels of copalyl diphosphate synthase 1 (SmCPS1), kaurene synthase-like 1 (SmKSL1) and cytochrome P450 monooxygenase 76AH1 (SmCYP76AH1), whereas their expression levels were decreased when SmERF128 was silenced. Accordingly, the content of tanshinone was reduced in SmERF128 RNA interference (RNAi) hairy roots and dramatically increased in SmERF128 overexpression hairy roots, as demonstrated through Ultra Performance Liquid Chromatography (UPLC) and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis. Furthermore, SmERF128 activated the expression of SmCPS1, SmKSL1, and SmCYP76AH1 by binding to the GCC box, and to the CRTDREHVCBF2 (CBF2) and RAV1AAT (RAA) motifs within their promoters during in vivo and in vitro assays. Our findings not only reveal the molecular basis of how the AP2/ERF transcription factor SmERF128 regulates diterpenoid biosynthesis, but also provide useful information for improving tanshinone production through genetic engineering.

Trends in herbgenomics.

From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networks of herbs to clarify their molecular mechanism in the prevention and treatment of human diseases. The main theoretical system includes genomics, functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, metagenomics, synthetic biology, pharmacogenomics of TCM, and bioinformatics, among other fields. Herbgenomics is mainly applicable to the study of medicinal model plants, genomic-assisted breeding, herbal synthetic biology, protection and utilization of gene resources, TCM quality evaluation and control, and TCM drug development. Such studies will accelerate the application of cutting-edge technologies, revitalize herbal research, and strongly promote the development and modernization of TCM.

Application of phylogenomics in Chinese medicine resources / 中国中药杂志

China is rich in the diversified Chinese medicine resources and is notable for the wide and long-term applications of Chinese medicine. However,the lack of genomic information on medicinal taxa leads to problems in relation to resource conservation and the downstream application of traditional Chinese medicine resources,which restricts the modernization process of traditional Chinese medicine. Molecular phylogenetics is an important tool to understand the origin and evolution of the earth's biodiversity and promote the conservation and use of medicinal taxa. With the development of sequencing technology,the combination of genomic data extends the traditional molecular phylogenetics to the research level of phylogenomics,making it more powerfully applied to all aspects of biological research. Undoubtedly,carrying out phylogenomic research on Chinese medicine species will greatly promote their resources conservation,molecular evaluation and identification,and the exploration and utilization of natural pharmacodynamic components,promoting the modernization of traditional Chinese medicine. This article starts with a brief introduction of the developing history and basic research methods of phylogenomics,and then reviews the current research progress in phylogenomics related to traditional Chinese medicine resources. Finally,it discusses the problems existing in the current research and the next direction of phylogenomics research in medicinal taxa. The article will hopefully provide a reference for relevant researches in future.

Current Status and Prospect of Discipline Construction of Herbgenomics / 中国实验方剂学杂志

Herbgenomics is an interdisciplinary subject between traditional Chinese medicine(TCM) and genomics.It is a comprehensive discipline covering multi-omics research in both medicinal organisms of TCM and the relationship of TCM to human body.It has been widely used in the research fields of medicinal model organisms,synthetic biology of TCM,identification of TCM molecules and breeding of medicinal plant cultivars,pharmacokinetics,and the study on the geoherbalism and medicinal of TCM.With the release of important documents,such as the Law of the People's Republic of China on TCM and the Outline of TCM Development Strategy(2016-2030),the Chinese medicine industry has entered a new and high-level development opportunity and the herbgenomic research area has got a landmark achievement.The training of well-rounded students and researchers is a key point for the development of TCM industry and the reform of medical colleges and universities.Therefore,the establishment of herbgenomics is particularly important for the modernization of TCM.At present,many colleges and universities have set up the course of Herbgenomics among graduate students and undergraduates,and initially formed a distinctive herbal genomics talent training system.This paper introduces the herbgenomics from the progress of the research,the development of teaching courses,the background of the textbook,the main content and key technologies of the discipline and the prospect of discipline construction,in order to provide theoretical basis and methodological support for the discipline construction,personal training and scientific research of herbgenomics.

Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance.

Resurrection plants, which are the "gifts" of natural evolution, are ideal models for studying the genetic basis of plant desiccation tolerance. Here, we report a high-quality genome assembly of 301 Mb for the diploid spike moss Selaginella tamariscina, a primitive vascular resurrection plant. We predicated 27 761 protein-coding genes from the assembled S. tamariscina genome, 11.38% (2363) of which showed significant expression changes in response to desiccation. Approximately 60.58% of the S. tamariscina genome was annotated as repetitive DNA, which is an almost 2-fold increase of that in the genome of desiccation-sensitive Selaginella moellendorffii. Genomic and transcriptomic analyses highlight the unique evolution and complex regulations of the desiccation response in S. tamariscina, including species-specific expansion of the oleosin and pentatricopeptide repeat gene families, unique genes and pathways for reactive oxygen species generation and scavenging, and enhanced abscisic acid (ABA) biosynthesis and potentially distinct regulation of ABA signaling and response. Comparative analysis of chloroplast genomes of several Selaginella species revealed a unique structural rearrangement and the complete loss of chloroplast NAD(P)H dehydrogenase (NDH) genes in S. tamariscina, suggesting a link between the absence of the NDH complex and desiccation tolerance. Taken together, our comparative genomic and transcriptomic analyses reveal common and species-specific desiccation tolerance strategies in S. tamariscina, providing significant insights into the desiccation tolerance mechanism and the evolution of resurrection plants.

Molecular Mechanism for the Quality of Medicinal Plants Affected by Drought Stress / 世界科学技术-中医药现代化

Drought stress could significantly affect the growth of medical plants, while moderate drought stress can effectively improve the quality of medicinal plants. Recently Herbgenomics promotes innovative research on the molecular mechanism for the quality of medicinal plants affected by drought stress. Here, we summarized the effects of drought stress on active compounds including alkaloids, flavonoids, terpenoids, phenols and saponins, and biomass of medicinal plants. Moreover, the studies on the quality of medicinal plants affected by drought stress using Herbgenomic technologies, the reactive oxygen species metabolism, and ABA signaling pathway, were reviewed. It is proposed to reveal the molecular mechanism for the quality of medicinal plants affected by drought stress, and to explore molecular markers closely related to drought-tolerance traits using medicinal model plant system based on Herbgenomics. This review provides a theoretical basis for improving the quality of medicinal plants, breeding of drought-tolerant medicinal plants and guiding agricultural production of traditional Chinese medicine.

RNA Sequencing and Coexpression Analysis Reveal Key Genes Involved in α-Linolenic Acid Biosynthesis in Perilla frutescens Seed.

Perillafrutescen is used as traditional food and medicine in East Asia. Its seeds contain high levels of α-linolenic acid (ALA), which is important for health, but is scarce in our daily meals. Previous reports on RNA-seq of perilla seed had identified fatty acid (FA) and triacylglycerol (TAG) synthesis genes, but the underlying mechanism of ALA biosynthesis and its regulation still need to be further explored. So we conducted Illumina RNA-sequencing in seven temporal developmental stages of perilla seeds. Sequencing generated a total of 127 million clean reads, containing 15.88 Gb of valid data. The de novo assembly of sequence reads yielded 64,156 unigenes with an average length of 777 bp. A total of 39,760 unigenes were annotated and 11,693 unigenes were found to be differentially expressed in all samples. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, 486 unigenes were annotated in the "lipid metabolism" pathway. Of these, 150 unigenes were found to be involved in fatty acid (FA) biosynthesis and triacylglycerol (TAG) assembly in perilla seeds. A coexpression analysis showed that a total of 104 genes were highly coexpressed (r > 0.95). The coexpression network could be divided into two main subnetworks showing over expression in the medium or earlier and late phases, respectively. In order to identify the putative regulatory genes, a transcription factor (TF) analysis was performed. This led to the identification of 45 gene families, mainly including the AP2-EREBP, bHLH, MYB, and NAC families, etc. After coexpression analysis of TFs with highly expression of FAD2 and FAD3 genes, 162 TFs were found to be significantly associated with two FAD genes (r > 0.95). Those TFs were predicted to be the key regulatory factors in ALA biosynthesis in perilla seed. The qRT-PCR analysis also verified the relevance of expression pattern between two FAD genes and partial candidate TFs. Although it has been reported that some TFs are involved in seed development, more direct evidence is still needed to verify their function. However, these findings can provide clues to reveal the possible molecular mechanisms of ALA biosynthesis and its regulation in perilla seed.

Advances and Applications of Frontier Omics Technology of Chinese Materia Medica / 世界科学技术-中医药现代化

A lot of research achievements have been obtained in the field of Chinese materia medica (CMM) in recent years,which have been paid close attention to by the international community.It also promotes the internationalization of traditional Chinese medicine (TCM).However,the genetic background of CMM bioactive compounds and the effect on human genes of CMM composition after ingestion are not clear.As a frontier technology,herbgenomics provides a new method for the study of biosynthesis,breeding of new varieties and the identification of CMM.It will also promote more achievements in this field.This paper reviewed the research progress of study on the frontier omics technology of CMM in order to provide references for CMM research.

Estimation of Genome Size of Ginseng Based on Herbgenomics by Flow Cytometric Analysis And High-throughput Sequence / 世界科学技术-中医药现代化

Ginseng is the dried root and rhizome of Panax ginseng.The lack of genomic data has restricted the development of ginseng industry and basic research.The genome size of P.ginseng was estimated to be 3.42 Gb by using the genome data of Oryza sativa ssp.Nipponbare and Glycine max (L.) Merrill as the reference and the flow cytometric analysis.Meanwhile,shotgun libraries with the insert size of 250 bp and 500 bp were constructed,and sequenced for double terminal PE 150 by using Illumina Hiseq X Ten platform.Totally,183.82 Gb high quality data was obtained after filtering the raw data.The genome size of P.ginseng was 3.35 Gb and the sequencing depth was 54.87 X by K-mer analysis.In this study,flow cytometry and K-mer analysis were used to identify the genome size of ginseng,which provided basic data for the further whole genome sequencing and herbgenomics studies.

[Herbgenomics].

Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases. Herbgenomics includes herbal structural genomics, functional genomics, transcriptomics, proteomics, metabonomics, epigenomics and metagenomics. Genomic information, together with transcriptomic, proteomic, and metabolomic data, can therefore be used to predict secondary metabolite biosynthetic pathways and their regulation, triggering a revolution in discovery-based research aimed at understanding the genetics and biology of herbs. Herbgenomics provides an effective platform to support chemical and biological analyses of complex herbal products that may contain more than one active component. Herbgenomics is now being applied to many areas of herb related biological research to help understand the quality of traditional medicines and for molecular herb identification through the establishment of an herbal gene bank. Moreover, functional genomics can contribute to model herb research platforms, geoherbal research, genomics-assisted herb breeding, and herbal synthetic biology, all of which are important for securing the future of medicinal plants and their active compounds. In addition, Herbgenomics will facilitate the elucidation of the targets and mechanism of herbs in disease treatment and provide support for personalized precise medicine.Herbgenomics will accelerate the application of cutting-edge technologies in herbal research and provide an unprecedented opportunity to revolutionize the use and acceptance of traditional herbal medicines.

Herbgenomics / 中国中药杂志

Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases. Herbgenomics includes herbal structural genomics, functional genomics, transcriptomics, proteomics, metabonomics, epigenomics and metagenomics. Genomic information, together with transcriptomic, proteomic, and metabolomic data, can therefore be used to predict secondary metabolite biosynthetic pathways and their regulation, triggering a revolution in discovery-based research aimed at understanding the genetics and biology of herbs. Herbgenomics provides an effective platform to support chemical and biological analyses of complex herbal products that may contain more than one active component. Herbgenomics is now being applied to many areas of herb related biological research to help understand the quality of traditional medicines and for molecular herb identification through the establishment of an herbal gene bank. Moreover, functional genomics can contribute to model herb research platforms, geoherbal research, genomics-assisted herb breeding, and herbal synthetic biology, all of which are important for securing the future of medicinal plants and their active compounds. In addition, Herbgenomics will facilitate the elucidation of the targets and mechanism of herbs in disease treatment and provide support for personalized precise medicine.Herbgenomics will accelerate the application of cutting-edge technologies in herbal research and provide an unprecedented opportunity to revolutionize the use and acceptance of traditional herbal medicines.