Genetic and Epigenetic Diversities Shed Light on Domestication of Cultivated Ginseng (Panax ginseng)

Rapid discrimination of Panax ginseng powder adulterated with various root plants by FT-IR spectroscopy coupled with multivariate analysis

Panax ginseng powder adulterated with other root plants (arrowroot, bellflower, and lance asiabell) was discriminated using Fourier transform infrared (FT-IR) spectroscopy, combined with multivariate analysis. Principal component analysis visually diagnosed the adulteration by showing two distinct clusters based on presence of adulteration. Wavenumber regions (1000 cm-1 and 3300 cm-1) selected from the loading plot associated with the vibration of OH and CH bond in ginsenoside and aromatic compounds. A quantitative model for the content of ginsenosides and specific aromatic compounds as indicators of pure ginseng powder, was developed based on partial least square regression analysis. The performance of the prediction model preprocessed with the Savizky-Golay 1st derivative was improved to R2 of 0.9650, 0.9635, and 0.9591 for Rb1, Rc, and β-Panasinsene, respectively. Therefore, FT-IR technology makes it possible to rapidly authenticate pure ginseng product based on the ginsenoside contents and aroma compound.

The phenotypic variation mechanisms of Atractylodes lancea post-cultivation revealed by conjoint analysis of rhizomic transcriptome and metabolome

The wild Atractylodes lancea rhizomes have been traditionally used as herbal medicine. As the increasingly exhaustion of wild A. lancea, the artificial cultivation mainly contributed to the medicinal material production. However, besides the phenotypic variation of rhizome phenotypic trait alteration, the qualities of cultivated A. lancea decrease compared with the wild counterpart. To unveil the physiological and molecular mechanism beneath the phenotypic variation, GC-MS-based volatile organic compounds (VOCs) profiling and RNAseq-based transcriptome analysis were conducted. The volatile metabolomics profiling revealed 65 differentially accumulated metabolites (DAMs) while the transcriptomic profiling identified 12 009 differentially expressed unigenes (DEGs) post-cultivation. The volatile active compounds including atractylone, and eudesmol accumulated more in wild rhizome than in the cultivated counterpart, and several unigenes in terpene synthesis were downregulated under cultivated condition. Compared with the wild A. lancea rhizome, the contents of bioactive Jasmonic Acid (JAs) in cultivated A. lancea rhizome were higher, and evidences that JAs negatively regulate the terpenes biosynthesis in the cultivated A. lancea rhizome were also provided. The combinational omics analysis further indicated the high correlation between the ten cultivation-suppressed VOCs and the cultivation-altered genes for sesquiterpenoids biosynthesis in A. lancea. The network of the cultivation-altered transcription factors (TFs) and the ten VOCs suggested TFs (e.g. Arabidopsis ERF13 homologs and WRKY50) are involved in the regulation of terpenes biosynthesis. These results laid a theoretical basis for developing geo-herbalism medicinal plants with "high quality and optimal shape".

Advances in DNA methylation and demethylation in medicinal plants: a review

DNA methylation and demethylation are widely acknowledged epigenetic phenomena which can cause heritable and phenotypic changes in functional genes without changing the DNA sequence. They can thus affect phenotype formation in medicinal plants. However, a comprehensive review of the literature summarizing current research trends in this field is lacking. Thus, this review aims to provide an up-to-date summary of current methods for the detection of 5-mC DNA methylation, identification and analysis of DNA methyltransferases and demethyltransferases, and regulation of DNA methylation in medicinal plants. The data showed that polyploidy and environmental changes can affect DNA methylation levels in medicinal plants. Changes in DNA methylation can thus regulate plant morphogenesis, growth and development, and formation of secondary metabolites. Future research is required to explore the mechanisms by which DNA methylation regulates the accumulation of secondary metabolites in medicinal plants.

Transcriptome analysis provides insights into the cell wall and aluminum toxicity related to rusty root syndrome of Panax ginseng

Rusty root syndrome is a common and serious disease in the process of Panax ginseng cultivation. This disease greatly decreases the production and quality of P. ginseng and causes a severe threat to the healthy development of the ginseng industry. However, its pathogenic mechanism remains unclear. In this study, Illumina high-throughput sequencing (RNA-seq) technology was used for comparative transcriptome analysis of healthy and rusty root-affected ginseng. The roots of rusty ginseng showed 672 upregulated genes and 526 downregulated genes compared with the healthy ginseng roots. There were significant differences in the expression of genes involved in the biosynthesis of secondary metabolites, plant hormone signal transduction, and plant-pathogen interaction. Further analysis showed that the cell wall synthesis and modification of ginseng has a strong response to rusty root syndrome. Furthermore, the rusty ginseng increased aluminum tolerance by inhibiting Al entering cells through external chelating Al and cell wall-binding Al. The present study establishes a molecular model of the ginseng response to rusty roots. Our findings provide new insights into the occurrence of rusty root syndrome, which will reveal the underlying molecular mechanisms of ginseng response to this disease.

Combining Metabolomics and Transcriptomics to Reveal the Regulatory Mechanism of Taproot Enlargement in Panax ginseng

Ginseng is regarded as the “king of herbs” in China, with its roots and rhizomes used as medicine, and it has a high medicinal value. In order to meet the market demand, the artificial cultivation of ginseng emerged, but different growth environments significantly affect the root morphology of garden ginseng. In this study, we used ginseng cultivated in deforested land (CF-CG) and ginseng cultivated in farmland (F-CG) as experimental materials. These two phenotypes were explored at the transcriptomic and metabolomic levels so as to understand the regulatory mechanism of taproot enlargement in garden ginseng. The results show that, compared with those of F-CG, the thickness of the main roots in CF-CG was increased by 70.5%, and the fresh weight of the taproots was increased by 305.4%. Sucrose, fructose and ginsenoside were significantly accumulated in CF-CG. During the enlargement of the taproots of CF-CG, genes related to starch and sucrose metabolism were significantly up-regulated, while genes related to lignin biosynthesis were significantly down-regulated. Auxin, gibberellin and abscisic acid synergistically regulated the enlargement of the taproots of the garden ginseng. In addition, as a sugar signaling molecule, T6P might act on the auxin synthesis gene ALDH2 to promote the synthesis of auxin and, thus, participate in the growth and development of garden ginseng roots. In summary, our study is conducive to clarifying the molecular regulation mechanism of taproot enlargement in garden ginseng, and it provides new insights for the further exploration of the morphogenesis of ginseng roots.

Transcriptome reveals insights into biosynthesis of ginseng polysaccharides

BACKGROUND

Ginseng polysaccharides, have been used to treat various diseases as an important active ingredient. Nevertheless, the biosynthesis of ginseng polysaccharides is poorly understood. To elucidate the biosynthesis mechanism of ginseng polysaccharides, combined the transcriptome analysis and polysaccharides content determination were performed on the roots, stems, and leaves collected from four cultivars of ginseng.

RESULTS

The results indicated that the total contents of nine monosaccharides were highest in the roots. Moreover, the total content of nine monosaccharides in the roots of the four cultivars were different but similar in stems and leaves. Glucose (Glc) was the most component of all monosaccharides. In total, 19 potential enzymes synthesizing of ginseng polysaccharides were identified, and 17 enzymes were significantly associated with polysaccharides content. Among these genes, the expression of phosphoglucomutase (PGM), glucose-6-phosphate isomerase (GPI), UTP-glucose-1-phosphate uridylyltransferase (UGP2), fructokinase (scrK), mannose-1-phosphate guanylyltransferase (GMPP), phosphomannomutase (PMM), UDP-glucose 4-epimerase (GALE), beta-fructofuranosidase (sacA), and sucrose synthase (SUS) were correlated with that of MYB, AP2/ERF, bZIP, and NAC transcription factors (TFs). These TFs may regulate the expression of genes involved in ginseng polysaccharides synthesis.

CONCLUSION

Our findings could provide insight into a better understanding of the regulatory mechanism of polysaccharides biosynthesis, and would drive progress in genetic improvement and plantation development of ginseng.

Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae)

Certain species within the genus Panax L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panaxvietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.

Ginsenosides regulate adventitious root formation in Panax ginseng via a CLE45-WOX11 regulatory module

Adventitious root branching is vital to plant growth and regeneration, but the regulation of this process remains unclear. We therefore investigated how ginsenosides regulate adventitious root branching in Panax ginseng. Cell proliferation and adventitious root branching were decreased in the presence of ginsenoside Rb1 and a high concentration of ginsenoside Re, but increased when treating with a low concentration of Re. Moreover, the exogenous application of a synthetic dodeca-amino acid peptide that has a CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) motif corresponding to PgCLE45 retarded root growth in both ginseng and Arabidopsis. The root Re levels and the expression of the DDS, CYP716A47, and CYP716A53 genes that encode enzymes involved in ginsenoside synthesis were decreased in the presence of PgCLE45. The expression profiles of PgWOX and PgCLE genes were determined to further investigate the CLE-WOX signaling pathway. The levels of PgWOX11 transcripts showed an inverse pattern to PgCLE45 transcripts. Using yeast one-hybrid assay, EMSA, and ChIP assay, we showed that PgWOX11 bound to the PgCLE45 promoter, which contained the HD motif. Transient expression assay showed that PgWOX11 induced the expression of PgCLE45 in adventitious roots, while PgCLE45 suppressed the expression of PgWOX11. These results suggest that there is a negative feedback regulation between PgCLE45 and PgWOX11. Taken together, these data show that ginsenosides regulate adventitious root branching via a novel PgCLE45-PgWOX11 regulatory loop, providing a potential mechanism for the regulation of adventitious root branching.

Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines

Long-term cultivation of Panax ginseng cell lines leads to a decreasing synthesis of the biologically active substances used in traditional medicine. To gain insight into the cellular mechanisms which may influence this process, we analyzed variations within the rDNA cluster of the Oriental ginseng cell lines. The cell lines were cultivated for 6 and 24 years; the number of nucleoli and chromosomes was analyzed. The complete 18S rDNA sequences were cloned and sequenced. The nucleotide polymorphism and phylogenetic relations of the sequences were analyzed, and the secondary structures for separate 18S rRNA regions were modeled. The 18S rDNA accumulated mutations during cell cultivation that correlate well with an increase in the number of chromosomes and nucleoli. The patterns of nucleotide diversity are culture-specific and the increasing polymorphism associates with cytosine methylation sites. The secondary structures of some 18S rRNA regions and their interaction can alter during cultivation. The phylogenetic tree topologies are particular for each cell line.The observed alterations in rDNA clusters are associated with a somaclonal variation, leading to changes in the pattern of intracellular synthesis during cell cultivation. The identified divergent rRNAs could provide additional gene expression regulation in P. ginseng cells by forming heterogeneous ribosomes.

The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation

Tea plant is an important economic crop, which is used to produce the world's oldest and most widely consumed tea beverages. Here, we present a high-quality reference genome assembly of the tea plant (Camellia sinensis var. sinensis) consisting of 15 pseudo-chromosomes. LTR retrotransposons (LTR-RTs) account for 70.38% of the genome, and we present evidence that LTR-RTs play critical roles in genome size expansion and the transcriptional diversification of tea plant genes through preferential insertion in promoter regions and introns. Genes, particularly those coding for terpene biosynthesis proteins, associated with tea aroma and stress resistance were significantly amplified through recent tandem duplications and exist as gene clusters in tea plant genome. Phylogenetic analysis of the sequences of 81 tea plant accessions with diverse origins revealed three well-differentiated tea plant populations, supporting the proposition for the southwest origin of the Chinese cultivated tea plant and its later spread to western Asia through introduction. Domestication and modern breeding left significant signatures on hundreds of genes in the tea plant genome, particularly those associated with tea quality and stress resistance. The genomic sequences of the reported reference and resequenced tea plant accessions provide valuable resources for future functional genomics study and molecular breeding of improved cultivars of tea plants.

Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta

Ilyonectria robusta causes rusty root rot, the most devastating chronic disease of ginseng. Here, we for the first time report the high-quality genome of the I. robusta strain CD-56. Time-course (36 h, 72 h, and 144 h) dual RNA-Seq analysis of the infection process was performed, and many genes, including candidate effectors, were found to be associated with the progression and success of infection. The gene expression profile of CD-56 showed a trend of initial inhibition and then gradually returned to a profile similar to that of the control. Analyses of the gene expression patterns and functions of pathogenicity-related genes, especially candidate effector genes, indicated that the stress response changed to an adaptive response during the infection process. For ginseng, gene expression patterns were highly related to physiological conditions. Specifically, the results showed that ginseng defenses were activated by CD-56 infection and persisted for at least 144 h thereafter but that the mechanisms invoked were not effective in preventing CD-56 growth. Moreover, CD-56 did not appear to fully suppress plant defenses, even in late stages after infection. Our results provide new insight into the chronic pathogenesis of CD-56 and the comprehensive and complex inducible defense responses of ginseng root to I. robusta infection.

Identification and 3D gene expression patterns of WUSCEHEL-related homeobox (WOX) genes from Panax ginseng

Wild ginseng (Panax ginseng) can survive in their natural habitat for hundreds of years, reflecting a remarkable plasticity. Plant stem cells (SCs) play a key role in the regenerative capacity and lifelong activity of these plants. WUSCHEL-RELATED HOMEOBOX (WOX) genes are master regulators of plant SC pluripotency, but their functions in medicinal plants have not been previously reported. To investigate whether these genes define different SC niches in ginseng, we cloned and analysed five WOX genes in ginseng (PgWOXs) and found that they might regulate root reconstruction. Then, the whole-mount RNA in situ hybridization was used to characterize the 3D gene expression pattern of PgWOXs in ginseng seedlings and cultured adventitious roots. PgWOX4 was expressed in vascular cambium SCs; PgWOX5 and PgWOX11 were mainly expressed in the tips of seedling and adventitious roots, which are the energetic centre of the meristem; and PgWOX13a and PgWOX13b were detected in the parenchyma cells of the main root of seedlings and cultured adventitious roots, suggesting that they are important for maintaining the balance between SC differentiation and self-renewal in the phloem and xylem. This is the first report of SC regulation in medical herbs; we expect that P. ginseng can serve as a model herb for investigating the relationship between SCs and their herbal morphological features, which would be a new research direction to improve the yield and quality of the medicinal materials by regulating the herbal SCs.

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.

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax

Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.

Genome-Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer)

Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions. In complement, the 45s rDNA, chloroplast and mitochondrial genomes were included to perform phylogenetic and population genetic analyses. The observed spatial genetic structure between northern cultivated ginseng (NCG) and southern cultivated ginseng (SCG) accessions suggested multiple independent origins of cultivated ginseng. Genome-wide scanning further demonstrated that NCG and SCG have undergone distinct selection pressures during the domestication process, with more genes identified in the NCG (97 genes) than in the SCG group (5 genes). Functional analyses revealed that these genes are involved in diverse pathways, including DNA methylation, lignin biosynthesis, and cell differentiation. These findings suggested that the SCG and NCG groups have distinct demographic histories. Candidate genes identified are useful for future molecular breeding of cultivated ginseng.

Development of highly transferable microsatellites for Panax ginseng (Araliaceae) using whole-genome data

PREMISE OF THE STUDY

Highly transferable expressed sequence tag (EST) microsatellites were developed for Panax ginseng (Araliaceae), one of the most celebrated traditional Chinese medicines and an endangered species in East Asia, using whole-genome data.

METHODS AND RESULTS

Twenty-one EST microsatellites were characterized from next-generation sequencing and were composed of di- and trinucleotide repeats. Polymorphisms and genetic diversity were evaluated for 45 accessions of three ginseng landraces. The number of alleles for each locus ranged from one to five among the landraces, and the polymorphism information content varied from 0.0000 to 0.6450. These microsatellites were also tested for congeneric amplification with P. notoginseng, P. stipuleanatus, P. quinquefolius, P. bipinnatifidus, and the closely related species Aralia elata.

CONCLUSIONS

These novel EST-derived microsatellite markers will facilitate further population genetic studies of the genera Panax and Aralia.

The impacts of polyploidy, geographic and ecological isolations on the diversification of Panax (Araliaceae)

BACKGROUND

Panax L. is a medicinally important genus within family Araliaceae, where almost all species are of cultural significance for traditional Chinese medicine. Previous studies suggested two independent origins of the East Asia and North America disjunct distribution of this genus and multiple rounds of whole genome duplications (WGDs) might have occurred during the evolutionary process.

RESULTS

We employed multiple chloroplast and nuclear markers to investigate the evolution and diversification of Panax. Our phylogenetic analyses confirmed previous observations of the independent origins of disjunct distribution and both ancient and recent WGDs have occurred within Panax. The estimations of divergence time implied that the ancient WGD might have occurred before the establishment of Panax. Thereafter, at least two independent recent WGD events have occurred within Panax, one of which has led to the formation of three geographically isolated tetraploid species P. ginseng, P. japonicus and P. quinquefolius. Population genetic analyses showed that the diploid species P. notoginseng harbored significantly lower nucleotide diversity than those of the two tetraploid species P. ginseng and P. quinquefolius and the three species showed distinct nucleotide variation patterns at exon regions.

CONCLUSION

Our findings based on the phylogenetic and population genetic analyses, coupled with the species distribution patterns of Panax, suggested that the two rounds of WGD along with the geographic and ecological isolations might have together contributed to the evolution and diversification of this genus.