Evolutionary roles of polyploidization-derived structural variations in the phenotypic diversification of Panax species.

Genomic structural variations (SVs) are widespread in plant and animal genomes and play important roles in phenotypic novelty and species adaptation. Frequent whole genome duplications followed by (re)diploidizations have resulted in high diversity of genome architecture among extant species. In this study, we identified abundant genomic SVs in the Panax genus that are hypothesized to have occurred through during the repeated polyploidizations/(re)diploidizations. Our genome-wide comparisons demonstrated that although these polyploidization-derived SVs have evolved at distinct evolutionary stages, a large number of SV-intersecting genes showed enrichment in functionally important pathways related to secondary metabolites, photosynthesis and basic cellular activities. In line with these observations, our metabolic analyses of these Panax species revealed high diversity of primary and secondary metabolites both at the tissue and interspecific levels. In particular, genomic SVs identified at ginsenoside biosynthesis genes, including copy number variation and large fragment deletion, appear to have played important roles in the evolution and diversification of ginsenosides. A further herbivore deterrence experiment demonstrated that, as major triterpenoidal saponins found exclusively in Panax, ginsenosides provide protection against insect herbivores. Our study provides new insights on how polyploidization-derived SVs have contributed to phenotypic novelty and plant adaptation.

Phenotypic and transcriptomic responses of the shade-grown species Panax ginseng to variable light conditions.

BACKGROUND AND AIMS: Elucidating how plant species respond to variable light conditions is important to understand the ecological adaptation to heterogeneous natural habitats. Plant performance and its underlying gene regulatory network have been well documented in sun-grown plants. However, the phenotypic and molecular responses of shade-grown plants under variable light conditions have remained largely unclear. METHODS: We assessed the differences in phenotypic performance between Panax ginseng (shade-grown) and Arabidopsis thaliana (sun-grown) under sunlight, shade and deep-shade conditions. To further address the molecular bases underpinning the phenotypic responses, we compared time-course transcriptomic expression profiling and candidate gene structures between the two species. KEY RESULTS: Our results show that, compared with arabidopsis, ginseng plants not only possess a lower degree of phenotypic plasticity among the three light conditions, but also exhibit higher photosynthetic efficiency under shade and deep-shade conditions. Further comparisons of the gene expression and structure reveal that differential transcriptional regulation together with increased copy number of photosynthesis-related genes (e.g. electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under the two shade conditions. In contrast, the inactivation of phytochrome-interacting factors (i.e. absent and no upregulation of the PIF genes) are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under variable light conditions. CONCLUSIONS: Our study provides new insights into how shade-grown plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops.

Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax.

All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the ancestral core-eudicot genome generates abundant genomic diversity, but the role of this diversity in shaping the hierarchical genome architecture, such as chromatin topology and gene expression, remains poorly understood. Here, we assemble chromosome-level genomes of one diploid and three tetraploid Panax species and conduct in-depth comparative genomic and epigenomic analyses. We show that chromosomal interactions within each duplicated ancestral chromosome largely maintain in extant Panax species, albeit experiencing ca. 100-150 million years of evolution from a shared ancestor. Biased genetic fractionation and epigenetic regulation divergence during polyploidization/(re)diploidization processes generate remarkable biochemical diversity of secondary metabolites in the Panax genus. Our study provides a paleo-polyploidization perspective of how reshuffling of the ancestral core-eudicot genome leads to a highly dynamic genome and to the metabolic diversification of extant eudicot plants.

Symmetrical drug-related intertriginous and flexural exanthema/baboon syndrome induced by traditional Chinese medicine.

BACKGROUND: Symmetrical drug-related intertriginous and flexural exanthema (SDRIFE) refers to an uncommon cutaneous adverse reaction that symmetrically involves the buttock and intertriginous areas after systemic exposure to the offending drug and is previously known as baboon syndrome. SDRIFE related with traditional Chinese medicine (TCM) has not been reported. OBJECTIVE: We presented a case of SDRIFE /baboon syndrome induced by TCM, Xi-Huang capsule. METHODS: A 57-years-old man presented with macular erythematous rash mainly on his intergluteal, inguinal, axillary, popliteal regions for a duration of 5 days. The lesions appeared a day after an oral Chinese patent medicine Xi-Huang capsule for arthralgia. Drug eruption was diagnosed. The rash disappeared completely within a week with immediate discontinuation of Xi-Huang capsule and a short term of systemic therapy with glucocorticosteroids. Patch testing was performed on the patient 1 month after complete resolution. He was patch tested with Xi-Huang capsule (5% and 10% in petroleum) using Finn Chambers on Scanpor tape and T.R.U.E. test system. Five heathy volunteers were also patch tested with the same Xi-Huang capsule. RESULTS: Patch testing to 20 common contact allergens including nickel and fragrance were negative. TCM patch test was positive. No positive results were found in five volunteers. Months later, the patient relapsed after an oral herbal Chinese medicine challenge for arthralgia. To avoid the rash recurrence, he stopped taking any Chinese herbal medicine and had complete resolution of disease. CONCLUSION: The Chinese patent drugs for external and oral have unique advantages and have been widely used in many diseases. It is important that dermatologists monitor for clinically significant manifestations of TCM, such as baboon syndrome. Patch testing could help make a definitive diagnosis.

Efficacy and Safety of Giant Condyloma Acuminatum with Monotherapy of Topical Traditional Chinese Medicine: Report of Eight Cases.

BACKGROUND: Giant condyloma acuminatum (GCA), also called Buschke-Löwenstein tumor, presents as a verrucous infiltrating lesion and is caused by sexual transmission of human papilloma virus. The optimal treatment is controversial and there are no standard guidelines because of its rarity and frequent recurrence. It has a relatively high local recurrence rate. OBJECTIVE: We here report eight patients (six men and two women) with GCA whose lesions were successfully treated topically with traditional Chinese medicine (TCM) preparations, paiteling. METHODS AND MATERIALS: We administered topical TCM preparations to eight patients diagnosed with GCA who had refused surgery. The treatment process included three stages, their durations depending on the speed of resolution of the lesions and the results of visual inspection with acetic acid. RESULTS: No significant complications occurred in any patient. The functional and esthetic outcomes were satisfactory. No recurrences were detected during follow-up. CONCLUSION: Topical treatment with TCM preparations may be a good alternative to surgery or other traditional methods for the treatment of GCA. This treatment has the advantages of being non-invasive, painless, and having a low risk of recurrence, and may be a useful adjunct to mainstream medical treatments.

Evolutionary Contribution of Duplicated Genes to Genome Evolution in the Ginseng Species Complex.

Genes duplicated by whole genome duplication (WGD) and small-scale duplication (SSD) have played important roles in adaptive evolution of all flowering plants. However, it still remains underinvestigated how the distinct models of duplication events and their contending evolutionary patterns have shaped the genome and epigenomes of extant plant species. In this study, we investigated the contribution of the WGD- and SSD-derived duplicate genes to the genome evolution of one diploid and three closely related allotetraploid Panax species based on genome, methylome, and proteome data sets. Our genome-wide comparative analyses revealed that although the ginseng species complex was recently diverged, they have evolved distinct overall patterns of nucleotide variation, cytosine methylation, and protein-level expression. In particular, genetic and epigenetic asymmetries observed in the recent WGD-derived genes are largely consistent across the ginseng species complex. In addition, our results revealed that gene duplicates generated by ancient WGD and SSD mechanisms exhibited distinct evolutionary patterns. We found the ancient WGD-derived genes (i.e., ancient collinear gene) are genetically more conserved and hypomethylated at the cytosine sites. In contrast, some of the SSD-derived genes (i.e., dispersal duplicated gene) showed hypermethylation and high variance in nucleotide variation pattern. Functional enrichment analyses of the duplicated genes indicated that adaptation-related traits (i.e., photosynthesis) created during the distant ancient WGDs are further strengthened by both the more recent WGD and SSD. Together, our findings suggest that different types of duplicated genes may have played distinct but relaying evolutionary roles in the polyploidization and speciation processes in the ginseng species complex.

Morphological and Transcriptome Analyses Provide Insights into Growth Inhibition of Trichophyton rubrum Caused by Laser Irradiation.

Trichophyton rubrum is one of the most common types of dermatophyte, causing superficial skin mycosis in human populations. Although laser treatment of onychomycosis has been proven to be effective in the clinic, the underlying mechanism of the effect of the laser on fungal growth is not clear. The objective of the present study was to observe the ultrastructural changes of Trichophyton rubrum following laser irradiation and compare the transcriptome differences between the laser irradiation group and control group. In the present study, scanning electron microscopy and transmission electron microscopy were used to observe the ultrastructural changes following the laser irradiation of Trichophyton rubrum. We also performed RNA-seq to investigate the effects of laser irradiation on Trichophyton rubrum by comparing the transcriptome pattern with the control. Morphological observation with electron microscopy indicated that laser irradiation resulted in the destruction of the cell membrane system. A significant induction of apoptosis was noted compared with the control group, which was confirmed by the formation of the myeloid body and protein aggregates in the cytoplasm. RNA-seq demonstrated that the expression levels of Acyl-CoA N-acyltransferase and S-adenosyl-L-methionine-dependent methyltransferase were increased in the laser irradiation group. This result indicated that laser irradiation triggered the initiation of the damage repair pathway. In conclusion, the present study suggested that laser irradiation caused physiological injury and therefore inhibited the growth of Trichophyton rubrum.

Efficacy and safety of Run Zao Zhi Yang capsule on chronic eczema: a multiple-center, randomized, double-blind, placebo-controlled clinical study.

Background: Run Zao Zhi Yang capsule (RZZYC) has been widely applied for eczema treatment as a traditional Chinese medicine, while its efficacy has not been scientifically investigated. Objective: We conducted this multiple-centers, randomized, double-blind, placebo-controlled study to investigate the effectiveness and safety of RZZYC on the treatment of patients with mild to moderate chronic eczema. Methods: 240 patients were randomly assigned into the experimental group and the placebo group. The primary efficacy indicator was the Eczama Area and Severity Index (EASI) score at week 4. The patient with an EASI score that decreases more than 95% from baseline (EASI 95) was judged as cured. The cured patients were followed up for another 8 weeks. The differences on EASI, Visual Analogue Score (VAS), and Dermatology Life Quality Index (DLQI) score were compared. Results: The proportions of EASI 95 and EASI 60 in the experimental group were significantly higher than those of the control group at week4 (p = .002 and p < .001, respectively), the VAS score decreased more significantly in the experimental group at week 4. After 8 weeks follow-up, no difference on recurrence rate and adverse event rate between the two groups was observed. Conclusion: RZZYC provides a good effect on the treatment of mild-to-moderate chronic eczema with a low recurrence and tolerable adverse events, and is a potential treatment that may be implemented in clinical practice.

Skin Biophysical Parameters and Patch Test Results in People Predisposing to Xiaotong Tiegao Induced Irritant Contact Dermatitis.

BACKGROUND: Xiaotong Tiegao (XTT) is an ancient topical Tibetan medicine plaster which is widely used in China. Irritant contact dermatitis (ICD) caused by XTT is very common. It is still unclear why some people are more prone to develop ICD. The aim of this study is to study the baseline skin biophysical parameters and patch test results in individuals predisposing to XTT induced ICD. METHODS: During a four-month period, 149 healthy volunteers with ICD and 50 volunteers without ICD after applying XTT were recruited. The skin biophysical parameters were measured, and contact allergy to 20 common allergens was patch tested, at two weeks after the ICD was recovered. RESULTS: There were no significant differences in age and sex between ICD and control groups. It was found that skin median melanin value (176.50 vs 189.50, P < 0.05, Mann-Whitney U-test) and erythema value (319.90 ± 70.49 vs 347.93 ± 84.55, P < 0.05, Independent-Samples T test) were much lower in ICD than control group. Overall patch test results were not different, but the positivity rate of nickel sulfate (15.44% vs 4.00%, P < 0.05, Fisher's exact test) was significantly higher in ICD group. CONCLUSIONS: In conclusion, people with nickel allergy, lower values of skin melanin, and erythema are predisposing to develop ICD.

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.

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

Chinese ginseng (Panax ginseng) is a medically important herb within Panax and has crucial cultural values in East Asia. As the symbol of traditional Chinese medicine, Chinese ginseng has been used as a herbal remedy to restore stamina and capacity in East Asia for thousands of years. To address the evolutionary origin and domestication history of cultivated ginseng, we employed multiple molecular approaches to investigate the genetic structures of cultivated and wild ginseng across their distribution ranges in northeastern Asia. Phylogenetic and population genetic analyses revealed that the four cultivated ginseng landraces, COMMON, BIANTIAO, SHIZHU, and GAOLI (also known as Korean ginseng), were not domesticated independently and Fusong Town is likely one of the primary domestication centers. In addition, our results from population genetic and epigenetic analyses demonstrated that cultivated ginseng maintained high levels of genetic and epigenetic diversity, but showed distinct cytosine methylation patterns compared with wild ginseng. The patterns of genetic and epigenetic variation revealed by this study have shed light on the domestication history of cultivated ginseng, which may serve as a framework for future genetic improvements.

A simple strategy for development of single nucleotide polymorphisms from non-model species and its application in Panax.

Single nucleotide polymorphisms (SNPs) are widely employed in the studies of population genetics, molecular breeding and conservation genetics. In this study, we explored a simple route to develop SNPs from non-model species based on screening the library of single copy nuclear genes (SCNGs). Through application of this strategy in Panax, we identified 160 and 171 SNPs from P. quinquefolium and P. ginseng, respectively. Our results demonstrated that both P. ginseng and P. quinquefolium possessed a high level of nucleotide diversity. The number of haplotype per locus ranged from 1 to 12 for P. ginseng and from 1 to 9 for P. quinquefolium, respectively. The nucleotide diversity of total sites (πT) varied between 0.000 and 0.023 for P. ginseng and 0.000 and 0.035 for P. quinquefolium, respectively. These findings suggested that this approach is well suited for SNP discovery in non-model organisms and is easily employed in standard genetics laboratory studies.

Topical application of a Chinese medicine, Qingpeng ointment, ameliorates 2, 4-dinitrofluorobenzene-induced allergic contact dermatitis in BALB/c mice.

BACKGROUND: Qingpeng ointment (QP) is a traditional Chinese medicine which has been used for treatment of eczema in China. However, the mechanisms of its anti-inflammatory activities are not known. OBJECTIVES: To assess the anti-inflammatory effects of QP using a mouse model of allergic contact dermatitis, compare the effects with mometasone furoate cream (MF), and to relate the effects to modulation of inflammatory cytokines. METHODS: Persistent dermatitis was induced in BALB/c mice using dinitrofluorobenzene. Topical treatment, including the vehicle of QP, 50%, 75%, 100% QP in vehicle, and MF was applied for 14 days. Dermatitis was evaluated macroscopically and microscopically at day 8 and day 15 after treatment. The levels of IL1B, IL2, TNFA, IFNG in both sera and skin tissue were detected with Enzyme-Linked Immunosorbent Assay (ELISA). RESULTS: Significant reductions of skin inflammation in mice skin were observed after treatment with QP and MF, but not with the vehicle of QP. Similar to MF, QP also suppressed the expression of IL1B, IL2, TNFA and IFNG. CONCLUSION: This study demonstrates that QP inhibits allergic contact dermatitis in mice, similar to MF. QP suppresses the expression of Th1 cytokines in both sera and skin tissue, by which it may exert its anti-inflammatory effects.

Anti-inflammatory effect of qingpeng ointment in atopic dermatitis-like murine model.

Qingpeng ointment (QP) is a Chinese medicine which has been used in treatment of atopic dermatitis (AD) in China. AD-like lesions were induced in BALB/c mice by repeated application of 2,4-dinitrofluorobenzene (DNFB) on shaved backs. The mice were then treated for 2 weeks with QP of different concentrations and Mometasone Furoate cream (MF), respectively. Macroscopic and microscopic changes of the skin lesions were observed after the treatment. The levels of serum immunoglobulin (Ig) E, tissue interferon (IFN)- γ , and interleukin (IL)-4 and IL-17A and the levels of involucrin, filaggrin, and kallikrein7 in epidermis were measured. The results show severe dermatitis with immune profiles similar to human acute AD. A significant infiltration of CD4(+) T and mast cells was observed in dermis of lesion but inhibited by QP after a 2-week treatment with it. The production of IgE, IL-4 and the mRNA expression of IL-17A were also suppressed, but the level of IFN- γ was increased. MF suppressed all production of these cytokines and IgE. Accordingly, the mechanism of QP on AD might correlate with its ability of modulating the immune dysfunctions rather than suppressing them. It had no effect on expressions of involucrin and filaggrin, except that its vehicle decreased the level of kallikrein7.

[Pilot-scale comparison research of different constructed wetland types to treat eutrophic lake water].

Comparison research of different constructed wetland types to treat lake Wulihu water was carried out. Under the condition of the loading rates 0.8 m3/(m2 x d), the removal efficiencies of the vertical flow wetland (VFW), subsurface flow wetland (SFW) and free surface wetland(FSW) had the following results: To ammonia nitrogen (NH4(+)-N) the average removal rates were 33.2%, 27.4% and 14.1%, respectively; To total nitrogen (TN) the average removal rates were 52.3% , 50.1% and 19.2%, respectively; To total phosphorus (TP) the average removal rates were 58.8%, 57.9% and 26.3%, respectively; To permanganate index the average removal rates were 37.2%, 38.3% and 14.8%, respectively; To chlorophyll a (Chl-a) the average removal rates were 86.9%, 96.1% and 55.3%, respectively. Obviously, VFW and SFW are more effective than FSW at treating eutrophicated water such as Lake Wulihu which with characters of low organically pollution and with high nitrogen and phosphorus pollution, and the VFW is the most effective on the removal of NH4(+)-N, TN and TP. SFW is the most effective on the removal of permanganate index and Chl-a. The effluent stability of VFW is better than SFW, and the SFW is better than FSW.

A clinical and patch test study of patients with positive patch test reactions to fragrance mix in China.

The clinical and patch test (PT) features of patients with positive PT reactions to fragrance mix (FM) were studied. 378 consecutive eczema outpatients patch tested with a modified European standard series were analysed. 60 patients (15.9%) reacted to FM. No significant differences could be found between the ages of FM PT-positive and PT-negative patients [median age 40.5 (range from 18 years to 69 years) versus median age 37.5 (range from 5 years to 81 years), rank sum test, P = 0.301]. FM PT-positive rate in confirmed non-cosmetic allergic contact dermatitis patients was 30.4%, which was similar to that in confirmed cosmetic allergic contact dermatitis patients (30.4% versus 30%, chi(2) test, chi(2) = 0.0010, P = 0.972). The FM PT-positive rates were 10.8% in males and 18.2% in females (chi(2) test, chi(2) = 3.3443, P = 0.067). 76.7% of the patients with fragrance contact dermatitis were allergic to Chinese traditional medicine, which is much higher than that for cosmetic allergy (76.7% versus 43.3%, chi(2) test, chi(2) = 6.9446, P = 0.008). The positive PT rate to colophonium in the patients with positive PT reactions to FM is higher than that in the FM PT-negative patients (18.9% versus 3.0%, chi(2) test, chi(2) = 15.5471, P < 0.01). 62.5% of the patients reacted to colophonium were positive to FM. These results show that age has little effect on fragrance contact allergy. Other fragrant products besides cosmetics are also important sources of fragrance contact allergy. Chinese traditional medicine was an important factor in fragrance allergy in China. Patients with positive PT reactions to FM are more likely to react to colophonium.