Genomic analyses reveal evolutionary and geologic context for the plateau fungus Ophiocordyceps sinensis.

BACKGROUND: Ophiocordyceps sinensis, which is only naturally found in the high-elevation extreme environment of the Tibetan Plateau, has been used in traditional Chinese medicine. Information concerning the evolutionary and geologic context of O. sinensis remains limited, however. METHODS: We constructed the high-quality genome of O. sinensis and provided insight into the evolution and ecology of O. sinensis using comparative genomics. RESULTS: We mapped the whole genome of the anamorph/asexual form Hirsutella of O. sinensis using Illumina and PacBio sequencing technologies and obtained a well assembled genome of 119.2 Mbp size. Long-read Single Molecule Real Time (SMRT) sequencing technology generated an assembly with more accurate representation of repeat sequence abundances and placement. Evolutionary analyses indicated that O. sinensis diverged from other fungi 65.9 Mya in the Upper Cretaceous, during the uplift of the Tibetan Plateau. Gene family expansions and contractions in addition to genome inflation via long terminal repeat (LTR) retrotransposon insertions were implicated as an important driver of O. sinensis divergence. The insertion rate of LTR sequences into the O. sinensis genome peaked ~ 30-40 Mya, when the Tibetan Plateau rose rapidly. Gene Ontology (GO) enrichment analysis suggested that O. sinensis contained more genes related to ice binding compared to other closely related fungi, which may aid in their adaptability to the cold Tibetan Plateau. Further, heavy metal resistance genes were in low abundance in the O. sinensis genome, which may help to explain previous observations that O. sinensis tissues contain high levels of heavy metals. CONCLUSIONS: Our results reveal the evolutionary, geological, and ecological context for the evolution of the O. sinensis genome and the factors that have contributed to the environmental adaptability of this valuable fungus. These findings suggest that genome inflation via LTR retrotransposon insertions in O. sinensis coincided with the uplift of the Tibetan Plateau. LTRs and the specific genetic mechanisms of O. sinensis contributed to its adaptation to the environment on the plateau.

[HPLC specific chromatogram of Vernonia anthelmintica and determination of six components].

This work aims to establish an HPLC specific chromatogram and determine six components of Vernonia anthelmintica with chlorogenic acid, isochlorogenic acid B, isochlorogenic acid A, isochlorogenic acid C, scutellarein and luteolin as index components. HPLC analysis was performed on a Waters Xbridge C_(18) column(4.6 mm×250 mm, 5 µm) with gradient elution of acetonitrile-0.05% trifluoroacetic acid solution at a flow rate of 1.0 mL·min~(-1). The detection wave length was 360 nm and the column temperature was 30 ℃. Chemometrics software Chempattern was employed to analyze the data. HPLC specific chromatogram of V. anthelmintica was established and six characteristic peaks were marked. Six characteristic peaks were simultaneously determined by HPLC within 50 min. The contents of the six components in 13 batch samples of V. anthelmintica were 0.14%-0.68%, 0.44%-0.74%, 0.63%-1.01%, 0.14%-0.71%, 0.15%-0.26% and 0.010%-0.030%, respectively. The HPLC specific chromatogram of V. anthelmintica, together with determination of six components showed strong specificity, and it can be used for the quality control of the crude drug.

[Comparative studies of three Cistanche speices based on UPLC specific chromatogram and determination of main components].

Based on UPLC specific chromatogram and determination of seven main components,this study aimed at evaluating the quality of Cistanche deserticola,C. tubulosa and C. sinensis. Echinacoside,cistanoside A,verbascoside,tubuloside A,isoacteoside,2'-acetylacteoside,tubuloside B were used as reference substances. UPLC analysis was performed on a Waters ACQUITY UPLC HSS T3 column( 2. 1 mm×100 mm,1. 8 µm). The mobile phase was acetonitrile-0. 08% trifluoroacetic acid solution. The flow rate was0. 3 mL·min-1,and the injection amount was 10 µL. The column temperature was 40 ℃,and the detection wavelength was 330 nm.The UPLC specific chromatograms were processed with ChemPattern software. UPLC specific chromatograms of C. deserticola and C.tubulosa from different samples were of high similarity,but the similarities of their counterfeit C. sinensis were less than 0. 06. Both of cluster and principal component analysis can distinguish certified products and counterfeits. The content ratios of echinacoside/verbascoside and verbascoside/isoacteoside were quite different between C. deserticola and C. tubulosa,which had distinct significance.The UPLC specific chromatogram and contents of seven main components can provide a basis for quality evaluation of Cistanches Herba.

[Comparative study for freeze-drying and sun-drying on multi-index ingredients of Cordyceps sinensis].

The aim of this paper was to compare the influence of freeze-drying and sun-drying on six main nucleosides and nucleobases of Cordyceps sinensis by HPLC. Hypoxanthine,xanthine,uridine,inosine,guanosine and adenosine were reference substances. HPLC analysis was performed on a GL Inertsustain AQ-C_(18) column( 4. 6 mm×250 mm,5 µm),with mobile phase consisting of water( A)-acetonitrile( B) at the flow rate of 1. 0 mL·min~(-1)( 0-10 min,0-1% B; 10-65 min,1%-3% B). The detection wavelength was 260 nm,the column temperature was controlled at 30 ℃,and the injection volume was 5 µL. The linear ranges of hypoxanthine,xanthine,uridine,inosine,guanosine and adenosine were 1. 025-20. 50( r = 0. 999 8),0. 545-10. 90( r = 0. 999 9),4. 051-81. 02( r = 0. 999 8),4. 044-80. 88( r= 0. 999 9),2. 075-41. 50( r= 0. 999 9),4. 032-80. 64( r = 0. 999 9) mg·L~(-1),respectively. The average recoveries of them( n = 6)were as follows: 102. 3%( RSD 2. 1%),101. 1%( RSD 2. 4%),97. 80%( RSD 1. 7%),101. 8%( RSD 1. 8%),98. 90%( RSD2. 0%) and 98. 10%( RSD 1. 4%),respectively. Each sample was processed by freeze-drying and sun-drying so as to compare the difference between the two drying methods. The contents of six index ingredients were significantly different between freeze-drying and sun-drying sample of C. sinensis. The total contents of six index ingredients in sun-drying sample were higher than that in the corresponding freeze-drying sample. This research results provide the scientific basis for the drying methods and quality evaluation of C. sinensis.

[Study on ethnic medicine quantitative reference herb,Tibetan medicine fruits of Capsicum frutescens as a case].

High price and difficult to get of reference substance have become obstacles to HPLC assay of ethnic medicine. A new method based on quantitative reference herb (QRH) was proposed. Specific chromatograms in fruits of Capsicum frutescens were employed to determine peak positions, and HPLC quantitative reference herb was prepared from fruits of C. frutescens. The content of capsaicin and dihydrocapsaicin in the quantitative control herb was determined by HPLC. Eleven batches of fruits of C. frutescens were analyzed with quantitative reference herb and reference substance respectively. The results showed no difference. The present method is feasible for quality control of ethnic medicines and quantitative reference herb is suitable to replace reference substances in assay.

[Content determination of four diester diterpenoid alkaloids in leaves of Aconitum kusnezoffii by HPLC].

This present study is to develop an HPLC method for simultaneous determination of four diester diterpenoid alkaloids, beiwutine, mesaconitine, hypaconitine and aconitine in the leaves of Aconitum kusnezoffii, so as to provide evidence of the quality control of this herb. The four constituents were measured on a Waters XBridge CC18 column(4.6 mmχ250 mm, 5 µm). The mobile phase was acetonitrile-40 mmol·L⁻¹ ammonium acetate solution(adjusted pH to 10.5 with ammonia solution)(33:67) with isocratic elution at a flow rate of 1.0 mL·min⁻¹; the detection wavelength was 235 nm; the column temperature was 30 °C, and the injection volume was 10 µL. Next, this contents of the four diester diterpenoid alkaloids in 12 samples were 0.025 5-0.088 5, 0.039 1-0.071 5, 0.026 6-0.081 0 and 0.008 12-0.031 2 mg·g⁻¹, respectively. Next, this method has been successfully applied to the analysis of A. kusnezoffii folium in different harvest periods. The contents of the four alkaloids decreased primarily, and then increased with the postponing of harvest. The established method is proved to be accurate and sensitive for the determination of alkaloids in A. kusnezoffii folium, and may be useful for the quality improvement of this herbal medicine. Moreover, these results indicated the scientific significance for the toxicity and the suitable harvest time of this herb.

[Comparative study on specific chromatograms and main nucleosides of cultivated and wild Cordyceps sinensis].

This study is to establish the HPLC specific chromatogram and determine four main nucleosides of wild and cultivated Cordyceps sinensis. Uridine, inosine, guanosine and adenosine were selected as reference substance. HPLC analysis was performed on a Waters XSelect HSS T3 C18 (4.6 mm×250 mm, 5 µm), with a mobile phase consisting of water(A)-acetonitrile (B) at a flow rate of 0.6 mL•min⁻¹ (0-5 min,0% B;5-15 min,0%-10% B, 15-30 min,10%-20% B, 30-33 min, 20%-50% B, 33-35 min, 50%-0% B, 35-40 min, 0% B). The detection wavelength was 260 nm and the column temperature was controlled at 30 ℃, and the injection volume was 5 µL. HPLC specific chromatogram of wild and cultivated C. sinensis was established and four main nucleosides were simultaneously determined by the above method. Specific chromatograms and contents of four main nucleosides showed no significant differences between cultivated and wild C. sinensis. These results can provide scientific evidences for further development and utilization of cultivated C. sinensis.

[Comparative study on specific chromatograms and main active components of wild and cultivated rhizomes of Paris polyphylla var. yunnanensis].

The present study is to compare specific chromatograms and main acitive components between wild and cultivated rhizomes of Paris polyphylla var. yunnanensis by HPLC. HPLC analysis was performed on a Waters XSelect HSS T3 C18 clumn (4.6 mm×250 mm, 5 µm), with a mobile phase consisting of acetonitrile (A)-water (B) at a flow rate of 1 mL•min⁻¹ (0-50 min,30%-50%A;50-80 min,50% A,80-85 min,50%-30%A;85-100 min,30% A). The detection wavelength was 203 nm and the column temperature was controlled at 30 ℃, and the injection volume was 10 µL. HPLC specific chromatograms of wild and cultivated rhizomes of P. polyphylla var. yunnanensis were established and nine steroidal saponins were simultaneously determined by the above method. The mean contents of paris saponin Ⅶ, paris saponin H and total average contents of four pennogenyl saponins in Rhizomes of wild samples were significantly higher than those of cultivated ones. However, this result is opposite from the average content of paris saponin Ⅰ and total average contents of five dioscins in the wild and cultivated samples. Because the significant differences occurred for the specific chromatograms and main active components between the wild and cultivated P. polyphylla var. yunnanensis, much more pharmacological and clinical researches are therefore necessary.

[Simultaneous determination of eight hydroxyl naphthoquinones in different parts of Arnebiae euchroma by HPLC].

This present study is to develop an HPLC method for simultaneous determination of eight hydroxyl naphthoquinones, shikonin, ß-hydroxy-isovalerylshikonin, acetylshikonin, ß-acetoxy-isovalerylshikonin, deoxyshikonin, isobutyrylshikonin, ß,ß'-dimethylacrylshikonin and isovalerylshikonin. The eight constituents were measured on a Waters Xbridge C18 column (4.6 mm×250 mm，5 µm) with isocratic elution of acetonitrile-0.05% formic acid solution (70∶30) at a flow rate of 1.0 mL•min⁻¹. The detection wavelength was 275 nm and the column temperature was 30 ℃. The results of content determination indicated that significant differences of the eight compounds exist in every part of Arnebia euchroma，in which the highest part was the root bark, followed with the root, then the stem residues. The content of the xylem of root and aerial part was lower than the above parts. The results provided scientific basis for the medicinal parts of A. euchroma.

Application of COI barcode sequence for the identification of snake medicine (Zaocys).

Counterfeits in the medicine market make the authentication of snakes used for Chinese medicine a challenge to Chinese drug regulatory control agencies. This paper explores existing methods that can be used to quickly and accurately distinguish Zaocys (Z. dhumnades) from its counterfeits for routine identification of snake meats in food and drug control laboratories. In this research, the Cytochrome Oxidase I (COI) fragments of 51 samples from 17 species of snakes were amplified using Polymerase Chain Reaction (PCR) and sequenced. The inter- and intra-specific variations of COI sequences were analyzed and compared based on Kimura-2-parameter (K-2P) distances; the minimal interspecific K-2P distance was 0.0934, which was bigger than the maximum intraspecific K-2P distance in Z. dhumnades (0.0523), indicating that Zaocys can be separated from its counterfeits. The Neighbor-Joining (N-J) tree of the snakes was constructed and the results show that snakes of the same species cluster with 100% bootstrap values. Since the Zaocys and its counterfeits are of different species, they can be distinguished using the N-J tree method. Another 10 samples of Zaocys from markets and drug stores were identified at the species level, among which 5 samples were proven to be the counterfeits--Ptyas korros.

[HPLC specific chromatogram of Lamiophlomis Herba and its counterfeit and determination of four effective components].

This study is to establish the HPLC specific chromatogram and determine four main effective components of Lamiophlomis Herba and its counterfeit.Chlorogenic acid, forsythoside B, acteoside and luteoloside were reference substance.HPLC analysis was performed on a Waters XSelect C18 column (4.6 mm×250 mm,5 µm).The mobile phase was acetonitrile-0.5% phosphoric acid solution (18∶82) with isocratic elution.The flow rate was 1.0 mL•min⁻¹, the detection wavelength was 332 nm and the column temperature was 30 ℃.Chemometrics software Chempattern was employed to analyze the research data.HPLC specific chromatogram of Lamiophlomis Herba from different samples were of high similarity, but the similarity of the HPLC specific chromatogram of its counterfeit were less than 0.65.Both of cluster and principal component analysis can distinguish certified products and adulterants.The HPLC specific chromatogram and contents of four effective components can be used for the quality control of Lamiophlomis Herba and its preparations.It provided scientific basis to standardize the use of the crude drug.

[Chemical constituents of ethnic medicine Cynanchum otophyllum].

In order to isolate and purify the reference compounds and improve the quality standard of ethnic medicine of Radix of Cynanchum otophyllum, the ethanol extracts were isolated by column chromatography onsilica gel, C18 reverse-phase silica gel, and semi-preparative HPLC. Twelve compounds were isolated and their structures were elucidated as 2,4-dihydroxy-6-methoxyphenylethanone(1), 4,6-dihydroxy-2-methoxyphenylethanone(2), p-hydroxyacetophenone(3), baishouwubenzophenone(4), 2,4-dihydroxyacetophenone(5), 2,5-dihydroxyacetophenone(6), otophylloside A(7),otophylloside B(8), caudatin-3-O-ß-D-cymaropyranosyl-(1→4)-ß-D-digitoxopyranoside(9),caudatin-3-O-ß-D-glucopyranosyl-(1→4)-ß-D-oleandropyranosyl-(1→4)-ß-D-cymaropyranosyl-(1→4)-ß-D-digitoxopyranoside(10),qingyangshengenin-3-O-ß-D-oleandropyranosyl-(1→4)-ß-D-cymaropyranoside(11),caudatin-3-O-ß-D-oleandropyranosyl-(1→4)-ß-D-cymaropyranosyl-(1→4)-ß-D-cymaropyranoside(12) on the basis of spectral analysis. Compounds 1 and 2 were isolated from the genus Cynanchum for the first time, and compounds 3-4, 9-12 were obtained from this plant for the first time.These compounds are main active components of Radix of C.otophyllum and can be used as reference substances for the quality control of this ethnic medicine.