RNA-seq analysis of Paris polyphylla var.yunnanensis roots identified candidate genes for saponin synthesis

Paris polyphylla Smith var.yunnanensis(Franch.) Hand.-Mazz.is a rhizomatous,herbaceous,perennial plant that has been used for more than a thousand years in traditional Chinese medicine.It is facing extinction due to overharvesting.Steroids are the major therapeutic components in Paris roots,the commercial value of which increases with age.To date,no genomic data on the species have been available.In this study,transcriptome analysis of an 8-year-old root and a 4-year-old root provided insight into the metabolic pathways that generate the steroids.Using Illumina sequencing technology,we generated a high-quality sequence and demonstrated de novo assembly and annotation of genes in the absence of prior genome information.Approximately 87,577 unique sequences,with an average length of 614 bases,were obtained from the root cells.Using bioinformatics methods,we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database.The unique transcripts were functionally classified using the Gene Ontology hierarchy and the Kyoto Encyclopedia of Genes and Genomes database.Of 3082 genes that were identified as significantly differentially expressed between roots of different ages,1518(49.25%) were upregulated and 1564(50.75%) were downregulated in the older root.Metabolic pathway analysis predicted that 25 unigenes were responsible for the biosynthesis of the saponins steroids.These data represent a valuable resource for future genomic studies on this endangered species and will be valuable for efforts to genetically engineer P.polyphylla and facilitate saponin-rich plant development.

Enhanced selective catalytic reduction of NO with NH3 via porous micro-spherical aggregates of Mn–Ce–Fe–Ti mixed oxide nanoparticles

We rationally designed a high performance denitration(De-NOx) catalyst based on a micrometer-sized spherical Mn–Ce–Fe–Ti(CP-SD)catalyst for selective catalytic reduction(SCR). This was prepared by a co-precipitation and spray drying(CP-SD) method. The catalyst was systematically characterized, and its morphological structure and surface properties were identified. Compare with conventional Mn–Ce–Fe–Ti(CP) catalysts, the Mn–Ce–Fe–Ti(CP-SD) catalyst had superior surface-adsorbed oxygen leading to enhanced 'fast NH3-SCR' reaction. The asobtained Mn–Ce–Fe–Ti(CP-SD) catalyst offered excellent NO conversion and N2 selectivity of 100.0% and 84.8% at 250℃, respectively, with a gas hourly space velocity(GHSV) of 40,000 h-1. The porous micro-spherical structure provides a larger surface area and more active sites to adsorb and activate the reaction gases. In addition, the uniform distribution and strong interaction of manganese, iron, cerium, and titanium oxide species improved H2O and SO2 resistance. The results showed that the Mn–Ce–Fe–Ti(CP-SD) catalyst could be used prospectively as a denitration(De-NOx) catalyst.

Analysis of changes in the Panax notoginseng glycerolipidome in response to long-term chilling and heat

Long-term moderately high or low temperatures can damage economically important plants.In the present study,we treated Panax notoginseng,an important traditional Chinese medicine,with temperatures of 10,20,and 30℃for 30 days.We then investigated P.notoginseng glycerolipidome responses to these moderate temperature stresses using an ESI/MS-MS-based lipidomic approach.Both long-term chilling(LTC,10℃)and long-term heat(LTH,30℃)decreased photo pigment levels and photosynthetic rate.LTH-induced degradation of photo pigments and glycerolipids may further cause the decline of photosynthesis and thereafter the senescence of leaves.LTC-induced photosynthesis decline is attributed to the degradation of photo synthetic pigments rather than the degradation of chloroplastidic lipids.P.notoginseng has an especially high level of lysophosphatidylglycerol,which may indicate that either P.notoginseng phospholipase A acts in a special manner on phosphatidylglycerol(PG),or that phospholipase B acts.The ratio of sulfoquinovosyldiacylglycerol(SQDG)to PG increased significantly after LTC treatment,which may indicate that SQDG partially substitutes for PG.After LTC treatment,the increase in the degree of unsaturation of plastidic lipids was less than that of extraplastidic lipids,and the increase in the unsaturation of PG was the largest among the ten lipid classes tested.These results indicate that increasing the level of unsaturated PG may play a special role in maintaining the function and stability of P.notoginseng photosystems after LTC treatment.

Submergence induced changes of molecular species in membrane lipids in Arabidopsis thaliana

The composition of membrane lipids is sensitive to environmental stresses.Submergence is a type of stress often encountered by plants.However,how the molecular species of membrane lipids respond to submergence has not yet been characterised.In this study,we used a lipidomic approach to profile the molecular species of membrane lipids in whole plants of Arabidopsis thaliana that were completely submerged for three days.The plants survived one day of submergence,after which,we found that the total membrane lipids were only subtly decreased,showing significant decreases of monogalactosyldiacylglycerol(MGDG)and phosphatidylcholine(PC)and an increase of phosphatidic acid(PA);however,the basic lipid composition was retained.In contrast,three days of submergence caused plants to die,and the membranes deteriorated via the rapid loss of 96% of lipid content together with a 229% increase in PA.The turnover of molecular species from PG and MGDG to PA indicated that submergenceinduced lipid changes occurred through PA-mediated degradation.In addition,molecular species of extraplastidic PG degraded sooner than plastidic ones,lyso-phospholipids exhibited various patterns of change,and the double-bond index(DBI)remained unchanged until membrane deterioration.Our results revealed the unique changes of membrane lipids upon submergence and suggested that the major cause of the massive lipid degradation could be anoxia.

Effects of Organic and Medium and Trace Element Fertilizers on Yield and Quality of Panax notoginseng

[Objectives]This study aimed to investigate the effects of organic and medium and trace element fertilizers(Ca,Zn,B)on yield and quality of Panax notoginseng to provide theoretical support for rational fertilization in cultivation of P.notoginseng.[Methods]Five fertilization treatments,control(CK),organic fertilizer(OM),zinc fertilizer(ZF),boron fertilizer(BF)and lime(LF),were designed.A two-consecutive-year field plot trail was conducted.The biological traits,yield and saponin content of P.notoginseng were determined.[Results]The application of organic fertilizer had no significant effect on the biological traits of P.notoginseng.Trace element fertilizers significantly increased the scape length of P.notoginseng.Among the treatments,ZF significantly increased the single flower weight but reduced the inflorescence diameter,while the effects of BF were opposite to those of ZF;LF significantly increased the stem thickness and reduced the plant height.All treatments significantly increased the seedling rate of three-year-old P.notoginseng,and the increase in the LF group(20.49%)was the largest,followed by those in the ZF(16.80%)and OM(16.40%)groups,and the increase in the BF group(13.08%)was the smallest.Although OM,ZF and BF treatments caused the root weight of individual plants to decrease,the final yield of each treatment was higher than that of the control group,and the increases in the BF and LF groups exceeded 17%(P<0.05).The total saponin outputs of all the treatments except OM were significantly higher than that of the control group.[Conclusions]Under the conditions of this test,the supplementation of organic and medium and trace element fertilizers on the basis of conventional fertilization will help to increase the yield of P.notoginseng.However,the reduction of the total saponin output of P.notoginseng caused by organic fertilizer cannot be ignored.

Biosynthetic pathway of prescription cucurbitacin IIa and high-level production of key triterpenoid intermediates in engineered yeast and tobacco

Cucurbitacin IIa is a triterpenoid isolated exclusively from Hemsleya plants and a non-steroidal anti-inflammatory drug that functions as the main ingredient of prescription Hemslecin capsules and tablets in China.Synthetic biology provides new strategies for production of such valuable cucurbitacins at a large scale;however,the biosynthetic pathway of cucurbitacin IIa has been unknown,and the heterologous production of cucurbitacins in galactose medium has been expensive and low yielding.In this study,we characterized the functions of genes encoding two squalene epoxidases(HcSE1-2),six oxidosqualene cyclases(HcOSC1-6),two CYP450s(HcCYP87D20 and HcCYP81Q59),and an acyltransferase(HcAT1)in cucurbitacin IIa biosynthesis by heterologous expression in Saccharomyces cerevisiae and Nicotiana benthamiana.We achieved high-level production of the key cucurbitacin precursor 11-carbonyl-20b-hydroxy-Cuol from glucose in yeast via modular engineering of the mevalonate pathway and optimization of P450 expression levels.The resulting yields of 46.41 mg/l 11-carbonyl-20b-hydroxy-Cuol and 126.47 mg/l total cucurbitacin triterpenoids in shake flasks are the highest yields yet reported from engineered microbes.Subsequently,production of 11-carbonyl-20b-hydroxy-Cuol by transient gene expression in tobacco resulted in yields of 1.28 mg/g dry weight in leaves.This work reveals the key genes involved in biosynthesis of prescription cucurbitacin IIa and demonstrates that engineered yeast cultivated with glucose can produce high yields of key triterpenoid intermediates.We describe a low-cost and highly efficient platform for rapid screening of candidate genes and high-yield production of pharmacological triterpenoids.

Comparative genomics reveals the diversification of triterpenoid biosynthesis and origin of ocotilloltype triterpenes in Panax

Gene duplication is assumed to be the major force driving the evolution of metabolite biosynthesis in plants.Freed from functional burdens,duplicated genes can mutate toward novelties until fixed due to selective fitness.However,the extent to which this mechanism has driven the diversification of metabolite biosynthesis remains to be tested.Here we performed comparative genomics analysis and functional characterization to evaluate the impact of gene duplication on the evolution of triterpenoid biosynthesis using Panax species as models.Wefound that whole-genome duplications(WGDs)occurred independently in Araliaceae and Apiaceae lineages.Comparative genomics revealed the evolutionary trajectories of triterpenoid biosynthesis in plants,which was mainly promoted by WGDs and tandem duplication.Lanosterol synthase(LAS)was likely derived from a tandemduplicate of cycloartenol synthase that predated the emergence of Nymphaeales.Under episodic diversifying selection,the LAS gene duplicates produced by g whole-genome triplication have given rise to triterpene biosynthesis in core eudicots through neofunctionalization.Moreover,functional characterization revealed that oxidosqualene cyclases(OSCs)responsible for synthesizing dammarane-type triterpenes in Panax species were also capable of producing ocotilloltype triterpenes.Genomic and biochemical evidence suggested that Panax genes encoding the above OSCs originated from the specialization of one OSC gene duplicate produced from a recent WGD shared by Araliaceae(Pg-b).Our results reveal the crucial role of gene duplication in diversification of triterpenoid biosynthesis in plants and provide insight into the origin of ocotillol-type triterpenes in Panax species.

Multilayered regulation of secondary metabolism in medicinal plants

Medicinal plants represent a huge reservoir of secondary metabolites(SMs),substances with significant pharmaceutical and industrial potential.However,obtaining secondary metabolites remains a challenge due to their low-yield accumulation in medicinal plants;moreover,these secondary metabolites are produced through tightly coordinated pathways involving many spatiotemporally and environmentally regulated steps.The first regulatory layer involves a complex network of transcription factors;a second,more recently discovered layer of complexity in the regulation of SMs is epigenetic modification,such as DNA methylation,histone modification and small RNA-based mechanisms,which can jointly or separately influence secondary metabolites by regulating gene expression.Here,we summarize the findings in the fields of genetic and epigenetic regulation with a special emphasis on SMs in medicinal plants,providing a new perspective on the multiple layers of regulation of gene expression.

The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb

Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome se- quences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16- epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe.

Genome of Plant Maca （Lepidium meyenil） Illuminates Genomic Basis for High-Altitude Adaptation in the Central Andes

Maca （Lepidium meyenii Walp, 2n = 8x = 64）, belonging to the Brassicaceae family, is an economic plant cultivated in the central Andes sierra in Peru （4000-4500 m）. Considering that the rapid uplift of the central Andes occurred 5-10 million years ago （Ma）, an evolutionary question arises regarding how plants such as maca acquire high-altitude adaptation within a short geological period. Here, we report the high-quality genome assembly of maca, in which two closely spaced maca-specific whole-genome duplications （WGDs; ~6.7 Ma） were identified. Comparative genomic analysis between maca and closely related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway, and secondary metabolite biosynthesis via WGDs. The retention and subsequent functional divergence of many duplicated genes may account for the morphological and physiological changes （i.e., small leaf shape and self-fertility） in maca in a high-altitude environment. In addition, some duplicated maca genes were identified with functions in morphological adaptation （i.e., LEAF CURLING RESPONSIVENESS） and abiotic stress response （i.e., GL YClNE-RICH RNA-BINDING PROTEINS and DNA-DAMAGE-REPAIR/TOLERATION2） under positive selection. Collectively, the maca genome provides use- ful information to understand the important roles of WGDs in the high-altitude adaptation of plants in the Andes.

A Comprehensive Porosity Prediction Model for the Upper Paleozoic Tight Sandstone Reservoir in the Daniudi Gas Field, Ordos Basin

This paper investigated the porosity controlling factors for tight sandstone reservoir in the Daniudi gas field, Ordos Basin based on an integrated petrographic, petrophysical and geostatistical analyses, and proposed a comprehensive prediction model for reservoir porosity. Compaction was found to be a key factor for causing reservoir densification. The degree of sandstone compaction appears to be affected by grain sizes and sorting. Under normal compaction conditions（e.g., cement content less than 6%, and with no dissolution）, the variation in reservoir porosity with burial depth can be well correlated with grain compositions, grain sizes, and sorting. Based on qualitative examination of the controlling factors for reservoir porosities, geostatistics were used to quantify the effects of various geological parameters on reservoir porosities. A statistical model for comprehensive prediction of porosity was then established, on the assumption that the present reservoir porosity directly relates to both normal compaction and diagenesis. This model is easy to use, and has been validated with measured porosity data. The porosity controlling factors and the comprehensive porosity prediction can be used to quantify effects of the main controlling factors and their interaction on reservoir property evolution, and may provide a reference model for log interpretation.

Overwhelming electrochemical oxygen reduction reaction of zinc-nitrogen-carbon from biomass resource chitosan via a facile carbon bath method

Developing high efficiency and low cost electrocatalysts is critical for the enhancement of oxygen reduction reaction(ORR),which is the fundamental for the development and commercialization of renewable energy conversion technology.Herein,zinc-nitrogen-carbon(Zn-N-C)was prepared by using biomass resource chitosan via a facile carbon bath method.The obtained Zn-N-C delivered a high specific surface area(794.7 cm^2/g)together with pore volume(0.49 cm^3/g).During the electrochemical evaluation of oxygen reduction reaction(ORR),Zn-N-C displayed high activity for ORR with an onset pote ntial E0=0.96 VRHE and a half wave potential E1/2=0.86 VRHE,which were more positive than those of the comme rcial 20 wt%Pt/C benchmark catalyst(E0=0.96 VRHE and E1/2=0.81 VRHE).In addition,the ZnN-C catalyst also had a better stability and methanol tolerance than those of the Pt/C catalyst.

Metabolic engineering of Yarrowia lipolytica for scutellarin production

Scutellarin related drugs have superior therapeutic effects on cerebrovascular and cardiovascular diseases.Here,an optimal biosynthetic pathway for scutellarin was constructed in Yarrowia lipolytica platform due to its excellent metabolic potential.By integrating multi-copies of core genes from different species,the production of scutellarin was increased from 15.11 mg/L to 94.79 mg/L and the ratio of scutellarin to the main by-product was improved about 110-fold in flask condition.Finally,the production of scutellarin was improved 23-fold and reached to 346 mg/L in fed-batch bioreactor,which was the highest reported titer for de novo production of scutellarin in microbes.Our results represent a solid basis for further production of natural products on unconventional yeasts and have a potential of industrial implementation.

Whole-Genome Sequencing and Analysis of the Chinese Herbal Plant Panax notoginseng

Dear Editor Panax notoginseng （Burk.） F.H. Chen （2n = 2x = 24, common name sanqi or tianql）, belonging to the Araliaceae family, is a slow-growing plant species documented in the ancient Chinese medical literatures for its ability to ameliorate hemostasis and improve blood circulation （Wang et al., 2016）. After decades of pharmacological research, a variety of P. notoginseng-specific secondary metabolites （notably ginsenosides, notoginsenosides and gypenosides） were isolated, identified, and implicated in conferring medicinal properties （Wang et al., 2016）.

HMOD： An Omics Database for Herbal Medicine Plants

Dear Editor ,More than 50% of drugs are derived from chemical compounds that have been isolated from various plants （Fabricant and Farnsworth, 2001; Yarnell and Abascal, 2002）. With the development of sequencing technology and synthetic biology, we can obtain molecular information from the transcriptomic and genomic data of plants and then utilize bacteria to synthesize desired chemical compounds （Atanasov et al., 2015; Smanski et al., 2016）. Increasing numbers of researchers have started to publish omics data generated from herbal plants.

Synthesis of pH-responsive triazine skeleton nano-polymer composite containing AIE group for drug delivery

We exploited a unique porous structure of the nano-covalent triazinepolymer(NCTP)containing aggregation-induced emission(AlE)group to achievecontrolled release and drug tracking in tumor acidic microenvironment.NCTP wassynthesized by the Friedel-Crafts alkylation and the McMurry coupling reaction.It notonly had strong doxorubicin(DOX)-loading capacity due to its high specific surface areaand large pore volume,but also showed the significant cumulative drug release as aresult of the pH response of triazine polymers.NCTP was induced luminescence aftermass accumulation near tumor cells.Besides,it had excellent biocompatibility andobvious antineoplastic toxicity.The results demonstrate that NCTP as a utility-type drugcarrier provides a new route for designing the multi-functional drug delivery platform.