Publications by authors named "ZheZhi Wang"

50 Publications

Genome-wide identification, classification and expression profile analysis of the HSF gene family in .

PeerJ 2021 6;9:e11345. Epub 2021 May 6.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China.

Heat shock transcription factors (HSFs) are critical regulators of plant responses to various abiotic and biotic stresses, including high temperature stress. HSFs are involved in regulating the expression of heat shock proteins (HSPs) by binding with heat stress elements (HSEs) to defend against high-temperature stress. The genome was recently fully sequenced; this provides a valuable resource for genetic and functional analysis. In this study, 23 putative genes were identified and divided into three groups (A, B, and C) based on phylogeny and structural features. Gene structure and conserved motif analyses were performed on members; the DNA-binding domain (DBD), hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries exhibited specific phylogenetic relationships. In addition, the presence of various -acting elements in the promoter regions of underscored their regulatory function in abiotic stress responses. RT-qPCR analyses showed that most genes were expressed in response to heat conditions, suggesting that HpHSFs play potential roles in the heat stress resistance pathway. Our findings are advantageous for the analysis and research of the function of HpHSFs in high temperature stress tolerance in .
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http://dx.doi.org/10.7717/peerj.11345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106910PMC
May 2021

Genome-Wide Identification of the TIFY Family in Reveals That SmJAZ3 Interacts With SmWD40-170, a Relevant Protein That Modulates Secondary Metabolism and Development.

Front Plant Sci 2021 18;12:630424. Epub 2021 Feb 18.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, China.

Bunge (), a traditional Chinese medicinal herb, contains numerous bioactive components with broad range of pharmacological properties. By increasing the levels of endogenous jasmonate (JA) in plants or treating them with methyl jasmonate (MeJA), the level of tanshinones and salvianolic acids can be greatly enhanced. The jasmonate ZIM (JAZ) proteins belong to the TIFY family, and act as repressors, releasing targeted transcriptional factors in the JA signaling pathway. Herein, we identified and characterized 15 TIFY proteins present in . Quantitative reverse transcription PCR analysis indicated that the genes were all constitutively expressed in different tissues and were induced by MeJA treatments. SmJAZ3, which negatively regulates the tanshinones biosynthesis pathway in and the detailed molecular mechanism is poorly understood. SmJAZ3 acts as a bait protein to capture and identify a WD-repeat containing the protein SmWD40-170. Further molecular and genetic analysis revealed that SmWD40-170 is a positive regulator, promoting the accumulation of secondary metabolites in . Our study systematically analyzed the TIFY family and speculated a module of the JAZ-WD40 complex provides new insights into the mechanisms regulating the biosynthesis of secondary metabolites in .
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http://dx.doi.org/10.3389/fpls.2021.630424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7930841PMC
February 2021

Selection and evaluation of reference genes for qRT-PCR of Scutellaria baicalensis Georgi under different experimental conditions.

Mol Biol Rep 2021 Feb 28;48(2):1115-1126. Epub 2021 Jan 28.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.

Scutellaria baicalensis Georgi is a famous medicinal plant with its dried roots having been used as a traditional Chinese medicinal for more than 2000 years. Although its genome sequence has previously been published and molecular biology methods have been used to study this species, no suitable internal reference genes have been investigated for standardization of gene expression via quantitative real-time polymerase chain reaction (qRT-PCR). Here, the stabilities of 10 candidate reference genes, ACT11, ACT7, α-TUB, β-TUB, GAPDH, UBC, RPL, SAM, HSP70, and PP2A, were analyzed by four different procedures of GeNorm, NormFinder, BestKeeper, and RefFinder. Their expression stabilities were evaluated under various conditions, including different tissue types (root, stem, leaf, and flower), hormone stimuli treatments (methyl jasmonate, salicylic acid, and abscisic acid), and abiotic stresses (heavy metal, salt, drought, cold, and wounding). The results indicated that β-TUB was the most stable gene for all tested samples, while ACT11 was the most unstable. The most stable reference gene was not consistent under different conditions. β-TUB exhibited the highest stability for different tissue types and abiotic stresses, while for hormone stimuli treatments, ACT7 showed the highest stability. To confirm the applicability of suitable reference genes, we selected to SbF6H and SbF8H as target genes to analyze their expression levels in different tissues. This study helps to the accurate quantification of the relative expression levels of interest genes in S. baicalensis via qRT-PCR analysis.
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http://dx.doi.org/10.1007/s11033-021-06153-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7842394PMC
February 2021

Genome-Wide Analysis and the Expression Pattern of the ERF Gene Family in .

Plants (Basel) 2021 Jan 11;10(1). Epub 2021 Jan 11.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.

is a well-known medicinal herb currently used as a remedy for depression as it contains many high levels of secondary metabolites. The ethylene response factor (ERF) family encodes transcriptional regulators with multiple functions that play a vital role in the diverse developmental and physiological processes of plants, which can protect plants from various stresses by regulating the expression of genes. Although the function of several genes from other plants has been further confirmed, is the first sequenced species in Malpighiales, and no information regarding the has been reported thus far. In this study, a total of 101 genes were identified from . A systematic and thorough bioinformatic analysis of the ERF family was performed using the genomic database of . According to the phylogenetic tree analysis, were further classified into 11 subfamilies. Gene ontology (GO) analysis suggested that most of the likely participate in the biological processes of plants. The cis-elements were mainly divided into five categories, associated with the regulation of gene transcription, response to various stresses, and plant development. Further analysis of the expression patterns showed that the stress-responsive responded to different treatments. This work systematically analyzed using the genome sequences of . Our results provide a theoretical basis for further investigation of the function of stress-related in .
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http://dx.doi.org/10.3390/plants10010133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7827068PMC
January 2021

Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers.

Mol Biol Rep 2021 Jan 5;48(1):241-250. Epub 2021 Jan 5.

National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.

Akebia trifoliata (Lardizabalaceae) is an important medicinal plant with multiple pharmacological effects. However, the lack of genomic information had limited the further excavation and utilization of this plant. An initial survey of the genome A. trifoliata was performed by next-generation sequencing, and then the genome size was inferred by flow cytometry. The whole genome survey of A. trifoliata generated 61.90 Gb of sequence data with approximately 95.51 × coverage. The genome size, heterozygosity and GC content obtained by k-mer analysis were almost 648.07 Mb, 0.72% and 36.11%, respectively. The genome size calculated by flow cytometry was 685.77 Mb, which was consistent with the results of genome survey. A total of 851,957 simple sequence repeats (SSR) were identified in the A. trifoliata genome. Twenty-eight phenotypic traits and thirty pairs of SSR primers were selected for the analysis of the genetic diversity of 43 accessions of cultivated A. trifoliata. The results showed that 216 bands were generated by 30 pairs of SSR primers, of which 189 (87.5%) were polymorphic. In addition, the phenotypes and SSR markers were used for cluster analysis of 43 cultivated accessions. The results of the two clustering methods were partially consistent. The genome survey of A. trifoliata demonstrated that the genome size of this plant was about 648.07 Mb. In the present study, the size and characteristics of the genome of A. trifoliata were reported for the first time, which greatly enriched the genomic resources of A. trifoliata for the further research and utilization.
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http://dx.doi.org/10.1007/s11033-020-06042-wDOI Listing
January 2021

Whole-genome sequence data of Hypericum perforatum and functional characterization of melatonin biosynthesis by N-acetylserotonin O-methyltransferase.

J Pineal Res 2021 Mar 25;70(2):e12709. Epub 2020 Dec 25.

Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, China.

Hypericum perforatum is among the most commonly used herbal remedies and supplements. The aerial plant parts are often used to treat depression. Due to the lack of genomic information of H. perforatum, the gene networks regulating secondary metabolite synthesis remain unclear. Here, we present a high-quality genome for H. perforatum with a 2.3-Mb scaffold N50. The draft assembly covers 91.9% of the predicted genome and represents the fourth sequenced genus in the order Malpighiales. Comparing this sequence with model or related species revealed that Populus trichocarpa and Hevea brasiliensis could be grouped into one branch, while H. perforatum and Linum usitatissimum are grouped in another branch. Combined with transcriptome data, 40 key genes related to melatonin, hyperforin, and hypericin synthesis were screened and analyzed. Five N-acetylserotonin O-methyltransferases (HpASMT1-HpASMT5) were cloned and functionally characterized. Purified HpASMT3 protein converted N-acetylserotonin into melatonin with a V of about 1.35 pkat/mg protein. HpASMT1 and HpASMT3 overexpression in Arabidopsis mutants caused 1.5-2-fold higher melatonin content than in mutant and wild-type plants. The endogenous reactive oxygen species (ROS) in transgenic plants was significantly lower than ROS in mutant and wild-type plants, suggesting higher drought tolerance. The obtained genomic data offer new resources for further study on the evolution of Hypericaceae family, but also provide a basis for further study of melatonin biosynthetic pathways in other plants.
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http://dx.doi.org/10.1111/jpi.12709DOI Listing
March 2021

Microbial diversity and community structure changes in the rhizosphere soils of from different planting years.

Plant Signal Behav 2021 02 8;16(2):1854507. Epub 2020 Dec 8.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, the Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, the Ministry of Education, College of Life Sciences, Shaanxi Normal University , Xi'an, The People's Republic of China.

is a type of typical traditional Chinese medicinal (TCM) herb that is economically important in China. The traditional planting method of is to plant continuously for many years, which often leads to impediments for its growth and development and soil-borne diseases. The root-associated microbiome is believed to play an important role in plant resistance and the quality of products from the plant. This study aims to reveal detailed changes in the populations of rhizosphere microorganisms, and providing theoretical guidance for the prevention and control of soil-borne diseases in . A high-throughput sequencing approach was utilized to illustrate changes in the microbial community from different planting years. Results and conclusions: The results show that the diversity and composition of the root-associated microbiome was significantly impacted by the consecutive monoculture of . At the level of the comparisons of the phyla, Bacteroidetes, Proteobacteria, Ascomycota, and Basidiomycota declined significantly. In contrast, the relative abundance of Actinobacteria, Acidobacteria, and Mortierellomycota distinctly increased. Comparisons at the genus level indicated that , and decreased significantly, whereas , and distinctly increased. In conclusion, this study helps to develop an understanding of the impediments involved in the consecutive monoculture of .
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http://dx.doi.org/10.1080/15592324.2020.1854507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7849755PMC
February 2021

JA-Responsive Transcription Factor SmMYB97 Promotes Phenolic Acid and Tanshinone Accumulation in .

J Agric Food Chem 2020 Dec 7;68(50):14850-14862. Epub 2020 Dec 7.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.

Phenolic acids and tanshinones are active principles in Bunge administered for cardiovascular and cerebrovascular diseases. Jasmonic acid (JA) promotes secondary metabolite accumulation, but the regulatory mechanism is unknown in . We identified and characterized the JA-responsive gene . Multiple sequence alignment and phylogenetic tree analyses showed that SmMYB97 was clustered with AtMYB11, AtMYB12, and ZmP1 in the subgroup S7 regulating flavonol biosynthesis. was highly expressed in leaves and induced by methyl jasmonate (MeJA). SmMYB97 was localized in the nucleus and had strong transcriptional activation activity. overexpression increased phenolic acid and tanshinone biosynthesis and upregulated the genes implicated in these processes. Yeast one-hybrid and transient transcriptional activity assays disclosed that SmMYB97 binds the , , , and promoter regions. SmJAZ8 interacts with SmMYB97 and downregulates the genes that it controls. This study partially clarified the regulatory network of MeJA-mediated secondary metabolite biosynthesis in .
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http://dx.doi.org/10.1021/acs.jafc.0c05902DOI Listing
December 2020

Extraction, purification, and determination of the gastroprotective activity of glucomannan from Bletilla striata.

Carbohydr Polym 2020 Oct 12;246:116620. Epub 2020 Jun 12.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China. Electronic address:

In this study, a water-soluble polysaccharide (BSP) was extracted and purified from pseudobulb of Bletilla striata. The preliminary structure and gastroprotective activity of BSP were analyzed. Results indicate that BSP is a glucomannan with a molar ratio of 7.45:2.55 (Man:Glc), and its molecular weight is approximately 1.7 × 10 Da. BSP displayed outstanding protective action against ethanol-induced GES-1 cell injury in vitro, as well as, excellent gastroprotective activity in vivo. Especially, a high-dose of BSP (100 mg/kg) could reduce the ulcer index of the gastric mucosa and increase the percentage of ulcer inhibition, which possibly caused by enhancing the antioxidant capacity and inhibiting the apoptotic pathway in gastric tissue. Interestingly, BSP exhibited a comparative gastroprotective activity to that of positive control (omeprazole). In summary, our results indicated that BSP could be considered as a potential supplement for the prevention of gastric injury.
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http://dx.doi.org/10.1016/j.carbpol.2020.116620DOI Listing
October 2020

De novo sequencing of Bletilla striata (Orchidaceae) transcriptome and identification of genes involved in polysaccharide biosynthesis.

Genet Mol Biol 2020 26;43(3):e20190417. Epub 2020 Jun 26.

Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China.

Bletilla striata polysaccharide (BSP) is the main component of Bletilla striata, which has important pharmacological and pharmacological effects; however, due to the lack of genetic data, the metabolic pathways of BSP remain unclear. For this study, 11 representative resources of B. striata were analyzed, and the BSP contents of the different samples were significantly different; however, the monosaccharide composition of BSP was glucose and mannose. The representative samples were selected to observe their life history in situ, which were then divided and cultured in a greenhouse. Finally, samples from various organs of different plants were combined for transcriptome sequencing using the Illumina system. Our results summarized the BSP metabolic pathway, and we found that there were eight enzyme genes involved in biosynthesis, but these genes showed tissue specificity. Following qRT-PCR validation and comparative analysis, manA showed the highest expression; however, there were significant differences between the two germplasm resources in which the BSP content was significantly different, while UGP2, GPI, PMM, and GMPP had significant differences between the two samples. In summary, this study lays the foundation for further research into BSP metabolism and other physiological processes at the molecular level.
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http://dx.doi.org/10.1590/1678-4685-GMB-2019-0417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315133PMC
June 2020

The cytosolic protein GRP1 facilitates abscisic acid- and darkness-induced stomatal closure in Salvia miltiorrhiza.

J Plant Physiol 2020 Feb 7;245:153112. Epub 2020 Jan 7.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China. Electronic address:

By screening an expressed sequence tag (EST) library of Salvia miltiorrhiza, we detected an acidic protein, SmGRP1, with no significant similarities to the other sequences in public databases. SmGRP1 encodes a peptide of 151 amino acids, 33.77 % of which are glutamic acid residues, and the peptide was positive according to "stains-all" staining. Expression analysis revealed that SmGRP1 was expressed in all examined tissues of S. miltiorrhiza but was most highly expressed in the leaves and stems. Without a signal peptide, SmGRP1 localized to the cytoplasm in protoplasts in subcellular localization experiments. SmGRP1 expression was prominently enhanced by ABA and darkness treatments; the protein could also be induced by high temperature, NaCl, and dehydration treatments, while low temperature suppressed its expression. Furthermore, although there were no obvious phenotypic differences in SmGRP1 overexpression and SmGRP1 knockdown mutants compared with control plants under normal culture conditions, the stomata of the knockdown lines remained open when treated with ABA, darkness, NO, and HO. In addition, the water loss rate of the knockdown mutants was faster than that of the control lines and overexpression mutants when exposed to air. These observations indicate that SmGRP1 is a novel acidic protein with potential calcium-binding capability and is involved in stomatal movement and stress resistance.
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http://dx.doi.org/10.1016/j.jplph.2019.153112DOI Listing
February 2020

Genome-wide identification and characterization of R2R3-MYB family in Hypericum perforatum under diverse abiotic stresses.

Int J Biol Macromol 2020 Feb 17;145:341-354. Epub 2019 Dec 17.

Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China. Electronic address:

The R2R3-MYB family is one of the largest families of plant transcription factor playing significant roles in plant growth. Although this gene family has been studied in many species, the R2R3-MYBs in Hypericum perforatum which is the first sequenced species in Malpighiales have not been analyzed. A total of 109 R2R3-MYB genes were identified in H. perforatum and clustered into 36 clades. Gene Ontology analysis revealed that most of the R2R3-MYB genes were involved in biological processes. Four kinds of cis-acting elements were found within the promoter regions, the majority of which were related to the stress responses and plant growth/development. The transcriptome data of different tissues (root, stems, leaves, and flowers) showed that the spatial expression profiles of R2R3-MYBs were different. Also, real-time quantitative PCR analysis revealed that eleven stress-related R2R3-MYB genes showed specific expression patterns under diverse treatments. In addition, sub-cellular localization analysis indicated that five significant proteins HpMYB45, HpMYB48, HpMYB55, HpMYB63, and HpMYB70 were all localized in the nucleus. This study was the first report on identification and characterization of R2R3-MYB gene family in H. perforatum. It facilitated the identification of tissue-preferential and stress-related genes and provided deep insights into the function of R2R3-MYBs in H. perforatum.
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http://dx.doi.org/10.1016/j.ijbiomac.2019.12.100DOI Listing
February 2020

Glycyrrhizic acid promotes neural repair by directly driving functional remyelination.

Food Funct 2020 Jan;11(1):992-1005

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.

Natural compounds are a rich source of effective candidate drugs for the treatment of neurological disorders. Glycyrrhizic acid (GA), the major water-soluble ingredient isolated from Glycyrrhiza glabra, is reported to show anti-inflammatory and immunomodulatory activities. However, its effect on CNS demyelinating disease is unclear. In this study, we showed that GA ameliorated the clinical disease severity of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), especially at the chronic stage of clinical EAE. Histological evaluation demonstrated that, in the prophylactic treatment regimen, GA significantly inhibited inflammatory demyelination in the CNS. During the chronic stage when myelin and axon damage has already occurred, GA induced oligodendrocyte progenitor cell (OPC) differentiation into mature oligodendrocytes, thus effectively accelerating remyelination. Evidence from the cuprizone-induced mouse model of de- and remyelination, ex vivo organotypic slice cultures, and in vitro OPC maturation experiments indicated that the observed efficacy of this compound resulted directly from enhanced remyelination rather than immune suppression. Furthermore, we found that GA promoted oligodendrocyte maturation through modulating GSK-3β signaling pathways. Our data led to the conclusion that GA could be used as a potential therapeutic candidate for the treatment of demyelinating diseases such as MS, which remains refractory to available treatments.
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http://dx.doi.org/10.1039/c9fo01459dDOI Listing
January 2020

Structure and anti-tumor activity of a polysaccharide from Bletilla ochracea Schltr.

Int J Biol Macromol 2020 Jul 13;154:1548-1555. Epub 2019 Nov 13.

National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China. Electronic address:

The polysaccharide fraction of Bletilla ochracea (BOP) was isolated from its tubers, and purified by DEAE-52 Cellulose and Sephadex G-200 column chromatography. The structural features of BOP were analyzed by GC-MS, HPLP, FT-IR, methylation and NMR. The average molecular weight of BOP was approximately 4.9 × 10 Da, and the monosaccharide composition was 7.88:2.12 mix of mannose and glucose. The FT-IR and NMR analyses revealed the following linkage: [→(4-β-D-Man-1) → (4-β-D-Glc-1) → 4-2-O-acetyl-β-D-Man-1 → 4-β-D-Man-1 → 4-3-O-acetyl-β-D-Man-1 → 4-2-O-acetyl-β-D-Man-1→]. Although BOP had no effect on the proliferation rate of CT26 colon carcinoma cells, it significantly inhibited tumor xenograft growth in vivo by stimulating CD4 T cell expansion in the spleen of the tumor-bearing mice. Taken together, BOP is a potent immunomodulatory agent that can be considered for anti-tumor therapy.
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http://dx.doi.org/10.1016/j.ijbiomac.2019.11.039DOI Listing
July 2020

Reference genes for qRT-PCR normalisation in different tissues, developmental stages, and stress conditions of .

PeerJ 2019 20;7:e7133. Epub 2019 Jun 20.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China.

. is a widely known medicinal herb used mostly as a remedy for depression because it contains high levels of naphthodianthrones, phloroglucinols, alkaloids, and some other secondary metabolites. Quantitative real-time PCR (qRT-PCR) is an optimized method for the efficient and reliable quantification of gene expression studies. In general, reference genes are used in qRT-PCR analysis because of their known or suspected housekeeping roles. However, their expression level cannot be assumed to remain stable under all possible experimental conditions. Thus, the identification of high quality reference genes is essential for the interpretation of qRT-PCR data. In this study, we investigated the expression of 14 candidate genes, including nine housekeeping genes (HKGs) (, , , , -α, , -α, -β, and ) and five potential candidate genes (, , , , and ). Three programs-GeNorm, NormFinder, and BestKeeper-were applied to evaluate the gene expression stability across four different plant tissues, four developmental stages and a set of abiotic stress and hormonal treatments. Integrating all of the algorithms and evaluations revealed that and -β were the most stable combination in different developmental stages samples and all of the experimental samples. , -β, and -α were identified as the three most applicable reference genes in different tissues and stress-treated samples. The majority of the conventional HKGs performed better than the potential reference genes. The obtained results will aid in improving the credibility of the standardization and quantification of transcription levels in future expression studies on .
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http://dx.doi.org/10.7717/peerj.7133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589333PMC
June 2019

AtPAP1 Interacts With and Activates SmbHLH51, a Positive Regulator to Phenolic Acids Biosynthesis in .

Front Plant Sci 2018 20;9:1687. Epub 2018 Nov 20.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.

Phenolic acids from have drawn considerable attention in recent years because of their remarkable pharmacological activities. We previously reported that transcription factor production of anthocyanin pigment 1 (AtPAP1) has strong capability to promote the production of phenolic acids in . However, the responsible molecular mechanism is unclear. Here, we analyzed the transcriptome of transgenic that over-expressed . Transcriptome analysis revealed 4,152 genes that were differentially expressed due to ectopic overexpression. , a novel bHLH gene significantly up-regulated by constitutive expression of , was isolated from for detailed functional characterization. SmbHLH51 localizes in the nuclei and interacts with AtPAP1, indicating that they probably comprise a regulatory transcription complex. Enhanced or reduced expression of was achieved in by gain- or loss-of-function assays, respectively, revealing that SmbHLH51 is a positive transcriptional regulator of the pathway for phenolic acid biosynthesis. We propose that applying this functional genomics approach through the transcriptomic analyses is an efficient means for identifying novel genes involved in plant secondary metabolism.
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http://dx.doi.org/10.3389/fpls.2018.01687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255977PMC
November 2018

Molecular Characterization and Overexpression of Increases the Production of Phenolic Acids in .

Int J Mol Sci 2018 Nov 28;19(12). Epub 2018 Nov 28.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.

Jasmonic acid (JA) carboxyl methyltransferase (JMT), a key enzyme in jasmonate-regulated plant responses, may be involved in plant defense and development by methylating JA to MeJA, thus influencing the concentrations of MeJA in plant. In this study, we isolated the gene from , an important medicinal plant widely used to treat cardiovascular disease. We present a genetic manipulation strategy to enhance the production of phenolic acids by overexpresion in . Global transcriptomic analysis using RNA sequencing showed that the expression levels of genes involved in the biosynthesis pathway of phenolic acids and MeJA were upregulated in the overexpression lines. In addition, the levels of endogenous MeJA, and the accumulation of rosmarinic acid (RA) and salvianolic acid (Sal B), as well as the concentrations of total phenolics and total flavonoids in transgenic lines, were significantly elevated compared with the untransformed control. Our results demonstrate that overexpression of promotes the production of phenolic acids through simultaneously activating genes encoding key enzymes involved in the biosynthesis pathway of phenolic acids and enhancing the endogenous MeJA levels in .
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http://dx.doi.org/10.3390/ijms19123788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6321555PMC
November 2018

SmMYB111 Is a Key Factor to Phenolic Acid Biosynthesis and Interacts with Both SmTTG1 and SmbHLH51 in Salvia miltiorrhiza.

J Agric Food Chem 2018 Aug 24;66(30):8069-8078. Epub 2018 Jul 24.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , Shaanxi Normal University , Xi'an , Shaanxi 710062 , People's Republic of China.

Transcription factors that include myeloblastosis (MYB), basic helix-loop-helix (bHLH), and tryptophan-aspartic acid (WD)-repeat protein often form a ternary complex to regulate the phenylpropanoid pathway. However, only a few MYB and bHLH members involved in the biosynthesis of salvianolic acid B (Sal B) have been reported, and little is known about Sal B pathway regulation by the WD40 protein transparent testa glabra 1 (TTG1)-dependent transcriptional complexes in Salvia miltiorrhiza. We isolated SmTTG1 from that species for detailed functional characterization. Enhanced or reduced expression of SmTTG1 was achieved by gain- or loss-of-function assays, respectively, revealing that SmTTG1 is necessary for Sal B biosynthesis. Interaction partners of the SmTTG1 protein were screened by yeast two-hybrid (Y2H) assays with the cDNA library of S. miltiorrhiza. A new R2R3-MYB transcription factor, SmMYB111, was found through this screening. Transgenic plants overexpressing or showing reduced expression of SmMYB111 upregulated or deregulated, respectively, the yields of Sal B. Both Y2H and bimolecular fluorescent complementation experiments demonstrated that SmMYB111 interacts with SmTTG1 and SmbHLH51, a positive regulator of the phenolic acid pathway. Our data verified the function of SmTTG1 and SmMYB111 in regulating phenolic acid biosynthesis in S. miltiorrhiza. Furthermore, ours is the first report of the potential ternary transcription complex SmTTG1-SmMYB111-SmbHLH51, which is involved in the production of Sal B in that species.
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http://dx.doi.org/10.1021/acs.jafc.8b02548DOI Listing
August 2018

Genome survey sequencing of Dioscorea zingiberensis.

Genome 2018 Aug 8;61(8):567-574. Epub 2018 Jun 8.

a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China.

Dioscorea zingiberensis (Dioscoreceae) is the main plant source of diosgenin (steroidal sapogenins), the precursor for the production of steroid hormones in the pharmaceutical industry. Despite its large economic value, genomic information of the genus Dioscorea is currently unavailable. Here, we present an initial survey of the D. zingiberensis genome performed by next-generation sequencing technology together with a genome size investigation inferred by flow cytometry. The whole genome survey of D. zingiberensis generated 31.48 Gb of sequence data with approximately 78.70× coverage. The estimated genome size is 800 Mb, with a high level of heterozygosity based on K-mer analysis. These reads were assembled into 334 288 contigs with a N50 length of 1079 bp, which were further assembled into 92 163 scaffolds with a total length of 173.46 Mb. A total of 4935 genes, 81 tRNAs, 69 rRNAs, and 661 miRNAs were predicted by the genome analysis, and 263 484 repeated sequences were obtained with 419 372 simple sequence repeats (SSRs). Among these SSRs, the mononucleotide repeat type was the most abundant (up to 54.60% of the total SSRs), followed by the dinucleotide (29.60%), trinucleotide (11.37%), tetranucleotide (3.53%), pentanucleotide (0.65%), and hexanucleotide (0.25%) repeat types. The 1C-value of D. zingiberensis was calibrated against Salvia miltiorrhiza and calculated as 0.87 pg (851 Mb) by flow cytometry, which was very close to the result of the genome survey. This is the first report of genome-wide characterization within this taxon.
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http://dx.doi.org/10.1139/gen-2018-0011DOI Listing
August 2018

The complete chloroplast genome sequence of Epipremnum aureum and its comparative analysis among eight Araceae species.

PLoS One 2018 12;13(3):e0192956. Epub 2018 Mar 12.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P.R. China.

Epipremnum aureum is an important foliage plant in the Araceae family. In this study, we have sequenced the complete chloroplast genome of E. aureum by using Illumina Hiseq sequencing platforms. This genome is a double-stranded circular DNA sequence of 164,831 bp that contains 35.8% GC. The two inverted repeats (IRa and IRb; 26,606 bp) are spaced by a small single-copy region (22,868 bp) and a large single-copy region (88,751 bp). The chloroplast genome has 131 (113 unique) functional genes, including 86 (79 unique) protein-coding genes, 37 (30 unique) tRNA genes, and eight (four unique) rRNA genes. Tandem repeats comprise the majority of the 43 long repetitive sequences. In addition, 111 simple sequence repeats are present, with mononucleotides being the most common type and di- and tetranucleotides being infrequent events. Positive selection pressure on rps12 in the E. aureum chloroplast has been demonstrated via synonymous and nonsynonymous substitution rates and selection pressure sites analyses. Ycf15 and infA are pseudogenes in this species. We constructed a Maximum Likelihood phylogenetic tree based on the complete chloroplast genomes of 38 species from 13 families. Those results strongly indicated that E. aureum is positioned as the sister of Colocasia esculenta within the Araceae family. This work may provide information for further study of the molecular phylogenetic relationships within Araceae, as well as molecular markers and breeding novel varieties by chloroplast genetic-transformation of E. aureum in particular.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192956PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5846728PMC
June 2018

Overexpression of Increases the Production of Phenolic Acids in .

Front Plant Sci 2017 18;8:1804. Epub 2017 Oct 18.

Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, China.

MYC2 is a core transcription factor in the plant response to jasmonates. It also functions in secondary metabolism and various processes for growth and development. However, the knowledge about its role in is still very limited. We determined that the biosynthesis of salvianolic acid B (Sal B) was strongly induced in 2-month-old transgenic plants that over-expressed . In the roots of transgenic line 12 that over-expressed (OEM-12), the Sal B concentration was as high as 5.95 ± 0.07 mg g, a level that was 1.88-fold higher than that in control plants that had been transformed with an empty vector. Neither tanshinone IIA nor cryptotanshinone was detected by high-performance liquid chromatography in any of the genotypes. Global transcriptomic analysis using RNA sequencing revealed that most enzyme-encoding genes for the phenylpropanoid biosynthesis pathway were up-regulated in the overexpression lines. Furthermore, both the phenylalanine and tyrosine biosynthesis pathways were activated in those transgenics. Our data demonstrate that overexpression of promotes the production of phenolic acids by simultaneously activating both primary and secondary pathways for metabolism in .
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http://dx.doi.org/10.3389/fpls.2017.01804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708653PMC
October 2017

Genome-Wide Comprehensive Analysis the Molecular Phylogenetic Evaluation and Tissue-Specific Expression of SABATH Gene Family in Salvia miltiorrhiza.

Genes (Basel) 2017 Dec 5;8(12). Epub 2017 Dec 5.

National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.

The plant SABATH gene family is a group of -methyltransferases (-MTs), which belongs to the -adenosyl-l-methionine-dependent methyltransferases (SAM-MTs). The resulting reaction products of SABATH genes play an important role in various processes of plant development. In this study, a total of 30 SABATH genes were detected in , which is an important medicinal plant, widely used to treat cardiovascular disease. Multiple sequence alignment and phylogenetic analyses showed that genes could be classified into three groups. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of 11 pairs paralogous of genes revealed that the genes had gone through purifying selection. Positive selection analyses using site models and branch-site models indicated that genes had undergone selective pressure for adaptive evolution. Functional divergence analyses suggested that the subgroup genes were divergent in terms of functions and positive selection sites that contributed to a functional divergence among the subgroups that were detected. Tissue-specific expression showed that the SABATH gene family in was primarily expressed in stems and leaves.
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http://dx.doi.org/10.3390/genes8120365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748683PMC
December 2017

De Novo Assembly and Analysis of Polygonatum sibiricum Transcriptome and Identification of Genes Involved in Polysaccharide Biosynthesis.

Int J Mol Sci 2017 Sep 12;18(9). Epub 2017 Sep 12.

National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, Shaanxi, China.

polysaccharides (PSPs) are used to improve immunity, alleviate dryness, promote the secretion of fluids, and quench thirst. However, the PSP biosynthetic pathway is largely unknown. Understanding the genetic background will help delineate that pathway at the molecular level so that researchers can develop better conservation strategies. After comparing the PSP contents among several different germplasms, we selected two groups with the largest contrasts in contents and subjected them to HiSeq2500 transcriptome sequencing to identify the candidate genes involved in PSP biosynthesis. In all, 20 kinds of enzyme-encoding genes were related to PSP biosynthesis. The polysaccharide content was positively correlated with the expression patterns of β-fructofuranosidase (), fructokinase (), UDP-glucose 4-epimerase (), Mannose-1-phosphate guanylyltransferase (), and UDP-glucose 6-dehydrogenase (), but negatively correlated with the expression of Hexokinase (). Through qRT-PCR validation and comprehensive analysis, we determined that , , and are key genes for enzymes within the PSP metabolic pathway in Our results provide a public transcriptome dataset for this species and an outline of pathways for the production of polysaccharides in medicinal plants. They also present more information about the PSP biosynthesis pathway at the molecular level in and lay the foundation for subsequent research of gene functions.
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http://dx.doi.org/10.3390/ijms18091950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5618599PMC
September 2017

The complete chloroplast genome sequence of the medicinal and economic plant woad (Brassicaceae).

Mitochondrial DNA B Resour 2017 Aug 8;2(2):514-515. Epub 2017 Aug 8.

Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P.R. China.

Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis. It becomes a popular useful tool for population and phylogeny in recently report. Here, the complete chloroplast genome of the has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 156,670 bp in size and comprises a pair of inverted repeat (IR) regions of 26,995 bp each, a large single-copy (LSC) region of 84,907 bp and a small single-copy (SSC) region of 17,773 bp. The total GC content is 36.5%, while the corresponding values of the LSC, SSC and IR region are 34.2%, 29.7% and 42.3%, respectively. The chloroplast genome contains 140 genes, including 94 protein-coding genes. The phylogenetic analysis showed a strong sister relationship with in Brassicaceae. These findings provide a foundation for further investigation of cp genome evolution in and other higher plants.
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http://dx.doi.org/10.1080/23802359.2017.1361356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799964PMC
August 2017

Selection and Validation of Appropriate Reference Genes for qRT-PCR Analysis in Fort.

Front Plant Sci 2017 28;8:1139. Epub 2017 Jun 28.

Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shannxi Normal UniversityXi'an, China.

Due to its sensitivity and specificity, real-time quantitative PCR (qRT-PCR) is a popular technique for investigating gene expression levels in plants. Based on the Minimum Information for Publication of Real-Time Quantitative PCR Experiments (MIQE) guidelines, it is necessary to select and validate putative appropriate reference genes for qRT-PCR normalization. In the current study, three algorithms, geNorm, NormFinder, and BestKeeper, were applied to assess the expression stability of 10 candidate reference genes across five different tissues and three different abiotic stresses in Fort. Additionally, the gene associated with IAA biosynthesis was applied to validate the candidate reference genes. The analysis results of the geNorm, NormFinder, and BestKeeper algorithms indicated certain differences for the different sample sets and different experiment conditions. Considering all of the algorithms, and were recommended as the most stable reference genes for total and different tissue samples, respectively. Moreover, and were considered to be the most suitable reference genes for abiotic stress treatments. The obtained experimental results might contribute to improved accuracy and credibility for the expression levels of target genes by qRT-PCR normalization in
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http://dx.doi.org/10.3389/fpls.2017.01139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5487591PMC
June 2017

Total Flavonoids of Drynariae Rhizoma Prevent Bone Loss Induced by Hindlimb Unloading in Rats.

Molecules 2017 Jun 22;22(7). Epub 2017 Jun 22.

Key Laboratory for Space Bioscience and Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.

Drynariae Rhizoma is a kidney-tonifying herb that has a long history in clinical practice for the treatment of bone fractures and joint diseases in China. Flavonoids are considered to be its major active ingredients and are reported to ease bone loss in ovariectomized rats. However, the beneficial effects of the total flavonoids of Drynariae Rhizoma on osteoporosis caused by microgravity or mechanical inactivity remain unknown. This study assessed the effects of total Drynariae Rhizoma flavonoids (DRTF, Qihuang, Beijing, China, national medicine permit No. Z20030007, number of production: 04080081, content of DRTF ≥80%) against bone loss induced by simulated microgravity. A hindlimb unloading tail-suspended rat model was established to determine the effect of DRTF on bone mineral density (BMD), biomechanical strength and trabecular bone microarchitecture. Twenty-eight male Sprague-Dawley rats were divided into four groups: the baseline, control, hindlimb unloading with vehicle (HLU), and hindlimb unloading treated with DRTF (HLU-DRTF, 75 mg/kg/day) groups. Oral DRTF was administered for 4 weeks. The underlying mechanisms of the DRTF actions on disuse-induced osteoporosis are discussed. The results showed that DRTF treatment significantly increased the BMD and mechanical strength of tail-suspended rats. Enhanced bone turnover markers with HLU treatment were attenuated by DRTF administration. Deterioration of trabecular bone induced by HLU was prevented through elevated bone volume/tissue volume (BV/TV), trabecular number (Tb. N), trabecular thickness (Tb. Th) and decreased trabecular separation (Tb. Sp). The present study provides the first evidence that DRTF prevents bone loss induced by HLU treatment, indicating its potential application in the treatment of disuse-induced osteoporosis.
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http://dx.doi.org/10.3390/molecules22071033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6152118PMC
June 2017

Transcriptional Responses and Gentiopicroside Biosynthesis in Methyl Jasmonate-Treated Gentiana macrophylla Seedlings.

PLoS One 2016 16;11(11):e0166493. Epub 2016 Nov 16.

Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, China.

Gentiana macrophylla, a medicinal plant with significant pharmacological properties, contains the bioactive compound gentiopicroside. Methyl jasmonate (MeJA) is an effective elicitor for enhancing the production of such compounds. However, little is known about MeJA-mediated biosynthesis of gentiopicroside. We investigated this phenomenon as well as gene expression profiles to determine the molecular mechanisms for MeJA-mediated gentiopicroside biosynthesis and regulation in G. macrophylla. Our HPLC results showed that Gentiana macrophylla seedlings exposed to MeJA had significantly higher concentrations of gentiopicroside when compared with control plants. We used RNA sequencing to compare transcriptional profiles in seedlings treated for 5 d with either 0 μmol L-1 MeJA (C) or 250 μmol L-1 MeJA (M5) and detected differentially expressed genes (DEGs). In total, 77,482 unique sequences were obtained from approximately 34 million reads. Of these, 48,466 (57.46%) sequences were annotated based on BLASTs performed against public databases. We identified 5,206 DEGs between the C and M5 samples, including genes related to the α-lenolenic acid degradation pathway, JA signaling pathway, and gentiopicroside biosynthesis. Expression of numerous enzyme genes in the glycolysis pathway was significantly up-regulated. Many genes encoding transcription factors (e.g. ERF, bHLH, MYB, and WRKY) also responded to MeJA elicitation. Rapid acceleration of the glycolysis pathway that supplies precursors for IPP biosynthesis and up-regulates the expression of enzyme genes in that IPP pathway are probably most responsible for MeJA stimulation of gentiopicroside synthesis. Our qRT-PCR results showed that the expression profiles of 12 gentiopicroside biosynthesis genes were consistent with the RNA-Seq data. These results increase our understanding about how the gentiopicroside biosynthesis pathway in G. macrophylla responds to MeJA.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166493PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112864PMC
June 2017

Function Analysis of Caffeoyl-CoA O-Methyltransferase for Biosynthesis of Lignin and Phenolic Acid in Salvia miltiorrhiza.

Appl Biochem Biotechnol 2017 Feb 9;181(2):562-572. Epub 2016 Sep 9.

Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China.

In this study, we cloned a full-length cDNA and the genomic DNA sequence of SmCCoAOMT (GenBank ID JQ007585) from Salvia miltiorrhiza. The 744-bp open-reading frame encodes a protein of 247 amino acids that shares 95 % similarity with one in Vitis vinifera. Real-time quantitative PCR analysis revealed that SmCCoAOMT is most highly expressed in the stems and can be induced by methyl jasmonate (MeJA) and XC-1 treatment. To evaluate its function in vivo, we generated RNA interference transgenic plants through Agrobacterium tumefaciens-mediated gene transfer. Compared with untransformed control plants, the transgenics had significantly less lignin and the expression of lignin-biosynthetic genes SmCCR and SmCOMT was depressed. In 90-day-old roots from plants of transgenic line M5, accumulations of rosmarinic acid and salvianolic acid B (Sal B) were greatly reduced by 0.89- and 0.69-fold, respectively. This low-Sal B phenotype was stable in the roots, with the level of accumulation being approximately 43.58 mg g dry weight, which was 52 % of the amount measured in the untransformed control. Our results suggest that SmCCoAOMT is involved in lignin biosynthesis and affects the accumulation of phenolic acids. This study also provides potential guidance for using lignin-related genes to genetically engineer Salvia miltiorrhiza.
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http://dx.doi.org/10.1007/s12010-016-2231-4DOI Listing
February 2017

Selection and Validation of Reference Genes for Quantitative Real-time PCR in Gentiana macrophylla.

Front Plant Sci 2016 29;7:945. Epub 2016 Jun 29.

Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University Xi'an, China.

Real time quantitative PCR (RT-qPCR or qPCR) has been extensively applied for analyzing gene expression because of its accuracy, sensitivity, and high throughput. However, the unsuitable choice of reference gene(s) can lead to a misinterpretation of results. We evaluated the stability of 10 candidates - five traditional housekeeping genes (UBC21, GAPC2, EF-1α4, UBQ10, and UBC10) and five novel genes (SAND1, FBOX, PTB1, ARP, and Expressed1) - using the transcriptome data of Gentiana macrophylla. Common statistical algorithms ΔC t, GeNorm, NormFinder, and BestKeeper were run with samples collected from plants under various experimental conditions. For normalizing expression levels from tissues at different developmental stages, GAPC2 and UBC21 had the highest rankings. Both SAND1 and GAPC2 proved to be the optimal reference genes for roots from plants exposed to abiotic stresses while EF-1α4 and SAND1 were optimal when examining expression data from the leaves of stressed plants. Based on a comprehensive ranking of stability under different experimental conditions, we recommend that SAND1 and EF-1α4 are the most suitable overall. In this study, to find a suitable reference gene and its real-time PCR assay for G. macrophylla DNA content quantification, we evaluated three target genes including WRKY30, G10H, and SLS, through qualitative and absolute quantitative PCR with leaves under elicitors stressed experimental conditions. Arbitrary use of reference genes without previous evaluation can lead to a misinterpretation of the data. Our results will benefit future research on the expression of genes related to secoiridoid biosynthesis in this species under different experimental conditions.
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http://dx.doi.org/10.3389/fpls.2016.00945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4925707PMC
July 2016

The complete chloroplast genome sequence of Dieffenbachia seguine (Araceae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 07 8;27(4):2913-4. Epub 2015 Jul 8.

a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University , Xi'an , PR China .

The nucleotide sequence of the chloroplast genome from Dieffenbachia seguine is the first to have complete genome sequence from genus of Dieffenbachia family Araceae. The genome size is 163 699 bp in length, with 36.4% GC content. A pair of inverted repeats (IRs, 25 235 bp) is separated by a large single copy region (LSC, 90 780 bp) and a small single copy region (SSC, 22 449 bp). The chloroplast genome contains 113 unique genes, 88 protein-coding genes, 37 tRNA genes, and four rRNA genes. In these genes, 16 genes contained single intron and two genes composed of double introns. A maximum likelihood phylogenetic analysis using complete chloroplast genome revealed that Dieffenbachia seguine belongs to the Araceae family of the Arecidae group, which is conform to the traditional classification.
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http://dx.doi.org/10.3109/19401736.2015.1060436DOI Listing
July 2016
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