Jianping Han

Chinese Academy of Medical Sciences & Peking Union Medical College

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Shilin Chen

Chinese Academy of Medical Sciences & Peking Union Medical College

Jingyuan Song

Chinese Academy of Medical Sciences & Peking Union Medical College

Xiaohui Pang

Chinese Academy of Medical Sciences & Peking Union Medical College

Hui Yao

Wuhan Children's Hospital

Xuemin Wei

State Administration of Traditional Chinese Medicine of the People's Republic of China

Gang Wang

Chinese Academy of Medical Sciences & Peking Union Medical College

Xiaoyue Wang

Chinese Academy of Medical Sciences & Peking Union Medical College

Linchun Shi

Chinese Academy of Medical Sciences & Peking Union Medical College

Zitong Gao

University of Hawaiʻi at Mānoa

Xuanjiao Bai

Chinese Academy of Medical Sciences & Peking Union Medical College

Cooperative Institutions

Chinese Academy of Medical Sciences & Peking Union Medical College

State Administration of Traditional Chinese Medicine of the People's Republic of China

Chinese Academy of Sciences

Ministry of Education of the People's Republic of China

Peking Union Medical College Hospital

Huazhong University of Science and Technology

China Academy of Chinese Medical Sciences

Beijing University of Chinese Medicine

Chengdu University of Traditional Chinese Medicine

Academy of Medical Sciences

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Identification ofDendrobiumSpecies by a Candidate DNA Barcode Sequence: The ChloroplastpsbA-trnHIntergenic Region

Planta Medica (2009)

Hui Yao Jingyuan Song Xinye Ma Chang Liu Ying Li

DNA barcoding is a novel technology that uses a standard DNA sequence to facilitate species identification. Although a consensus has not been reached regarding which DNA sequences can be used as the best plant barcodes, the psbA-trnH spacer region has been tested extensively in recent years. In this study, we hypothesize that the psbA-trnH spacer regions are also effective barcodes for Dendrobium species. We have sequenced the chloroplast psbA-trnH intergenic spacers of 17 Dendrobium species to test this hypothesis. The sequences were found to be significantly different from those of other species, with percentages of variation ranging from 0.3 % to 2.3 % and an average of 1.2 %. In contrast, the intraspecific variation among the Dendrobium species studied ranged from 0 % to 0.1 %. The sequence difference between the psbA-trnH sequences of 17 Dendrobium species and one Bulbophyllum odoratissimum ranged from 2.0 % to 3.1 %, with an average of 2.5 %. Our results support the notion that the psbA-trnH intergenic spacer region could be used as a barcode to distinguish various Dendrobium species and to differentiate Dendrobium species from other adulterating species.

Dendrobium

DNA Barcoding

Intergenic region

Barcode

10.1055/s-0029-1185385

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Citations (137)

Comparison of DNA barcoders in identifying medicinal materials

China Journal of Chinese Materia Medica (2012)

Jianping Han Jingyuan Song Hui Yao Xiaochen Chen Shilin Chen

The DNA barcoding of traditional Chinese medicine was summarized in this article. Based on analyzing a number of research findings, the authors discussed the possibility of nuclear DNA sequence and chloroplast genes in identifying medicinal materials. ITS was considered to evolve faster, which was used for plant molecular systematics analysis and species identification,while ITS2 was more suitable to identify medicinal materials. So, it is important that we should select suitable DNA sequences as barcodes based on the objective of a study. With the cost reduction of sequencing, identifying medicinal materials by cp-genome barcoding would be applied broadly and effectively in the future.

DNA Barcoding

Identification

10.4268/cjcmm20120802

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Citations (1)

Algorithm-based fault tolerance in computation of power flow

Y. Chen Jianping Han

The LU decomposition followed by forward/backward substitution is a very powerful technique for power flow studies. In order to ensure the reliability of computation, the algorithm-based fault tolerance (ABFT) is applied to LU decomposition in power flow studies. This technique is proposed not only to detect and correct errors caused by hardware failure but also to debug programs. Since the ABFT often suffers from roundoff errors when applied to the floating-point number system, a new technique called significant-bit maintenance arithmetic (SBMA) is also suggested for handling numerical problems.< >

Software fault tolerance

10.1109/mwscas.1990.140674

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Citations (0)

Overview of sesquiterpenes and chromones of agarwood originating from four main species of the genus Aquilaria

RSC Advances (2019)

Mei Gao Xiaomin Han Ying Sun Hongjiang Chen Yun Yang

The main chemical constituents of agarwood are sesquiterpenes and chromones, which can be divided into different categories depending on their molecular skeletons. Agarwoods are obtained from different plant species:

Agarwood

10.1039/c8ra09409h

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Citations (66)

Microbial inoculants and garbage fermentation liquid reduced root-knot nematode disease and As uptake in Panax quinquefolium cultivation by modulating rhizosphere microbiota community

Chinese Herbal Medicines (2021)

Pei Cao Xuemin Wei Gang Wang Xiaochen Chen Jianping Han

To find a suitable ecological cultivation measure to solve the problem of root-knot nematode disease of Panax quinquefolium (Panacis Quinquefolii Radix) and the heavy metals accumulating in its roots.Three-year-old P. quinquefolium was treated with four different combinations of microbial inoculant (MI) and garbage fermentation liquid (GFL) [the joint application of 'TuXiu' MI and Fifty potassium MI (TF), the combination use of 'No. 1' MI and Fifty potassium MI (NF), 'Gulefeng' poly-γ-glutamic acid MI (PGA), GFL], and the untreated control (CK). Here, high-throughput sequencing, ICP-MS and UPLC were employed to systematically characterize changes of microbial diversity and structure composition, heavy metals (As, Cd and Pb) content and ginsenoside content among different treatments.The results revealed that different MIs and GFL could increase the root dry weight of P. quinquefolium, PGA enhanced it by 83.24%, followed by GFL (49.93%), meanwhile, PGA and GFL were able to lessen root-knot nematode disease incidence by 57.25% and 64.35%. The treatment of PGA and GFL can also effectively reduce heavy metals in roots. The As content in GFL and PGA was decreased by 52.17% and 43.48% respectively, while the Cd and Pb contents of GFL and PGA was decreased somewhat. Additionally, the content of total ginsenosides was increased by 42.14% and 42.07%, in response to TF and NF, respectively. Our metagenomic analysis showed that the relative abundance of particular soil microbial community members related to the biocontrol of root-knot nematode disease and plant pathogen (i.e., Chaetomium in NF, Xylari in GFL, and Microascus in PGA), heavy metal bioremediation (Hyphomacrobium in PGA and Xylaria in GFL), and nitrogen fixation (Nordella and Nitrospira in TF) was significantly increased; notably, potential harmful microflora, such as Plectosaphaerella and Rhizobacter, were more abundant in the control group.MI and GFL could improve the quality of P. quinquefolium by modifying its rhizosphere microbial community structure and composition, both of them are beneficial to the development of ecological cultivation of P. quinquefolium.

10.1016/j.chmed.2021.11.001

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Molecular Mechanism Underlying Mechanical Wounding-Induced Flavonoid Accumulation in Dalbergia odorifera T. Chen, an Endangered Tree That Produces Chinese Rosewood

Genes (2020)

Ying Sun Mei Gao Seogchan Kang Chengmin Yang Hui Meng

Dalbergia odorifera, a critically endangered tree species, produces heartwood containing a vast variety of flavonoids. This heartwood, also known as Chinese rosewood, has high economic and medicinal value, but its formation takes several decades. In this study, we showed that discolored wood induced by pruning displays similar color, structure, and flavonoids content to those of natural heartwood, suggesting that wounding is an efficient method for inducing flavonoid production in D. odorifera. Transcriptome analysis was performed to investigate the mechanism underlying wounding-induced flavonoids production in D. odorifera heartwood. Wounding upregulated the expression of 90 unigenes, which covered 19 gene families of the phenylpropanoid and flavonoid pathways, including PAL, C4H, 4CL, CHS, CHI, 6DCS, F3’5’H, F3H, FMO, GT, PMAT, CHOMT, IFS, HI4’OMT, HID, IOMT, I2’H, IFR, and I3’H. Furthermore, 47 upregulated unigenes were mapped to the biosynthesis pathways for five signal molecules (ET, JA, ABA, ROS, and SA). Exogenous application of these signal molecules resulted in the accumulation of flavonoids in cell suspensions of D. odorifera, supporting their role in wounding-induced flavonoid production. Insights from this study will help develop new methods for rapidly inducing the formation of heartwood with enhanced medicinal value.

Dalbergia

Phenylpropanoid

Flavonoid Biosynthesis

10.3390/genes11050478

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Citations (23)

Transcriptome analysis provides insights into key gene(s) involved in steroidal alkaloid biosynthesis in the medicinally important herb Fritillaria taipaiensis

Research Square (Research Square) (2019)

Xiaoyue Wang Hongmei Luo Xuemin Wei Pei Cao Zitong Gao

Abstract Background Fritillariae Cirrhosae Bulbus, which is a traditional antitussive and expectorant medicine in China, is derived from six original plants. Among these six species, all except for Fritillaria taipaiensis and Fritillaria unibracteata var. wabuensis have been recorded in the National Protected Plants III. Their major bioactive compounds, including imperialine and peimisine, are steroidal alkaloids, derived from the steroid synthesis pathway. However, research on the F. taipaiensis genome, transcriptomes and steroid-synthesis-related genes has been lacking for a long time. In this study, the first transcriptome sequencing of F. taipaiensis was performed. Results A total of 94,396,694 (~11.4 Gb) high-quality reads obtained using paired-end Illumina sequencing were de novo assembled into 190,350 transcripts. Functional annotation with multiple public databases identified an array of genes involved in steroidal alkaloid biosynthesis and other secondary metabolite pathways, including steroid and terpenoid backbone biosynthesis, and important oxidoreductases. The large number of differentially expressed transcripts together with CYPs suggests the involvement of these candidates in tissue-specific expression. The expression analysis revealed that bulbs may be the main site of the upstream steroidal alkaloid biosynthesis pathway, and we speculated that the downstream reactions, including the oxidation-reduction reaction catalyzed by CYPs, might also occur primarily in bulbs. Conclusion In conclusion, the comprehensive transcriptome dataset created in this study will serve as a resource for the identification of potential candidates for the genetic manipulation of targeted bioactive metabolites and will also contribute to the development of functionally relevant molecular marker resources to expedite molecular breeding and conservation efforts for F. taipaiensis.

Secondary metabolite

Steroid biosynthesis

10.21203/rs.2.10690/v1

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Citations (3)

Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

PLoS ONE (2010)

Shilin Chen Hui Yao Jianping Han Chang Liu Jingyuan Song

The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over.Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level.The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

Barcode

DNA Barcoding

Identification

10.1371/journal.pone.0008613

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Citations (1,478)

Identification and poisoning diagnosis of Aconitum materials using a genus-specific nucleotide signature

Ecotoxicology and Environmental Safety (2022)

Gang Wang Yang Liu Xuanjiao Bai Pei Cao Xiaohui Pang

Aconitum genus generally contains hypertoxic alkaloids. Poisoning incidents due to the improper ingestion of Aconitum materials frequently occur around the world. DNA barcoding is considered as a powerful tool for species identification, but complete sequences of conventional DNA barcodes are sometimes unattainable from food and highly processed products due to severe DNA degradation. Therefore, a shorter molecular marker will be more profitable for the authentication and poisoning diagnosis of Aconitum materials. In this study, 1246 psbA-trnH sequences and chloroplast genomes representing 183 taxa of Aconitum were collected, and a 23-bp nucleotide signature unique to Aconitum genus (5'-TATATGAGTCATTGAAGTTGCAG-3') was developed. The nucleotide signature was conserved and universal within Aconitum while divergent among other genera. The specific molecular signature was then successfully applied to the detection of processed Aconitum ingredients. To further evaluate the application potential of nucleotide signature in completely unknown mixture samples, boiled food mixtures, containing different ratios of Aconitum materials, were sequenced by high-throughput sequencing technology. The results showed that the nucleotide signature sequence could be directly extracted from raw sequencing data, even at a low DNA concentration of 0.2 ng/µl. Consequently, the 23-bp genus-specific nucleotide signature represents a significant step forward in the use of DNA barcoding to identify processed samples and food mixtures with degraded DNA. This study undoubtedly provides a new perspective and strong support for the identification and detection of Aconitum-containing products, which can be further introduced to the diagnosis of food poisoning.

Aconitum

DNA Barcoding

10.1016/j.ecoenv.2022.113539

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Citations (10)

Identification of commercial Ganoderma (Lingzhi) species by ITS2 sequences

Chinese Medicine (2015)

Baosheng Liao Xiaochen Chen Jianping Han Yang Dan Lili Wang

DNA barcoding can be used to authenticate Ganoderma species for safe use. This study aims to identify commercial products containing Ganoderma using DNA barcoding.We used 63 internal transcribed spacer (ITS) 2 sequences of Ganoderma species from 33 newly-sequenced wild samples, crude drugs, mycelia, spores, and authentic extracts and spore oils collected from various locations and markets, as well as 30 sequences from GenBank. Sequences were assembled and aligned using CodonCode Aligner V3.71. Intra- and inter-specific distances were estimated by MEGA 6.0, and phylogeny reconstruction was based on the K2P model. SNP(s) and RNA secondary structure of ITS2 were analyzed and compared among closely related Ganoderma species.G. lucidum cultivated in China was different from those cultivated in Europe. "Chizhi" (G. lucidum) and "Zizhi" (G. sinense) were clustered into two clades that were separated from the other Ganoderma species. The fruiting bodies and commercial products of G. lucidum and G. sinense were successfully distinguished from those of other Ganoderma species by comparing the ITS2 sequences and RNA secondary structures.The DNA barcoding method is applicable to the authentication of commercial products containing Ganoderma species.

Identification

10.1186/s13020-015-0056-7

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Citations (41)