Ying Li

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

Chao Sun

Chinese Academy of Medical Sciences & Peking Union Medical College

Hongmei Luo

University of Science and Technology of China

Yingjie Zhu

Qufu Normal University

Xiwen Li

Chinese Academy of Medical Sciences & Peking Union Medical College

Hui Yao

Wuhan Children's Hospital

Zhichao Xu

Northeast Forestry University

Yongzhen Sun

Zhongda Hospital Southeast University

Jun Qian

Chinese Academy of Medical Sciences & Peking Union Medical College

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Chinese Academy of Medical Sciences & Peking Union Medical College

176

Chinese Academy of Sciences

Peking Union Medical College Hospital

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

Academy of Medical Sciences

Shanghai Jiao Tong University

Ministry of Agriculture and Rural Affairs

Ministry of Education of the People's Republic of China

Peking University

Yunnan Agricultural University

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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)

High‐accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy

New Phytologist (2014)

Qiushi Li Ying Li Jingyuan Song Haibin Xu Jiang Xu

Summary A circular consensus sequencing ( CCS ) strategy involving single molecule, real‐time ( SMRT ) DNA sequencing technology was applied to de novo assembly and single nucleotide polymorphism ( SNP ) detection of chloroplast genomes. Chloroplast DNA was purified from enriched chloroplasts of pooled individuals to construct a shotgun library for each species. The sequencing reactions were performed on a PacBio RS platform. CCS sub‐reads were generated from polymerase reads that passed the native dumbbell‐shaped DNA templates multiple times. The complete chloroplast genome sequence was generated by mapping all reads to the draft sequence constructed in a step‐by‐step manner. The full‐chain, PCR ‐free approach eliminates the possible context‐specific biases in library construction and sequencing reaction. The chloroplast genome was easily and completely assembled using the data generated from one SMRT Cell without requiring a reference genome. Comparisons of the three assembled Fritillaria genomes to 34.1 kb of validation Sanger sequences revealed 100% concordance, and the detected intraspecies SNP s at a minimum variant frequency of 15% were all confirmed. This simple approach with potential for parallel sequencing yields high‐quality chloroplast genomes for sensitive SNP detection and comparative analyses. We recommend this approach for its powerful applicability for evolutionary genetics and genomics studies in plants based on the sequences of chloroplast genomes.

Sequence assembly

Sanger sequencing

Hybrid genome assembly

10.1111/nph.12966

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Citations (97)

The Wolfiporia Cocos Genome and Transcriptome Shed Light on the Formation of Its Edible and Medicinal Sclerotium

Genomics Proteomics & Bioinformatics (2020)

Hongmei Luo Jun Qian Zhichao Xu Wanjing Liu Lei Xu

Wolfiporia cocos (F. A. Wolf) has been praised as a food delicacy and medicine for centuries in China. Here, we present the genome and transcriptome of the Chinese strain CGMCC5.78 of W. cocos. High-confidence functional prediction was made for 9277 genes among the 10,908 total predicted gene models in the W. cocos genome. Up to 2838 differentially expressed genes (DEGs) were identified to be related to sclerotial development by comparing the transcriptomes of mycelial and sclerotial tissues. These DEGs are involved in mating processes, differentiation of fruiting body tissues, and metabolic pathways. A number of genes encoding enzymes and regulatory factors related to polysaccharide and triterpenoid production were strikingly regulated. A potential triterpenoid gene cluster including the signature lanosterol synthase (LSS) gene and its modified components were annotated. In addition, five nonribosomal peptide synthase (NRPS)-like gene clusters, eight polyketide synthase (PKS) gene clusters, and 15 terpene gene clusters were discovered in the genome. The differential expression of the velevt family proteins, transcription factors, carbohydrate-active enzymes, and signaling components indicated their essential roles in the regulation of fungal development and secondary metabolism in W. cocos. These genomic and transcriptomic resources will be valuable for further investigations of the molecular mechanisms controlling sclerotial formation and for its improved medicinal applications.

Secondary metabolism

Gene cluster

Nonribosomal peptide

10.1016/j.gpb.2019.01.007

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Citations (16)

Feasibility of transbronchial lung cryobiopsy in patients with veno-venous extracorporeal membrane oxygenation support

ERJ Open Research (2022)

Shiyao Wang Guowu Zhou Yingying Feng Yi Zhang Ye Tian

Background Veno-venous extracorporeal membrane oxygenation (VV-ECMO) is essential life support in patients with severe acute hypoxaemic respiratory failure. However, biopsies should be considered for some patients with unknown aetiology. This study aims to evaluate the feasibility of transbronchial lung cryobiopsy (TBLC) in such patients. Methods All patients with acute hypoxaemic respiratory failure of unknown aetiology who underwent TBLC with VV-ECMO support were retrospectively reviewed. Patients’ characteristics, ventilation settings, procedure parameters, complications, pathological diagnosis and survival were summarised and analysed. Results Eight female and five male patients with VV-ECMO support underwent TBLC. The median age was 58 (interquartile range (IQR) 38–67) years old. Concurrent diseases were present in 10 of the 13 patients, seven of which were immunosuppressed. The median time between biopsy and VV-ECMO establishment was 2.0 (IQR 0.5–6.5) days. No patient died from the procedure. Neither pneumothorax nor severe bleeding occurred in any of the patients. Five of the 13 patients experienced moderate bleeding, and all bleeding events were successfully controlled with prophylactic balloon blockers. Pathological diagnosis by TBLC was obtained in all patients, and the diagnosis of diffuse alveolar damage was made in nine of them. Conclusions In patients with VV-ECMO support, the TBLC procedure is generally safe when standardised bleeding prophylaxis is in place. TBLC contributes to identifying underlying aetiologies in patients with acute hypoxaemic respiratory failure of unknown aetiology.

Interquartile range

Etiology

10.1183/23120541.00383-2022

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DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae

Ecology and Evolution (2019)

Feng‐Ming Ren Yingwei Wang Zhichao Xu Ying Li Tianyi Xin

The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya-Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA-trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P-distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia-recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well-supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.

DNA Barcoding

Papaveraceae

10.1002/ece3.4886

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Citations (26)

Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria

Chinese Medicine (2021)

Lan Wu Mingli Wu Ning Cui Li Xiang Ying Li

Abstract Background Although molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species. Methods We here compared 26 complete cp genomes of ten Fritillaria species including 18 new sequences sequenced in this study. Each species had repeats and the cp genomes were used as a whole DNA barcode to test whether they can distinguish Fritillaria species . Results The cp genomes of Fritillaria medicinal plants were conserved in genome structure, gene type, and gene content. Comparison analysis of the Fritillaria cp genomes revealed that the intergenic spacer regions were highly divergent compared with other regions. By constructing the phylogenetic tree by the maximum likelihood and maximum parsimony methods, we found that the entire cp genome showed a high discrimination power for Fritillaria species with individuals of each species in a monophyletic clade. These results indicate that cp genome can be used to effectively differentiate medicinal plants from the genus Fritillaria at the species level. Conclusions This study implies that cp genome can provide distinguishing differences to help identify closely related Fritillaria species, and has the potential to be served as a universal super-barcode for plant identification.

Monophyly

DNA Barcoding

Intergenic region

Identification

Barcode

Maximum parsimony

10.1186/s13020-021-00460-z

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Citations (47)

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)

Generation and analysis of expressed sequence tags from a cDNA library of the fruiting body of Ganoderma lucidum

Chinese Medicine (2010)

Hongmei Luo Chao Sun Jingyuan Song Jin Lan Ying Li

Abstract Background Little genomic or trancriptomic information on Ganoderma lucidum ( Lingzhi ) is known. This study aims to discover the transcripts involved in secondary metabolite biosynthesis and developmental regulation of G. lucidum using an expressed sequence tag (EST) library. Methods A cDNA library was constructed from the G . lucidum fruiting body. Its high-quality ESTs were assembled into unique sequences with contigs and singletons. The unique sequences were annotated according to sequence similarities to genes or proteins available in public databases. The detection of simple sequence repeats (SSRs) was preformed by online analysis. Results A total of 1,023 clones were randomly selected from the G . lucidum library and sequenced, yielding 879 high-quality ESTs. These ESTs showed similarities to a diverse range of genes. The sequences encoding squalene epoxidase (SE) and farnesyl-diphosphate synthase (FPS) were identified in this EST collection. Several candidate genes, such as hydrophobin , MOB2 , profilin and PHO84 were detected for the first time in G . lucidum . Thirteen (13) potential SSR-motif microsatellite loci were also identified. Conclusion The present study demonstrates a successful application of EST analysis in the discovery of transcripts involved in the secondary metabolite biosynthesis and the developmental regulation of G. lucidum .

10.1186/1749-8546-5-9

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Citations (17)

Supplementary Table 1 from Gene Silencing Associated with SWI/SNF Complex Loss during NSCLC Development

Shujie Song Vonn Walter Mehmet Karaca Ying Li Christopher S. Bartlett

<p>XLSX file - 623K, Genes that are upregulated or downregulated by BRG1.</p>

Table (database)

10.1158/1541-7786.22511415

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Hybrid Sequencing of Full-Length cDNA Transcripts of the Medicinal Plant Scutellaria baicalensis

International Journal of Molecular Sciences (2019)

Ting Gao Zhichao Xu Xiaojun Song Kai Huang Ying Li

Scutellaria baicalensis is a well-known medicinal plant that produces biologically active flavonoids, such as baicalin, baicalein, and wogonin. Pharmacological studies have shown that these compounds have anti-inflammatory, anti-bacterial, and anti-cancer activities. Therefore, it is of great significance to investigate the genetic information of S. baicalensis, particularly the genes related to the biosynthetic pathways of these compounds. Here, we constructed the full-length transcriptome of S. baicalensis using a hybrid sequencing strategy and acquired 338,136 full-length sequences, accounting for 93.3% of the total reads. After the removal of redundancy and correction with Illumina short reads, 75,785 nonredundant transcripts were generated, among which approximately 98% were annotated with significant hits in the protein databases, and 11,135 sequences were classified as lncRNAs. Differentially expressed gene (DEG) analysis showed that most of the genes related to flavonoid biosynthesis were highly expressed in the roots, consistent with previous reports that the flavonoids were mainly synthesized and accumulated in the roots of S. baicalensis. By constructing unique transcription models, a total of 44,071 alternative splicing (AS) events were identified, with intron retention (IR) accounting for the highest proportion (44.5%). A total of 94 AS events were present in five key genes related to flavonoid biosynthesis, suggesting that AS may play important roles in the regulation of flavonoid biosynthesis in S. baicalensis. This study provided a large number of highly accurate full-length transcripts, which represents a valuable genetic resource for further research of the molecular biology of S. baicalensis, such as the development, breeding, and biosynthesis of active ingredients.

Wogonin

Baicalin

Baicalein

Flavonoid Biosynthesis

10.3390/ijms20184426

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Citations (12)