51
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Zhao Z, Wang X, Yu Y, Yuan S, Jiang D, Zhang Y, Zhang T, Zhong W, Yuan Q, Huang L. Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses. PeerJ 2018; 6:e6032. [PMID: 30533315 PMCID: PMC6284424 DOI: 10.7717/peerj.6032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/30/2018] [Indexed: 11/29/2022] Open
Abstract
Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.
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Affiliation(s)
- Zhenyu Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xin Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,Tianjin University of Traditional Chinese Medicine,Tianjin, China
| | - Yi Yu
- Infinitus (China) Company Ltd, Guangzhou, China
| | - Subo Yuan
- Department of Immunology, Medical College, Wuhan University of Science and Technology, Wuhan, China
| | - Dan Jiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yujun Zhang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Teng Zhang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenhao Zhong
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qingjun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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52
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Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq. Sci Rep 2018; 8:17404. [PMID: 30479362 PMCID: PMC6258696 DOI: 10.1038/s41598-018-35654-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/09/2018] [Indexed: 11/08/2022] Open
Abstract
Chloroplast genomes (cp genomes) are widely used in comparative genomics, population genetics, and phylogenetic studies. Obtaining chloroplast genomes from RNA-Seq data seems feasible due to the almost full transcription of cpDNA. However, the reliability of chloroplast genomes assembled from RNA-Seq instead of genomic DNA libraries remains to be thoroughly verified. In this study, we assembled chloroplast genomes for three Erysimum (Brassicaceae) species from three RNA-Seq replicas and from one genomic library of each species, using a streamlined bioinformatics protocol. We compared these assembled genomes, confirming that assembled cp genomes from RNA-Seq data were highly similar to each other and to those from genomic libraries in terms of overall structure, size, and composition. Although post-transcriptional modifications, such as RNA-editing, may introduce variations in the RNA-seq data, the assembly of cp genomes from RNA-seq appeared to be reliable. Moreover, RNA-Seq assembly was less sensitive to sources of error such as the recovery of nuclear plastid DNAs (NUPTs). Although some precautions should be taken when producing reference genomes in non-model plants, we conclude that assembling cp genomes from RNA-Seq data is a fast, accurate, and reliable strategy.
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53
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Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment. Sci Rep 2018; 8:16635. [PMID: 30413776 PMCID: PMC6226466 DOI: 10.1038/s41598-018-35061-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/15/2018] [Indexed: 01/07/2023] Open
Abstract
Dryopteris fragrans (L.) Schott is a fern growing on the surface of hot rocks and lava. It is exposed to sunlight directly and bears local hot environment. We sequenced the complete nucleotide sequence of its chloroplast (cp) genome. The cp genome was 151,978 bp in length, consisting of a large single-copy region (85,332 bp), a small single-copy region (31,947 bp) and a pair of inverted repeats (17,314 bp). The cp genome contained 112 genes and 345 RNA editing sites in protein-coding genes. Simple sequence repeats (SSRs) and long repeat structure pairs (30–55 bp) were identified. The number and percent of repeat structures are extremely high in ferns. Thermal denaturation experiments showed its cp genome to have numerous, dispersed and high GC percent repeat structures, which conferred the strongest thermal stability. This repeat-heavy genome may provide the molecular basis of how D. fragrans cp survives its hot environment.
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54
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Zhang X, Rong C, Qin L, Mo C, Fan L, Yan J, Zhang M. Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships. Molecules 2018; 23:E2917. [PMID: 30413097 PMCID: PMC6278565 DOI: 10.3390/molecules23112917] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 12/29/2022] Open
Abstract
Malus hupehensis belongs to the Malus genus (Rosaceae) and is an indigenous wild crabapple of China. This species has received more and more attention, due to its important medicinal, and excellent ornamental and economical, values. In this study, the whole chloroplast (cp) genome of Malus hupehensis, using a Hiseq X Ten sequencing platform, is reported. The M. hupehensis cp genome is 160,065 bp in size, containing a large single copy region (LSC) of 88,166 bp and a small single copy region (SSC) of 19,193 bp, separated by a pair of inverted repeats (IRs) of 26,353 bp. It contains 112 genes, including 78 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). The overall nucleotide composition is 36.6% CG. A total of 96 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition, a total of 49 long repeats were identified, including 24 forward repeats, 21 palindromic repeats, and four reverse repeats. Comparisons of the IR boundaries of nine Malus complete chloroplast genomes presented slight variations at IR/SC boundaries regions. A phylogenetic analysis, based on 26 chloroplast genomes using the maximum likelihood (ML) method, indicates that M. hupehensis clustered closer ties with M. baccata, M. micromalus, and M. prunifolia than with M. tschonoskii. The availability of the complete chloroplast genome using genomics methods is reported here and provides reliable genetic information for future exploration on the taxonomy and phylogenetic evolution of the Malus and related species.
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Affiliation(s)
- Xin Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chunxiao Rong
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Ling Qin
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chuanyuan Mo
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lu Fan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jie Yan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Manrang Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Li J, Zhang D, Ouyang K, Chen X. The complete chloroplast genome of the miracle tree Neolamarckia cadamba and its comparison in Rubiaceae family. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1496034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Jingjian Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, PR China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, PR China
| | - Deng Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Kunxi Ouyang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Xiaoyang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, PR China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, PR China
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56
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Khan AL, Asaf S, Lee IJ, Al-Harrasi A, Al-Rawahi A. First reported chloroplast genome sequence of Punica granatum (cultivar Helow) from Jabal Al-Akhdar, Oman: phylogenetic comparative assortment with Lagerstroemia. Genetica 2018; 146:461-474. [PMID: 30159822 DOI: 10.1007/s10709-018-0037-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/23/2018] [Indexed: 12/14/2022]
Abstract
Pomegranate (Punica granatum L.) is one of the oldest known edible fruits. It has grown in popularity and is a profitable fruit crop due to its attractive features including a bright red appearance and its biological activities. Scientific exploration of the genetics and evolution of these beneficial traits has been hampered by limited genomic information. In this study, we sequenced the complete chloroplast (cp) genome of the native P. granatum (cultivar Helow) cultivated in the mountains of Jabal Al-Akhdar, Oman. The results revealed a P. granatum cp genome length of 158,630 bp, characterized by a relatively conserved structure containing 2 inverted repeat regions of 25,466 bp, an 18,686 bp small single copy regions, and an 89,015 bp large single copy region. The 86 protein-coding genes included 37 transfer RNA genes and 8 ribosomal RNA genes. Comparison of the P. granatum whole cp genome with seven Lagerstroemia species revealed an overall high degree of sequence similarity with divergence among intergenic spacers. The location, distribution, and divergence of repeat sequences and shared genes of the Punica and Lagerstroemia species were highly similar. Analyses of nucleotide substitution, insertion/deletions, and highly variable regions in these cp genomes identified potential plastid markers for taxonomic and phylogenetic studies in Myrtales. A phylogenetic study of the cp genomes and 76 shared coding regions generated similar cladograms. The complete cp genome of P. granatum will aid in taxonomical studies of the family Lythraceae.
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Affiliation(s)
- Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
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57
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Khan AL, Asaf S, Lee IJ, Al-Harrasi A, Al-Rawahi A. First chloroplast genomics study of Phoenix dactylifera (var. Naghal and Khanezi): A comparative analysis. PLoS One 2018; 13:e0200104. [PMID: 30063732 PMCID: PMC6067692 DOI: 10.1371/journal.pone.0200104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/19/2018] [Indexed: 12/16/2022] Open
Abstract
Date palm (Phoenix dactylifera L.) is one of the oldest fruit crops in the arid regions of the Middle East. However, little information is available regarding its plastid genomes. In this study, we sequenced the chloroplast (cp) genomes of two economically important but genomically unexplored date palm cultivars of Phoenix dactylifera (var. Naghal and Khanezi). The data assembly and genome annotation revealed a typical quadripartite structure similar to Arecaceae, and the genome sizes of Naghal and Khanezi were 158,210 bp and 158,211 bp, respectively. Structurally, both cp genomes were comprised of four regions: a pair of inverted repeats (27,273 bp for Khanezi and for Naghal 27,272 bp), a large single-copy region (86,090 bp and 86,092 bp) and a small single-copy region (17,575 bp and 17,574 bp). Both genomes had 138 representative genes, whereas 227 and 229 randomly distributed microsatellites were also observed in Khanezi and Naghal, respectively. Phylogenetic analysis based on the whole cp genomes and 68 shared genes showed identical phylogenetic trees of Khanezi and Naghal forming clades with Khalas and Aseel cultivars, respectively. The current study showed detailed comparative cp genome analysis, which could be essential for broader population genetics and molecular studies of these four date palm cultivars.
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Affiliation(s)
- Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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58
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Zhou J, Cui Y, Chen X, Li Y, Xu Z, Duan B, Li Y, Song J, Yao H. Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis. Molecules 2018; 23:E437. [PMID: 29462921 PMCID: PMC6017017 DOI: 10.3390/molecules23020437] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/11/2018] [Accepted: 02/14/2018] [Indexed: 11/17/2022] Open
Abstract
Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence divergence analysis of four species from Papaveraceae indicated that the most divergent regions are found in the non-coding spacers with minimal differences among three Papaver species. These differences include the ycf1 gene and intergenic regions, such as rpoB-trnC, trnD-trnT, petA-psbJ, psbE-petL, and ccsA-ndhD. These regions are hypervariable regions, which can be used as specific DNA barcodes. This finding suggested that the chloroplast genome could be used as a powerful tool to resolve the phylogenetic positions and relationships of Papaveraceae. These results offer valuable information for future research in the identification of Papaver species and will benefit further investigations of these species.
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Affiliation(s)
- Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Yingxian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Xinlian Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| | - Yonghua Li
- Department of Pharmacy, Guangxi Traditional Chinese Medicine University, Nanning 530200, China.
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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59
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Guo S, Guo L, Zhao W, Xu J, Li Y, Zhang X, Shen X, Wu M, Hou X. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii. Molecules 2018; 23:molecules23020246. [PMID: 29373520 PMCID: PMC6017096 DOI: 10.3390/molecules23020246] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 01/21/2023] Open
Abstract
Paeonia ostii, a common oil-tree peony, is important ornamentally and medicinally. However, there are few studies on the chloroplast genome of Paeonia ostii. We sequenced and analyzed the complete chloroplast genome of P. ostii. The size of the P. ostii chloroplast genome is 152,153 bp, including a large single-copy region (85,373 bp), a small single-copy region (17,054 bp), and a pair of inverted repeats regions (24,863 bp). The P. ostii chloroplast genome encodes 111 genes, including 77 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The genome contains forward repeats (22), palindromic repeats (28), and tandem repeats (24). The presence of rich simple-sequence repeat loci in the genome provides opportunities for future population genetics work for breeding new varieties. A phylogenetic analysis showed that P. ostii is more closely related to Paeonia delavayi and Paeonialudlowii than to Paeoniaobovata and Paeoniaveitchii. The results of this study provide an assembly of the whole chloroplast genome of P. ostii, which may be useful for future breeding and further biological discoveries. It will provide a theoretical basis for the improvement of peony yield and the determination of phylogenetic status.
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Affiliation(s)
- Shuai Guo
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Lili Guo
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Wei Zhao
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Jiang Xu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Yuying Li
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Xiaoyan Zhang
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
- College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Mingli Wu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, Hubei China
| | - Xiaogai Hou
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
- Correspondence: ; Tel: +86-0379-6998-0776
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