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Huang J, Hu X, Zhou Y, Peng YJ, Liu Z. Phylogeny, Genetic Diversity and Population Structure of Fritillaria cirrhosa and Its Relatives Based on Chloroplast Genome Data. Genes (Basel) 2024; 15:730. [PMID: 38927666 PMCID: PMC11202927 DOI: 10.3390/genes15060730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Fritillaria cirrhosa and its relatives have been utilized in traditional Chinese medicine for many years and are under priority protection in China. Despite their medicinal and protective value, research on their phylogeny, genetic diversity, and divergence remains limited. Here, we investigate the chloroplast genome variation architecture of 46 samples of F. cirrhosa and its relatives collected from various regions, encompassing the majority of wild populations across diverse geographical areas. The results indicate abundant variations in 46 accessions including 1659 single-nucleotide polymorphisms and 440 indels. Six variable markers (psbJ, ndhD, ycf1, ndhG, trnT-trnL, and rpl32-trnL) were identified. Phylogenetic and network analysis, population structure analysis, and principal component analysis showed that the 46 accessions formed five clades with significant divergence, which were related to their geographical distribution. The regions spanning from the southern Hengduan Mountains to the Qinghai-Tibet Plateau exhibited the highest levels of genetic diversity. F. cirrhosa and its relatives may have suffered a genetic bottleneck and have a relatively low genetic diversity level. Moreover, geographical barriers and discrete patches may have accelerated population divergence. The study offers novel perspectives on the phylogeny, genetic diversity, and population structure of F. cirrhosa and its relatives, information that can inform conservation and utilization strategies in the future.
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Affiliation(s)
- Jiao Huang
- College of Life Science, Leshan Normal University, Leshan 614000, China
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2
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Ciborowski K, Szczecińska M, Maździarz M, Sawicki J, Paukszto Ł. Decoding Evolution of Rubioideae: Plastomes Reveal Sweet Secrets of Codon Usage, Diagnostides, and Superbarcoding. Genes (Basel) 2024; 15:562. [PMID: 38790191 PMCID: PMC11121115 DOI: 10.3390/genes15050562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Galium genus belongs to the Rubiaceae family, which consists of approximately 14,000 species. In comparison to its well-known relatives, the plastomes of the Galium genus have not been explored so far. The plastomes of this genus have a typical, quadripartite structure, but differ in gene content, since the infA gene is missing in Galium palustre and Galium trfidum. An evaluation of the effectiveness of using entire chloroplast genome sequences as superbarcodes for accurate plant species identification revealed the high potential of this method for molecular delimitation within the genus and tribe. The trnE-UUC-psbD region showed the biggest number of diagnostides (diagnostic nucleotides) which might be new potential barcodes, not only in Galium, but also in other closely related genera. Relative synonymous codon usage (RSCU) appeared to be connected with the phylogeny of the Rubiaceae family, showing that during evolution, plants started preferring specific codons over others.
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Affiliation(s)
| | | | | | - Jakub Sawicki
- Department of Botany and Evolutionary Ecology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland; (K.C.); (M.S.); (M.M.); (Ł.P.)
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3
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Milarska SE, Androsiuk P, Paukszto Ł, Jastrzębski JP, Maździarz M, Larson KW, Giełwanowska I. Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis. Sci Rep 2023; 13:18774. [PMID: 37907682 PMCID: PMC10618263 DOI: 10.1038/s41598-023-46017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.
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Affiliation(s)
- Sylwia E Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Keith W Larson
- Climate Impacts Research Centre, Umeå University, 90187, Umeå, Sweden
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Mao J, Liang Y, Wang X, Zhang D. Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization. BMC PLANT BIOLOGY 2023; 23:101. [PMID: 36800941 PMCID: PMC9940437 DOI: 10.1186/s12870-023-04088-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with medicinal values. Gentiana cephalantha Franchet is a sister species to G. rigescens possessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences. RESULTS The plastid genomes were highly similar between G. rigescens and G. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp in G. rigescens and from 146,856 to 147,016 bp in G. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed that G. rigescens and G. cephalantha formed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports that G. rigescens and G. cephalantha are closely related, but independent species. However, hybridization was confirmed to occur frequently between G. rigescens and G. cephalantha in sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction of G. rigescens. CONCLUSION G. rigescens and G. cephalantha are recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species, G. rigescens faces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.
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Affiliation(s)
- Jiuyang Mao
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Yuze Liang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China.
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali, 671000, Yunnan, China.
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Liu C, Liu S, Tse WM, Tse KWG, Erbu A, Xiong H, Lanzi G, Liu Y, Ye B. A distinction between Fritillaria Cirrhosa Bulbus and Fritillaria Pallidiflora Bulbus via LC-MS/MS in conjunction with principal component analysis and hierarchical cluster analysis. Sci Rep 2023; 13:2735. [PMID: 36792675 PMCID: PMC9931167 DOI: 10.1038/s41598-023-29631-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Fritillaria Cirrhosa Bulbus (known as chuanbeimu in Chinese, FCB) is one of the most used Chinese medicines for lung disease. However, a variety of substitutes have entered the market, with Fritillaria Pallidiflora Bulbus (FPB) being the most common. Due to their similarity in appearance, morphology, and chemical composition but a large price difference, the FCB has frequently been adulterated with the FPB, posing a serious challenge to the distinction and quality of the FCB. Therefore, we aimed to distinguish FCB and FPB based on their main nine isosteroidal alkaloid contents and test the potential of chemometrics as a discrimination approach for evaluating quality. The nine major isosteroidal alkaloids were measured using a liquid chromatography with tandem mass spectrometry (LC-MS/MS) approach in 41 batches of FCB and 17 batches of FPB. Additionally, they were categorized and distinguished using the methods of hierarchical cluster analysis (HCA) and principal component analysis (PCA). Quantitative analysis revealed that the nine alkaloids were present in different amounts in the two types of Fritillariae bulbus. In FCB, the highest amount was peimisine (17.92-123.53 μg/g) and the lowest was delavine (0.42-29.18 μg/g), while in FPB, imperialine was higher (78.05-344.09 μg/g), but verticinone and verticine were less than the other seven alkaloids. The FCB and FPB were successfully classified and distinguished by the HCA and PCA. Taken together, the method has a good linear relationship (R2 > 0.9975). The LOD and LOQ of the nine alkaloids were in the range of 0.0651-0.6510 and 0.1953-1.9531 ng/mL, respectively. The intra- and inter-day precision were shown to be excellent, with relative standard deviations (RSDs) below 1.63% and 2.39%, respectively. The LC-MS/MS method in conjunction with HCA and PCA can effectively differentiate FCB and FPB. It may be a promising strategy for quality evaluation and control at the FCB.
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Affiliation(s)
- Chuanlan Liu
- Medical College of Tibet University, Lasa, 850002, People's Republic of China
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug, and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Simei Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug, and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Wai Ming Tse
- Nin Jiom Medicine Manufactory (H.K.) Limited, 16/F. Block A, Texaco Road, Tsuen Wan, N.T., Hong Kong, People's Republic of China
| | - Kathy Wai Gaun Tse
- Nin Jiom Medicine Manufactory (H.K.) Limited, 16/F. Block A, Texaco Road, Tsuen Wan, N.T., Hong Kong, People's Republic of China
| | - Aga Erbu
- Medical College of Tibet University, Lasa, 850002, People's Republic of China
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug, and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Hai Xiong
- Medical College of Tibet University, Lasa, 850002, People's Republic of China
| | - Gongga Lanzi
- Medical College of Tibet University, Lasa, 850002, People's Republic of China
| | - Yanyong Liu
- Medical College of Tibet University, Lasa, 850002, People's Republic of China
| | - Bengui Ye
- Medical College of Tibet University, Lasa, 850002, People's Republic of China.
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug, and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, People's Republic of China.
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The Curious Case of Fritillaria sonnikovae (Liliaceae) in South Siberia: New Insights into Its Origin and Phylogeny. DIVERSITY 2023. [DOI: 10.3390/d15020193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fritillaria Tourn. ex L. is a genus of Liliaceae including a little more than 150 species occurring in the temperate Holarctic. Fritillaria sonnikovae Shaulo & Erst is the most recently described Siberian species in the genus. In the affinity section of the F. sonnikovae diagnosis, only F. dagana Turcz. and F. roylei Hook. are mentioned. Our study is an original attempt to shed light on the F. sonnikovae origin and its evolutionary relationships with other Fritillaria using nuclear (ITS) and plastid (matK + rps16 + trnH-psbA) DNA markers. Our results showed that F. sonnikovae together with F. dagana and F. maximowiczii Freyn belongs to the North Asian lineage of the Liliorhiza subgenus and produced no evidence supporting relationship between F. sonnikovae and F. roylei. Monophyly of Fritillaria sonnikovae was not reliably confirmed in our study since its close affinity with F. maximowiczii was demonstrated by phylogenetic analysis and morphology. Fritillaria dagana was shown to be a sister to the F. maximowiczii + F. sonnikovae group. Most authors of the present study suggest considering F. sonnikovae as a synonym for F. maximowiczii. In this view, F. sonnikovae may be considered a narrow endemic and one of the light-perianth morphs of F. maximowiczii, which has emerged in the Western Sayan and remained there as a tertiary relict.
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Wang W, Wang X, Shi Y, Yin Q, Gao R, Wang M, Xiang L, Wu L. Identification of Laportea bulbifera using the complete chloroplast genome as a potentially effective super-barcode. J Appl Genet 2023; 64:231-245. [PMID: 36633756 DOI: 10.1007/s13353-022-00746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/12/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Laportea bulbifera, a Miao medicine grown in karst areas, has exerted a unique curative effect on skin itching in the elderly, with an annual sales of > 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. bulbifera, it is difficult to identify the species correctly using only traditional methods, which seriously affects the safety of drug usage for patients. This study obtained the complete high-quality L. bulbifera chloroplast (cp) genome, using second- and third-generation high-throughput sequencing. The cp genome was 149,911 bp in length, with a typical quadripartite structure. A total of 127 genes were annotated, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There was an inverted small single copy (SSC) structure in the L. bulbifera cp genome, one large-scale rearrangement of ~ 39 kb excised in the SSC and IR regions. The complete cp genome sequence is used as a potentially effective super-barcode and the highly variable regions (ycf1, matK, and ndhD) can be used as potentially specific barcodes to accurately distinguish L. bulbifera from counterfeits and closely related species. This study is important for the identification of L. bulbifera and lays a theoretical foundation for elucidating the phylogenetic relationship of the species.
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Affiliation(s)
- Wenting Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xingwen Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qinggang Yin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ranran Gao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengyue Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia. Int J Mol Sci 2022; 23:ijms232415570. [PMID: 36555212 PMCID: PMC9779425 DOI: 10.3390/ijms232415570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.
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An YL, Wei WL, Guo DA. Application of Analytical Technologies in the Discrimination and Authentication of Herbs from Fritillaria: A Review. Crit Rev Anal Chem 2022; 54:1775-1796. [PMID: 36227577 DOI: 10.1080/10408347.2022.2132374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Medicinal plants of Fritillaria are widely distributed in numerous countries around the world and possess excellent antitussive and expectorant effects. In particular, Fritillariae Bulbus (FB) as a precious traditional medicine has thousands of years of medical history in China. Herbs of Fritillaria have a high market value and demand while limited by harsh growing circumstances and scarce wild resources. As a consequence, fraudulent behaviors are regularly engaged by the unscrupulous merchants in an attempt to reap greater profits. It is of an urgent need to evaluate the quality of Fritillaria herbs and their products using various analytical instruments and techniques. This review has scrutinized approximately 160 articles from 1995 to 2022 published on the investigation of Fritillaria herbs and related herbal products. The botanical classification of genus Fritillaria, types of counterfeits, technologies applied for differentiating Fritillaria species were comprehensively summarized and discussed in the current review. Molecular and chromatographic identification were the dominant technologies in the authentication of Fritillaria herbs. Additionally, we brought some potential and promising technologies and analytical strategies into attention, which are worthy attempting in the future researches. This review could conduce to excellent reference value for further investigations of the authenticity assessment of Fritillaria species.
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Affiliation(s)
- Ya-Ling An
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Long Wei
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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Yin D, Pang B, Li H, Liu Q, Zhai Y, Ma N, Chen T, Shen H, Jia Q, Wang D. The complete chloroplast genome of the medical plant Huperzia crispata from the Huperziaceae family: structure, comparative analysis, and phylogenetic relationships. Mol Biol Rep 2022; 49:11729-11741. [PMID: 36197623 DOI: 10.1007/s11033-022-07979-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/21/2022] [Indexed: 10/10/2022]
Abstract
BACKGROUND Huperzia crispata, belonging to the Huperziaceae family, is one of the most essential resources of huperzine A for candidate drugs to treat Alzheimer's diseases. However, there is very limited information about H. crispat, and its taxonomic status and interspecific relationships between Huperzia species are still unclear. To investigate the taxonomic classification of Huperzia species and identify species discrimination markers, the complete chloroplast (cp) genome of H. crispata was sequenced and characterized for the first time. METHODS AND RESULTS Total genomic DNA was isolated and sequenced using the next-generation Illumina NovaSeq 6000 platform. The data were filtered, assembled and annotated by a series software and web service. The results were as follows: the cp genome of H. crispata was 154,320 bp long with a large single-copy (LSC) region of 104,023 bp, a small single-copy (SSC) region of 19,671 bp, and a pair of inverted repeat (IRa and IRb) regions of 15,313 bp. A total of 131 genes, including 87 protein-coding genes, 36 transfer RNA genes (tRNAs), and eight ribosome RNA genes (rRNAs), were annotated in the cp genome. The contraction and expansion of the inverted repeat (IR) regions were relatively conserved in the Huperzia genus. Codon usage bias analysis showed that the encoding rate at the 3-end of codon A/T (74.34%) was significantly higher than that of C/G (25.66%). A total of 8 hotspot loci with high Pi values (> 0.06) were identified in the four Huperzia species based on nucleic acid diversity analysis. Ka/Ks selective pressure analysis demonstrated that the cemA gene is the most common gene undergoing positive selection among Huperzia. In addition, a total of 261 simple sequence repeats and 179 interspersed repeats were identified in the cp genome. Phylogenetic tree analysis based on the complete protein sequences of 23 related species of H. crispata indicated that H. serrata f. longipetiolata is a sister of H. crispata, suggesting that H. serrata f. longipetiolata and H. crispata are more closely related than H. serrata and H. lucidula. CONCLUSIONS The results strongly supported that H. crispata was more closely related to H. serrata f. longipetiolata than to H. serrata and H. lucidula within the Huperzia genus. The outcome provided important information for the phylogenetic analysis of the subsequent specific molecular species identification in Huperzia. The present results will provide valuable information for further research into the classification, phylogeny and species identification of Huperzia plants.
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Affiliation(s)
- Dengpan Yin
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Bo Pang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Haibo Li
- Yuyao Seedling Management Station, Ningbo, 315400, Zhejiang, China
| | - Qiao Liu
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Yufeng Zhai
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Nan Ma
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Tongtong Chen
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Hongjun Shen
- Ningbo Delai Medicinal Material Planting Co., Ltd, Ningbo, 315444, Zhejiang, China
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Dekai Wang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China.
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Dong S, Zhou M, Zhu J, Wang Q, Ge Y, Cheng R. The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination. BMC Genomics 2022; 23:620. [PMID: 36028808 PMCID: PMC9412808 DOI: 10.1186/s12864-022-08755-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins. RESULT This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124 bp of Jiangxi Province to 160,618 bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56-57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into four groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas. CONCLUSION Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family.
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Affiliation(s)
- Shujie Dong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Manjia Zhou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinxing Zhu
- Bureau of Agricultural and Rural Affairs of Suichang, Suichang, China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China. .,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China.
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12
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Yue J, Ni Y, Jiang M, Chen H, Chen P, Liu C. Characterization of Codonopsis pilosula subsp. tangshen plastome and comparative analysis of Codonopsis species. PLoS One 2022; 17:e0271813. [PMID: 35913971 PMCID: PMC9342729 DOI: 10.1371/journal.pone.0271813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
Codonopsis pilosula subsp. tangshen is one of the most important medicinal herbs used in traditional Chinese medicine. Correct identification of materials from C. pilosula subsp. tangshen is critical to ensure the efficacy and safety of the associated medicines. Traditional DNA molecular markers could distinguish Codonopsis species well, so we need to develop super or specific molecular markers. In this study, we reported the plastome of Codonopsis pilosula subsp. tangshen (Oliv.) D.Y. Hong conducted phylogenomic and comparative analyses in the Codonopsis genus for the first time. The entire length of the Codonopsis pilosula subsp. tangshen plastome was 170,672 bp. There were 108 genes in the plastome, including 76 protein-coding genes, 28 transfer RNA (tRNA), and four ribosomal RNA (rRNA) genes. Comparative analysis indicated that Codonopsis pilosula subsp. tangshen had an unusual large inversion in the large single-copy (LSC) region compared with the other three Codonopsis species. And there were two dispersed repeat sequences at both ends of the inverted regions, which might mediate the generation of this inversion. We found five hypervariable regions among the four Codonopsis species. PCR amplification and Sanger sequencing experiments demonstrated that two hypervariable regions could distinguish three medicinal Codonopsis species. Results obtained from this study will support taxonomic classification, discrimination, and molecular evolutionary studies of Codonopsis species.
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Affiliation(s)
- Jingwen Yue
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, P. R. China
| | - Yang Ni
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, P. R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Pinghua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, P. R. China
- * E-mail: (PHC); (CL)
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
- * E-mail: (PHC); (CL)
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13
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Wei Y, Ding S, Chen G, Dong J, Du F, Huang X, Cui X, Chen R, Tang Z. Real-time fluorescence and colorimetric identification of bulbus fritillariae using recombinase assisted loop-mediated isothermal DNA amplification (RALA). FRONTIERS IN PLANT SCIENCE 2022; 13:948879. [PMID: 35968097 PMCID: PMC9366889 DOI: 10.3389/fpls.2022.948879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Bulbus Fritillariae (BF) is a kind of herbal medicine widely used in many countries including China, Japan, Korea, and so on. Among the known BF medicinal materials, Bulbus Fritillariae cirrhosae (BF cirrhosae) was reported to have the best curative effect. Due to the limited resources of BF cirrhosae, a lot of adulterants have emerged in the market, impairing the market order, resource development, and above all, clinical efficacy. Here, a novel nucleic acid amplification technique, Recombinase Assisted Loop-mediated isothermal DNA Amplification (RALA), was used to establish a real-time fluorescence isothermal molecular authentication method for five commonly used BF drugs. Moreover, this RALA-based assay can also be developed as a colorimetric detection method for on-site detection. Both real-time fluorescence and visual methods could detect as low as 0.1% genuine targets in the mixed samples. In summary, we report an isothermal detection system for five kinds of BF circulating in the market, providing a new choice for the molecular identification of BF drugs and showing promise in the laboratory testing as well as field identification of other herbal medicines.
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Affiliation(s)
- Yinghua Wei
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Beijing, China
| | - Sheng Ding
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Beijing, China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Beijing, China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Beijing, China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Beijing, China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Beijing, China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Beijing, China
| | - Rong Chen
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, The Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Beijing, China
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14
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Rapid Identification of Fupenzi (Rubus chingii Hu) and Its Adulteration by AuNP Visualization. J FOOD QUALITY 2022. [DOI: 10.1155/2022/6278549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Fupenzi (Rubus chingii Hu) is a dried and immature fruit in East China, which has effects of nourishing kidneys, solidifying essence, and otherwise. Because Fupenzi was often adulterated and replaced with inferior things, this paper had researched Fupenzi and its adulterant raspberry. A new type of visible sensor was constructed by using Au nanoparticles (AuNPs), which was modified by the surface-active agent and combined with the ultraviolet-visible (UV-vis) spectrum technology. It was found that the change in particle size after the interaction of AuNPs and adulterants will lead to color change. In this paper, the RGB (red, green, and blue) values of the solution were extracted to correlate the color with the concentration of adulterants, and the relationship between the absorption peak intensity and the concentration of adulterants was established. The results showed that the intensity of an absorption peak is related to adulteration concentration, and the color of the solution changed from red to gray as the particle size changed. The visual sensor constructed based on the above principle is a fast and precise method to detect adulteration with different concentrations, which has a potential application value in real-time and rapid detection of Fupenzi’s quality.
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15
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Fan H, Li J, Landrein S. Complete chloroplast genome of Nyctocalos pinnatum: chloroplast features and phylogenetic relationships within Bignoniaceae. Mitochondrial DNA B Resour 2022; 7:1035-1037. [PMID: 35756448 PMCID: PMC9225756 DOI: 10.1080/23802359.2022.2081522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Nyctocalos is a genus of flowering lianas belonging to the family Bignoniaceae, and occurring from South-Central China to Malesia. In this study, we assembled the first complete chloroplast genome of N. pinnatum. The total length of the chloroplast genome is 159591 bp, with a GC content of 38.04%, which includes a pair of inverted repeats of 30,480 bp, a small single-copy region of 12,774 bp and a large single-copy region of 85,857 bp. The chloroplast genome contains 135 genes, consisting of 89 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. We constructed a phylogenomic tree with representative chloroplast genomes from Bignoniaceae. N. pinnatum is revealed to be sister to Oroxylum in the tribe Oroxyleae, with a high bootstrap support. This is the first chloroplast genome assembled in Nyctocalos, and it provides essential information for further ecology and evolutionary studies in this genus and Bignoniaceae.
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Affiliation(s)
- Huan Fan
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Jinyue Li
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy Sciences, Beijing, China
| | - Sven Landrein
- Center for Gardening and Horticulture, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
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16
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He X, Dong S, Gao C, Wang Q, Zhou M, Cheng R. The complete chloroplast genome of Carpesium abrotanoides L. (Asteraceae): structural organization, comparative analysis, mutational hotspots and phylogenetic implications within the tribe Inuleae. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Quan Y, Li L, Yin Z, Chen S, Yi J, Lang J, Zhang L, Yue Q, Zhao J. Bulbus Fritillariae Cirrhosae as a Respiratory Medicine: Is There a Potential Drug in the Treatment of COVID-19? Front Pharmacol 2022; 12:784335. [PMID: 35126123 PMCID: PMC8811224 DOI: 10.3389/fphar.2021.784335] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/03/2021] [Indexed: 01/08/2023] Open
Abstract
Bulbus fritillariae cirrhosae (BFC) is one of the most used Chinese medicines for lung disease, and exerts antitussive, expectorant, anti-inflammatory, anti-asthmatic, and antioxidant effects, which is an ideal therapeutic drug for respiratory diseases such as ARDS, COPD, asthma, lung cancer, and pulmonary tuberculosis. Through this review, it is found that the therapeutic mechanism of BFC on respiratory diseases exhibits the characteristics of multi-components, multi-targets, and multi-signaling pathways. In particular, the therapeutic potential of BFC in terms of intervention of “cytokine storm”, STAT, NF-κB, and MAPK signaling pathways, as well as the renin-angiotensin system (RAS) that ACE is involved in. In the “cytokine storm” of SARS-CoV-2 infection there is an intense inflammatory response. ACE2 regulates the RAS by degradation of Ang II produced by ACE, which is associated with SARS-CoV-2. For COVID-19, may it be a potential drug? This review summarized the research progress of BFC in the respiratory diseases, discussed the development potentiality of BFC for the treatment of COVID-19, explained the chemical diversity and biological significance of the alkaloids in BFC, and clarified the material basis, molecular targets, and signaling pathways of BFC for the respiratory diseases. We hope this review can provide insights on the drug discovery of anti-COVID-19.
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Affiliation(s)
- Yunyun Quan
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
- Department of Pharmacognosy, West China School of Pharmacy Sichuan University, Chengdu, China
| | - Li Li
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Zhujun Yin
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Shilong Chen
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Jing Yi
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Jirui Lang
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Lu Zhang
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Qianhua Yue
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Junning Zhao
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
- Department of Pharmacognosy, West China School of Pharmacy Sichuan University, Chengdu, China
- *Correspondence: Junning Zhao,
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18
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Zhang T, Huang S, Song S, Zou M, Yang T, Wang W, Zhou J, Liao H. Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics. PeerJ 2022; 9:e12612. [PMID: 35003925 PMCID: PMC8684722 DOI: 10.7717/peerj.12612] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/18/2021] [Indexed: 02/04/2023] Open
Abstract
The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.
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Affiliation(s)
- Tian Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Sipei Huang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Simin Song
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Meng Zou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Tiechui Yang
- Qinghai lvkang Biological Development Co., Ltd, Xining, Qinghai, China
| | - Weiwei Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
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19
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Jiang R, Zou M, Qin Y, Tan G, Huang S, Quan H, Zhou J, Liao H. Modeling of the Potential Geographical Distribution of Three Fritillaria Species Under Climate Change. FRONTIERS IN PLANT SCIENCE 2022; 12:749838. [PMID: 35082804 PMCID: PMC8784777 DOI: 10.3389/fpls.2021.749838] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Fritillaria species, a well-known Chinese traditional medicine for more than 2,000 years, have become rare resources due to excessive harvesting. In order to balance the economical requirement and ecological protection of Fritillaria species, it is necessary to determine (1) the important environmental variables that were responsible for the spatial distribution, (2) distribution change in response to climate change in the future, (3) ecological niche overlap between various Fritillaria species, and (4) the correlation between spatial distribution and phylogenies as well. In this study, the areas with potential ecological suitability for Fritillaria cirrhosa, Fritillaria unibracteata, and Fritillaria przewalskii were predicted using MaxEnt based on the current occurrence records and bioclimatic variables. The result indicated that precipitation and elevation were the most important environmental variables for the three species. Moreover, the current suitable habitats of F. cirrhosa, F. unibracteata, and F. przewalskii encompassed 681,951, 481,607, and 349,199 km2, respectively. Under the scenario of the highest concentration of greenhouse gas emission (SSP585), the whole suitable habitats of F. cirrhosa and F. przewalskii reach the maximum from 2021 to 2100, while those of F. unibracteata reach the maximum from 2021 to 2100 under the scenario of moderate emission (SSP370) from 2021 to 2100. The MaxEnt data were also used to predict the ecological niche overlap, and thus high overlap occurring among three Fritillaria species was observed. The niche overlap of three Fritillaria species was related to the phylogenetic analysis despite the non-significance (P > 0.05), indicating that spatial distribution was one of the factors that contributed to the speciation diversification. Additionally, we predicted species-specific habitats to decrease habitat competition. Overall, the information obtained in this study provided new insight into the potential distribution and ecological niche of three species for the conservation and management in the future.
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Affiliation(s)
| | | | | | | | | | | | - Jiayu Zhou
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Hai Liao
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, China
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20
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Chen Q, Hu H, Zhang D. DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:764255. [PMID: 35283910 PMCID: PMC8914171 DOI: 10.3389/fpls.2022.764255] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/21/2022] [Indexed: 05/10/2023]
Abstract
The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.
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Affiliation(s)
- Qi Chen
- College of Pharmacy, Dali University, Dali, China
| | - Haisu Hu
- College of Pharmacy, Dali University, Dali, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, China
- Institute of Materia Medica, Dali University, Dali, China
- *Correspondence: Dequan Zhang,
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21
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Jamdade R, Upadhyay M, Al Shaer K, Al Harthi E, Al Sallani M, Al Jasmi M, Al Ketbi A. Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122741. [PMID: 34961211 PMCID: PMC8708657 DOI: 10.3390/plants10122741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 06/14/2023]
Abstract
Arabia is the largest peninsula in the world, with >3000 species of vascular plants. Not much effort has been made to generate a multi-locus marker barcode library to identify and discriminate the recorded plant species. This study aimed to determine the reliability of the available Arabian plant barcodes (>1500; rbcL and matK) at the public repository (NCBI GenBank) using the unsupervised and supervised methods. Comparative analysis was carried out with the standard dataset (FINBOL) to assess the methods and markers' reliability. Our analysis suggests that from the unsupervised method, TaxonDNA's All Species Barcode criterion (ASB) exhibits the highest accuracy for rbcL barcodes, followed by the matK barcodes using the aligned dataset (FINBOL). However, for the Arabian plant barcode dataset (GBMA), the supervised method performed better than the unsupervised method, where the Random Forest and K-Nearest Neighbor (gappy kernel) classifiers were robust enough. These classifiers successfully recognized true species from both barcode markers belonging to the aligned and alignment-free datasets, respectively. The multi-class classifier showed high species resolution following the two classifiers, though its performance declined when employed to recognize true species. Similar results were observed for the FINBOL dataset through the supervised learning approach; overall, matK marker showed higher accuracy than rbcL. However, the lower rate of species identification in matK in GBMA data could be due to the higher evolutionary rate or gaps and missing data, as observed for the ASB criterion in the FINBOL dataset. Further, a lower number of sequences and singletons could also affect the rate of species resolution, as observed in the GBMA dataset. The GBMA dataset lacks sufficient species membership. We would encourage the taxonomists from the Arabian Peninsula to join our campaign on the Arabian Barcode of Life at the Barcode of Life Data (BOLD) systems. Our efforts together could help improve the rate of species identification for the Arabian Vascular plants.
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Affiliation(s)
- Rahul Jamdade
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximillians University, 80539 Munich, Germany;
| | - Khawla Al Shaer
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Eman Al Harthi
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Mariam Al Sallani
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Mariam Al Jasmi
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
| | - Asma Al Ketbi
- Sharjah Seed Bank and Herbarium, Environment and Protected Areas Authority, Sharjah P.O. Box 2926, United Arab Emirates; (K.A.S.); (E.A.H.); (M.A.S.); (M.A.J.); (A.A.K.)
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22
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Dong S, Ying Z, Yu S, Wang Q, Liao G, Ge Y, Cheng R. Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships. BMC Genomics 2021; 22:880. [PMID: 34872502 PMCID: PMC8647421 DOI: 10.1186/s12864-021-08193-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 11/16/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. RESULTS The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy. CONCLUSIONS Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.
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Affiliation(s)
- Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zhiqi Ying
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Shuisheng Yu
- The Administration Bureau of Zhejiang Jiulongshan National Nature Reserve, Suichang, Zhejiang Province, People's Republic of China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Guanghui Liao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China.
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23
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Yang H, Bao L, Liu Y, Luo S, Zhao F, Chen G, Liu F. Identification and quantitative analysis of salt-adulterated honeysuckle using infrared spectroscopy coupled with multi-chemometrics. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Zhu H, Wang W, Zhou Y, Wang B, Nie J. Simultaneous identification of Fritillariae cirrhosae bulbus and its common adulterants in one reaction by multiplex ligation-dependent probe amplification and high-resolution melting curve assay. Gene 2021; 785:145620. [PMID: 33794327 DOI: 10.1016/j.gene.2021.145620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/24/2021] [Accepted: 03/24/2021] [Indexed: 11/25/2022]
Abstract
Fritillariae cirrhosae bulbus, a well-known and precious medicinal and edible herb in China, causes remarkable effects on swelling and relieving cough, with fewer side effects than other congeneric medicine. It has been subject to various cheaper congeneric adulteration because of its high price and limited production. In this paper, a rapid, high throughput, sensitive and efficient technique was described for simultaneous identification of F. cirrhosae bulbus and its common adulterants by employing multiplex ligation-dependent probe amplification coupled with high-resolution melting (MLPA-HRM) curve assay in their internal transcribed spacer 1 (ITS1) regions. This assay was highly sensitive with a detection limit of 0.19 ng genomic DNA, and highly specific with no cross-reaction with common adulterants. Mixed sample analysis showed as low as 10% adulteration can be detected from F. cirrhosae bulbus in one MLPA-HRM reaction. Overall, the method described in this paper is well suited for detecting adulteration in F. cirrhosae bulbus.
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Affiliation(s)
- Hailan Zhu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Wenbin Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Yuxin Zhou
- Hubei Institute for Drug Control, Wuhan 430012, China
| | - Bo Wang
- Hubei Institute for Drug Control, Wuhan 430012, China.
| | - Jing Nie
- Hubei Institute for Drug Control, Wuhan 430012, China
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25
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Russell S, Jackson C, Reyes-Prieto A. High Sequence Divergence but Limited Architectural Rearrangements in Organelle Genomes of Cyanophora (Glaucophyta) Species. J Eukaryot Microbiol 2020; 68:e12831. [PMID: 33142007 DOI: 10.1111/jeu.12831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/16/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
Abstract
Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3-fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups.
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Affiliation(s)
- Sarah Russell
- Department of Biology, University of New Brunswick, 10 Bailey Drive, Fredericton, NB, E3B 5A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher Jackson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Royal Botanic Gardens Victoria, Melbourne, Vic., Australia
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, 10 Bailey Drive, Fredericton, NB, E3B 5A3, Canada
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26
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Wu X, Duan L, Chen Q, Zhang D. Genetic diversity, population structure, and evolutionary relationships within a taxonomically complex group revealed by AFLP markers: A case study on Fritillaria cirrhosa D. Don and closely related species. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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27
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Xu W, Xia B, Li X. The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses. Sci Rep 2020; 10:20782. [PMID: 33247172 PMCID: PMC7699626 DOI: 10.1038/s41598-020-77661-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 11/23/2022] Open
Abstract
The six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.
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Affiliation(s)
- Wenbin Xu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Boshun Xia
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xinwei Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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28
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Wu CS, Sudianto E, Hung YM, Wang BC, Huang CJ, Chen CT, Chaw SM. Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses. Sci Rep 2020; 10:20650. [PMID: 33244113 PMCID: PMC7693304 DOI: 10.1038/s41598-020-77492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/16/2020] [Indexed: 11/23/2022] Open
Abstract
Cypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. formosana, and C. obtusa var. obtusa were sequenced, respectively. We show that the loss of plastid trnT-GGU readily distinguishes C. formosensis from its congeneric species. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We also discover three short hypervariable loci (i.e., 3′ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. Moreover, nine species-specific indels of > 100 bp were detected in the cypress plastomes. These indels, together with the three aforementioned short barcodes, constitute an alternative and powerful barcode system crucial for identifying specimens that are fragmentary or contain degraded/poor DNA. Our sequenced data and barcode systems not only enrich the genetic reference for cypresses, but also contribute to future reforestation, conservation, and forensic investigations.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Edi Sudianto
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Mei Hung
- Department of Forensic Science Investigation Bureau, Ministry of Justice, New Taipei City, 231209, Taiwan
| | - Bo-Cyun Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chiun-Jr Huang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chi-Tsong Chen
- Department of Forensic Science Investigation Bureau, Ministry of Justice, New Taipei City, 231209, Taiwan.
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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29
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Chen T, Zhong F, Yao C, Chen J, Xiang Y, Dong J, Yan Z, Ma Y. A Systematic Review on Traditional Uses, Sources, Phytochemistry, Pharmacology, Pharmacokinetics, and Toxicity of Fritillariae Cirrhosae Bulbus. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2020; 2020:1536534. [PMID: 33273948 PMCID: PMC7676930 DOI: 10.1155/2020/1536534] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/05/2020] [Accepted: 10/14/2020] [Indexed: 12/31/2022]
Abstract
Fritillariae Cirrhosae Bulbus (known as chuanbeimu in Chinese, FCB) is a famous folk medicine which has been widely used to relieve cough and eliminate phlegm for thousands of years in China. The medicine originates from dried bulbs of six species of Fritillaria which are distributed in the temperate zone of the Northern Hemisphere. Increasing attention has been paid to FCB because of its excellent medicinal value such as being antitussive, expectorant, analgesic, anticancer, anti-inflammatory, and antioxidative. During the past years, a large number of research studies have been conducted to investigate the phytochemistry, pharmacology, and pharmacokinetics of FCB. A range of compounds have been isolated and identified from FCB, including alkaloids, saponins, nucleosides, organic acids, terpenoids, and sterols. Among them, alkaloids as the main active ingredient have been illustrated to exert significant therapeutic effects on many diseases such as cancer, acute lung injury, chronic obstructive pulmonary disease, asthma, Parkinson's disease, and diabetes. Due to the excellent medical value and low toxicity, FCB has a huge market all over the world and triggers a growing enthusiasm among researchers. However, there is still a lack of systematic review. Hence, in this work, we reviewed the FCB-based articles published in Sci Finder, Web of Science, PubMed, Google Scholar, CNKI, and other databases in the recent years. The traditional uses, sources, phytochemistry, pharmacology, pharmacokinetics, and toxicity of FCB were discussed in the review, which aims to provide a reference for further development and utilization of FCB.
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Affiliation(s)
- Ting Chen
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Furong Zhong
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Cheng Yao
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Jia Chen
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Yiqing Xiang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Jijing Dong
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Zhuyun Yan
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Yuntong Ma
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
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30
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Tai Y, Shen J, Luo Y, Qu H, Gong X. Research progress on the ethanol precipitation process of traditional Chinese medicine. Chin Med 2020; 15:84. [PMID: 32793299 PMCID: PMC7418433 DOI: 10.1186/s13020-020-00366-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Ethanol precipitation is a purification process widely used in the purification of Chinese medicine concentrates. This article reviews the research progress on the process mechanism of ethanol precipitation, ethanol precipitation process application for bioactive component purification, ethanol precipitation and traditional Chinese medicine quality, ethanol precipitation equipment, critical parameters, parameter research methods, process modeling and calculation methods, and process monitoring technology. This review proposes that ethanol precipitation technology should be further developed in terms of five aspects, namely, an in-depth study of the mechanism, further study of the effects on traditional Chinese medicine quality, improvement of the quality control of concentrates, development of new process detection methods, and development of a complete intelligent set of equipment.
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Affiliation(s)
- Yanni Tai
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Jichen Shen
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Yu Luo
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Haibin Qu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Xingchu Gong
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang China
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