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Wang X, Zhang Z, Shi Y, Man J, Huang Y, Zhang X, Liu S, He G, An K, Amu L, Chen W, Liu Z, Wang X, Wei S. Population identification and genetic diversity analysis of Fritillaria ussuriensis (Fritillaria) based on chloroplast genes atpF and petB. J Appl Genet 2024:10.1007/s13353-024-00874-z. [PMID: 38684618 DOI: 10.1007/s13353-024-00874-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024]
Abstract
The chloroplast genomes of five Fritillaria ussuriensis materials from different production areas were comparatively analyzed, atpF and petB were screened as specific DNA barcodes, and the population identification and genetic diversity of F. ussuriensis were analyzed based on them. The F. ussuriensis chloroplast genome showed a total length of 151 515-151 548 bp with a typical tetrad structure and encoded 130 genes. atpF and petB were used to amplify 183 samples from 13 populations, and they could identify 6 and 9 haplotypes, respectively. Joint analysis of the two sequences revealed 18 haplotypes, named H1-H18, with the most widely distributed and most abundant being H4. Ten haplotypes were unique for 7 populations that they could be used to distinguish from others. Haplotype diversity and nucleotide diversity were 0.99 and 2.09 × 10-3, respectively, indicating the genetic diversity was relatively rich. The results of the intermediary adjacency network showed that H5 was the oldest haplotype, and stellate radiation was centered around it, indicating that population expansion occurred in genuine production areas. This study lays a theoretical foundation for the population identification, genetic evolution, and breed selection of F. ussuriensis.
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Affiliation(s)
- Xin Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Zhifei Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Yue Shi
- School of Life and Science, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
- Engineering Research Center of Good Agricultural Practice for Chinese Crude Drugs, Ministry of Education, Beijing, 102488, People's Republic of China
| | - Jinhui Man
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Yuying Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Xiaoqin Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Shanhu Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Gaojie He
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Kelu An
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Laha Amu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Wenqin Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Ziqi Liu
- Heilongjiang BCT Chinese Traditional Medicine Co.Ltd, Heilongjiang, 150600, People's Republic of China
| | - Xiaohui Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing Institute of Traditional Chinese Medicine,, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China.
- Engineering Research Center of Good Agricultural Practice for Chinese Crude Drugs, Ministry of Education, Beijing, 102488, People's Republic of China.
| | - Shengli Wei
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China.
- Engineering Research Center of Good Agricultural Practice for Chinese Crude Drugs, Ministry of Education, Beijing, 102488, People's Republic of China.
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Wang J, Wang J, Shang M, Dai G, Liao B, Zheng J, Hu Z, Duan B. Comparatively analyzing of chloroplast genome and new insights into phylogenetic relationships regarding the genus Stephania. Gene 2024; 893:147931. [PMID: 37898453 DOI: 10.1016/j.gene.2023.147931] [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: 08/15/2023] [Revised: 10/05/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
The medicinal plant of the genus Stephania holds significant economic importance in the pharmaceutical industry. However, accurately classifying and subdividing this genus remains a challenge. Herein, the chloroplast (cp) genomes of Stephania and Cyclea were sequenced, and the primary characteristics, repeat sequences, inverted repeats regions, simple sequence repeats, and codon usage bias of 17 species were comparatively analyzed. Twelve markers were identified through genome alignment and sliding window analysis. Moreover, a molecular clock analysis revealed the divergence between subgenus (subg.) Botryodiscia and the combined Cyclea, subg. Stephania and Tuberiphania during the early Oligocene epoch. Notably, the raceme-type inflorescence represents the ancestral state of the Stephania and Cyclea. The genetic relationships inferred from the cp genome and protein-coding genes exhibited similar topologies. Additionally, the paraphyletic relationship between the genera Cyclea and Stephania was confirmed. Bayesian inference, maximum likelihood, and neighbor-joining trees consistently showed that section Tuberiphania and Transcostula were non-monophyletic. In conclusion, this research provides valuable insights for further investigations into species identification, evolution, and phylogenetics within the Stephania genus.
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Affiliation(s)
- Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali 671000, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali 671000, China
| | - Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali 671000, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali 671000, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali 671000, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali 671000, China
| | - Zhigang Hu
- College of Pharmaceutical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
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Li Z, Duan B, Zhou Z, Fang H, Yang M, Xia C, Zhou Y, Wang J. Comparative analysis of medicinal plants Scutellaria baicalensis and common adulterants based on chloroplast genome sequencing. BMC Genomics 2024; 25:39. [PMID: 38191291 PMCID: PMC10773089 DOI: 10.1186/s12864-023-09920-2] [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: 08/02/2023] [Accepted: 12/17/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Scutellaria baicalensis Georgi has been extensively used as a medicinal herb in China for over 2000 years. They may be intentionally or inadvertently substituted or blended with comparable species in the local market, threatening clinical medication safety. Molecular markers are effective tools to prevent misidentification and eliminate doping and falsification among Scutellaria plants. This study screened four highly variable regions to identify Scutellaria and its adulterants. In addition, a phylogenetic analysis was performed using the complete cp genome combined with published Scutellaria species samples. Moreover, a comparative analysis of the cp genomes was conducted to investigate the cp genome evolution of S. baicalensis. RESULTS The complete cp genome of five species of Scutellaria was sequenced for the first time, and four previously published Scutellaria species were re-sequenced. They all exhibited a conserved quadripartite structure in their cp genomes, including two distinct regions, namely a small and large single copy region, respectively, and two inverted repeats encompassing the majority of ribosomal RNA genes. Furthermore, the nine species exhibited high conservation from aspects of the genome structure, codon usage, repeat sequences, and gene content. Four highly variable regions (matK-rps16, ndhC-trnV-UAC, psbE-petL, and rps16-trnQ-UUG) may function as potential molecular markers for differentiating S. baicalensis from its adulterants. Additionally, the monophyly of Scutellaria was ascertained and could be reclassified into two subgenera, subgenus Anaspis and subgenus Scutellaria, as evidenced by the phylogenetic analyses on sequences of cp genome and shared protein-coding sequences. According to the molecular clock analysis, it has been inferred that the divergence of Scutellaria occurred at approximately 4.0 Mya during the Pliocene Epoch. CONCLUSION Our study provides an invaluable theoretical basis for further Scutellaria species identification, phylogenetics, and evolution analysis.
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Affiliation(s)
- Zhen Li
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Zhongyu Zhou
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, 133002, China
| | - Hui Fang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Ying Zhou
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- Institute of Caulis Dendrobii of Longling County, Baoshan, 678300, China.
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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Shang M, Wang J, Dai G, Zheng J, Liao B, Wang J, Duan B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 14:1251829. [PMID: 37954994 PMCID: PMC10634298 DOI: 10.3389/fpls.2023.1251829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Introduction The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification. Methods In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized. Results exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago. Discussion The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.
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Affiliation(s)
- Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
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Zhang W, Zhang Z, Liu B, Chen J, Zhao Y, Huang Y. Comparative analysis of 17 complete chloroplast genomes reveals intraspecific variation and relationships among Pseudostellaria heterophylla (Miq.) Pax populations. FRONTIERS IN PLANT SCIENCE 2023; 14:1163325. [PMID: 37426955 PMCID: PMC10325831 DOI: 10.3389/fpls.2023.1163325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/17/2023] [Indexed: 07/11/2023]
Abstract
Pseudostellaria heterophylla (Miq.) Pax is a well-known medicinal and ecologically important plant. Effectively distinguishing its different genetic resources is essential for its breeding. Plant chloroplast genomes can provide much more information than traditional molecular markers and provide higher-resolution genetic analyses to distinguish closely related planting materials. Here, seventeen P. heterophylla samples from Anhui, Fujian, Guizhou, Hebei, Hunan, Jiangsu, and Shandong provinces were collected, and a genome skimming strategy was employed to obtain their chloroplast genomes. The P. heterophylla chloroplast genomes ranged from 149,356 bp to 149,592 bp in length, and a total of 111 unique genes were annotated, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. Codon usage analysis showed that leucine had the highest frequency, while UUU (encoding phenylalanine) and UGC (encoding cysteine) were identified as the most and least frequently used codons, respectively. A total of 75-84 SSRs, 16-21 short tandem repeats, and 27-32 long repeat structures were identified in these chloroplast genomes. Then, four primer pairs were revealed for identifying SSR polymorphisms. Palindromes are the dominant type, accounting for an average of 47.86% of all long repeat sequences. Gene orders were highly collinear, and IR regions were highly conserved. Genome alignment indicated that there were four intergenic regions (psaI-ycf4, ycf3-trnS, ndhC-trnV, and ndhI-ndhG) and three coding genes (ndhJ, ycf1, and rpl20) that were highly variable among different P. heterophylla samples. Moreover, 10 SNP/MNP sites with high polymorphism were selected for further study. Phylogenetic analysis showed that populations of Chinese were clustered into a monophyletic group, in which the non-flowering variety formed a separate subclade with high statistical support. In this study, the comparative analysis of complete chloroplast genomes revealed intraspecific variations in P. heterophylla and further supported the idea that chloroplast genomes could elucidate relatedness among closely related cultivation materials.
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Affiliation(s)
- Wujun Zhang
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Baocai Liu
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jingying Chen
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yunqing Zhao
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yingzhen Huang
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
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Fang H, Dai G, Liao B, Zhou P, Liu Y. Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 13:1099856. [PMID: 36684764 PMCID: PMC9853280 DOI: 10.3389/fpls.2022.1099856] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/13/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND Phyllanthus urinaria L. is extensively used as ethnopharmacological material in China. In the local marketplace, this medicine can be accidentally contaminated, deliberately substituted, or mixed with other related species. The contaminants in herbal products are a threat to consumer safety. Due to the scarcity of genetic information on Phyllanthus plants, more molecular markers are needed to avoid misidentification. METHODS In this study, the complete chloroplast genome of nine species of the genus Phyllanthus was de novo assembled and characterized. RESULTS This study revealed that all of these species exhibited a conserved quadripartite structure, which includes a large single copy (LSC) region and small single copy (SSC) region, and two copies of inverted repeat regions (IRa and IRb), which separate the LSC and SSC regions. And the genome structure, codon usage, and repeat sequences were highly conserved and showed similarities among the nine species. Three highly variable regions (trnS-GCU-trnG-UCC, trnT-UGU-trnL-UAA, and petA-psbJ) might be helpful as potential molecular markers for identifying P. urinaria and its contaminants. In addition, the molecular clock analysis results showed that the divergence time of the genus Phyllanthus might occur at ~ 48.72 Ma. CONCLUSION This study provides valuable information for further species identification, evolution, and phylogenetic research of Phyllanthus.
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Affiliation(s)
| | | | | | - Ping Zhou
- *Correspondence: Yinglin Liu, ; Ping Zhou,
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