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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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Chen S, Safiul Azam FM, Akter ML, Ao L, Zou Y, Qian Y. The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification. FRONTIERS IN PLANT SCIENCE 2024; 15:1356912. [PMID: 38745930 PMCID: PMC11092384 DOI: 10.3389/fpls.2024.1356912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024]
Abstract
Introduction Thalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety. Methods The present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum. Results and discussion The cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium. Conclusion Considering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.
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Affiliation(s)
- Shixi Chen
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Key Laboratory of Sichuan Province, Neijiang Normal University, Sichuan, China
| | - Fardous Mohammad Safiul Azam
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Mst. Lovely Akter
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Li Ao
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan, China
| | - Yuanchao Zou
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Key Laboratory of Sichuan Province, Neijiang Normal University, Sichuan, China
| | - Ye Qian
- Branch of The First Affiliated Hospital of Xinjiang Medical University, Changji, Xinjiang, China
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Hu H, Xu Z, Wei Y, Wang T, Zhao Y, Xu H, Mao X, Huang L. The Identification of Fritillaria Species Using Hyperspectral Imaging with Enhanced One-Dimensional Convolutional Neural Networks via Attention Mechanism. Foods 2023; 12:4153. [PMID: 38002210 PMCID: PMC10670081 DOI: 10.3390/foods12224153] [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: 09/06/2023] [Revised: 10/14/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Combining deep learning and hyperspectral imaging (HSI) has proven to be an effective approach in the quality control of medicinal and edible plants. Nonetheless, hyperspectral data contains redundant information and highly correlated characteristic bands, which can adversely impact sample identification. To address this issue, we proposed an enhanced one-dimensional convolutional neural network (1DCNN) with an attention mechanism. Given an intermediate feature map, two attention modules are constructed along two separate dimensions, channel and spectral, and then combined to enhance relevant features and to suppress irrelevant ones. Validated by Fritillaria datasets, the results demonstrate that an attention-enhanced 1DCNN model outperforms several machine learning algorithms and shows consistent improvements over a vanilla 1DCNN. Notably under VNIR and SWIR lenses, the model obtained 98.97% and 99.35% for binary classification between Fritillariae Cirrhosae Bulbus (FCB) and other non-FCB species, respectively. Additionally, it still achieved an extraordinary accuracy of 97.64% and 98.39% for eight-category classification among Fritillaria species. This study demonstrated the application of HSI with artificial intelligence can serve as a reliable, efficient, and non-destructive quality control method for authenticating Fritillaria species. Moreover, our findings also illustrated the great potential of the attention mechanism in enhancing the performance of the vanilla 1DCNN method, providing reference for other HSI-related quality controls of plants with medicinal and edible uses.
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Affiliation(s)
- Huiqiang Hu
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenyu Xu
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Yunpeng Wei
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Tingting Wang
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Yuping Zhao
- China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Huaxing Xu
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaobo Mao
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Luqi Huang
- China Academy of Chinese Medical Sciences, Beijing 100070, China
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Tian Y, Liu X, Xu Y, Yu B, Wang L, Qu X. Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots. Sci Rep 2023; 13:15622. [PMID: 37730791 PMCID: PMC10511529 DOI: 10.1038/s41598-023-42945-x] [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: 06/12/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023] Open
Abstract
Tiandong is a vital traditional Chinese herbal medicine. It is derived from the tuber root of the Asparagus cochinchinensis according to the Pharmacopoeia of the people's republic of China (2020 Edition). On account of the similar morphology, Asparagus meioclados and Asparagus munitus were used as Tian-Dong in southwest China. Chloroplast (cp) genomes are highly active genetic components of plants and play an extremely important role in improving the efficiency of the identification of plant species. To differentiate the medicinal plants belonging to the genus Asparagus, we sequenced and analyzed the complete plastomes (plastid genomes) of A. meioclados and A. munitus and obtained two plastomes whose length changed to 156,515 bp and 156,381 bp, respectively. A total of 111 unique genes have been detected in plastome, which included 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In plastomes of A. meioclados and A. munitus, 14,685 and 14,987 codons were detected, among which 9942 and 10,207 had the relative synonymous codon usage (RSCU) values higher than 1, respectively. A. meioclados and A. munitus have 26 SSRs patterns, among which A. meioclados was 25 and A. munitus 21. The average Ka/Ks value was 0.36, and positive selection was detected in genes of the photosynthetic system (ndhF and rbcL) in Asparagus species. To perform the comparative analysis of plastomes, the two newly sequenced plastomes of the A. meioclados and A. munitus species were compared with that of A. cochinchinensis, and 12 hotspots, including 5 coding regions and 7 inter-genomic regions, were identified. Based on the whole plastome of Asparagus, 2 divergent hotspots (accD and rpl32-trnL-UAG) and 1 international barcode fragment (rbcL) were screened, which may be used as particular molecular markers for the identification of Asparagus species. In addition, we determined the phylogenetic relationship between A. meioclados and A. munitus in the genus Asparagus. This study enriches our knowledge of the molecular evolutionary relationships of the Asparagus genus and provides treasured data records for species identification, molecular breeding, and evolutionary analysis of this genus.
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Affiliation(s)
- Yulu Tian
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, No. 1166 Liutai Avenue, Wenjiang District, Chengdu, 611137, China
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Xue Liu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
| | - Yuanjiang Xu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Benxia Yu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Le Wang
- College of Life Science and Food Engineering, Chongqing Three Gorges University, 666 Tianxing Road, Wanzhou District, Chongqing, 404100, China
| | - Xianyou Qu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
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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 2022:1-22. [PMID: 36227577 DOI: 10.1080/10408347.2022.2132374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Ren W, Liu C, Yan S, Jiang Z, Wang T, Wang Z, Zhang M, Liu M, Sun J, Gao J, Ma W. Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus. Front Genet 2022; 13:849182. [PMID: 35910210 PMCID: PMC9329572 DOI: 10.3389/fgene.2022.849182] [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: 04/21/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species’ ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constitutes the complete chloroplast genome of A. ukurunduense into a 156,645-bp circular DNA, which displayed a typical quadripartite structure. In addition, 133 genes were identified, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In total, 107 simple sequence repeats and 49 repetitive sequences were observed. Thirty-two codons indicated that biased usages were estimated across 20 protein-coding genes (CDS) in A. ukurunduense. Four hotspot regions (trnK-UUU/rps16, ndhF/rpl32, rpl32/trnL-UAG, and ycf1) were detected among the five analyzed Acer species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that A. ukurunduense is most closely associated with the species of Sect. Palmata. A. ukurunduense and A. pubipetiolatum var. pingpienense diverged in 22.11 Mya. We selected one of the hypervariable regions (trnK-UUU/rps16) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five Acer species through Sanger sequencing. By sequencing the cp genome of A. ukurunduense and comparing it with the relative species of Acer, we can effectively address the phylogenetic problems of Acer at the species level and provide insights into future research on population genetics and genetic diversity.
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Affiliation(s)
- Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Chi Liu
- Faculty of Electrical Engineering and Information Technology, Technical University of Chemnitz, Chemnitz, Germany
| | - Song Yan
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhehui Jiang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Tianhao Wang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Zhen Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Meiqi Zhang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Meiqi Liu
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jiaying Sun
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jinhui Gao
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
- *Correspondence: Jinhui Gao, ; Wei Ma,
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- Jiangsu Kanion Pharmaceutical Co. Ltd., Lianyungang, China
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Lianyungang, China
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, China
- *Correspondence: Jinhui Gao, ; Wei Ma,
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Wong KH, Kong BLH, Siu TY, Wu HY, But GWC, Shaw P, Lau DTW. Complete chloroplast genomes of Asparagus aethiopicus L., A. densiflorus (Kunth) Jessop 'Myers', and A. cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congenerics. PLoS One 2022; 17:e0266376. [PMID: 35468142 PMCID: PMC9037925 DOI: 10.1371/journal.pone.0266376] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/19/2022] [Indexed: 11/21/2022] Open
Abstract
Asparagus species are widely used for medicinal, horticultural, and culinary purposes. Complete chloroplast DNA (cpDNA) genomes of three Asparagus specimens collected in Hong Kong-A. aethiopicus, A. densiflorus 'Myers', and A. cochinchinensis-were de novo assembled using Illumina sequencing. Their sizes ranged from 157,069 to 157,319 bp, with a total guanine-cytosine content of 37.5%. Structurally, a large single copy (84,598-85,350 bp) and a small single copy (18,677-18,685 bp) were separated by a pair of inverted repeats (26,518-26,573 bp). In total, 136 genes were annotated for A. aethiopicus and A. densiflorus 'Myers'; these included 90 mRNA, 38 tRNA, and 8 rRNA genes. Further, 132 genes, including 87 mRNA, 37 tRNA, and 8 rRNA genes, were annotated for A. cochinchinensis. For comparative and phylogenetic analysis, we included NCBI data for four congenerics, A. setaceus, A. racemosus, A. schoberioides, and A. officinalis. The gene content, order, and genome structure were relatively conserved among the genomes studied. There were similarities in simple sequence repeats in terms of repeat type, sequence complementarity, and cpDNA partition distribution. A. densiflorus 'Myers' had distinctive long sequence repeats in terms of their quantity, type, and length-interval frequency. Divergence hotspots, with nucleotide diversity (Pi) ≥ 0.015, were identified in five genomic regions: accD-psaI, ccsA, trnS-trnG, ycf1, and ndhC-trnV. Here, we summarise the historical changes in the generic subdivision of Asparagus. Our phylogenetic analysis, which also elucidates the nomenclatural complexity of A. aethiopicus and A. densiflorus 'Myers', further supports their close phylogenetic relationship. The findings are consistent with prior generic subdivisions, except for the placement of A. racemosus, which requires further study. These de novo assembled cpDNA genomes contribute valuable genomic resources and help to elucidate Asparagus taxonomy.
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Affiliation(s)
- Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Bobby Lim-Ho Kong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Tin-Yan Siu
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Grace Wing-Chiu But
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Pang‑Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - David Tai-Wai Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
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Guzmán-Díaz S, Núñez FAA, Veltjen E, Asselman P, Larridon I, Samain MS. Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030448. [PMID: 35161429 PMCID: PMC8838774 DOI: 10.3390/plants11030448] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 05/13/2023]
Abstract
Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.
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Affiliation(s)
- Salvador Guzmán-Díaz
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
- Correspondence:
| | - Fabián Augusto Aldaba Núñez
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
| | - Emily Veltjen
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
- Ghent University Botanical Garden, Ghent University, 9000 Gent, Belgium
| | - Pieter Asselman
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
| | - Isabel Larridon
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Marie-Stéphanie Samain
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
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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: 3] [Impact Index Per Article: 1.5] [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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10
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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: 6] [Impact Index Per Article: 3.0] [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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11
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Li C, Cai C, Tao Y, Sun Z, Jiang M, Chen L, Li J. Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:754209. [PMID: 34721483 PMCID: PMC8551639 DOI: 10.3389/fpls.2021.754209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/21/2021] [Indexed: 06/02/2023]
Abstract
Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.
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Affiliation(s)
- Chenxin Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Yutian Tao
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
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12
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Wu L, Wu M, Cui N, Xiang L, Li Y, Li X, Chen S. Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria. Chin Med 2021; 16:52. [PMID: 34225754 PMCID: PMC8256587 DOI: 10.1186/s13020-021-00460-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/26/2021] [Indexed: 12/21/2022] Open
Abstract
Background Although molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species. Methods We here compared 26 complete cp genomes of ten Fritillaria species including 18 new sequences sequenced in this study. Each species had repeats and the cp genomes were used as a whole DNA barcode to test whether they can distinguish Fritillaria species. Results The cp genomes of Fritillaria medicinal plants were conserved in genome structure, gene type, and gene content. Comparison analysis of the Fritillaria cp genomes revealed that the intergenic spacer regions were highly divergent compared with other regions. By constructing the phylogenetic tree by the maximum likelihood and maximum parsimony methods, we found that the entire cp genome showed a high discrimination power for Fritillaria species with individuals of each species in a monophyletic clade. These results indicate that cp genome can be used to effectively differentiate medicinal plants from the genus Fritillaria at the species level. Conclusions This study implies that cp genome can provide distinguishing differences to help identify closely related Fritillaria species, and has the potential to be served as a universal super-barcode for plant identification. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-021-00460-z.
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Affiliation(s)
- 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, 100700, China
| | - Mingli 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, 100700, China
| | - Ning Cui
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, 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, 100700, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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13
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Ren F, Wang L, Li Y, Zhuo W, Xu Z, Guo H, Liu Y, Gao R, Song J. Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola. Ecol Evol 2021; 11:4158-4171. [PMID: 33976800 PMCID: PMC8093665 DOI: 10.1002/ece3.7312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 01/27/2023] Open
Abstract
The increasingly wide application of chloroplast (cp) genome super-barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. Corydalis is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, there currently are few reports about cp genomes of the genus Corydalis. In this study, we sequenced four complete cp genomes of two endangered lithophytes Corydalis saxicola and Corydalis tomentella in Corydalis, conducted a comparison of these cp genomes among each other as well as with others of Papaveraceae. The cp genomes have a large genome size of 189,029-190,247 bp, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955-42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola, and Papaveraceae species, five NADH dehydrogenase-like genes (ndhF, ndhD, ndhL, ndhG, and ndhE) with psaC, rpl32, ccsA, and trnL-UAG normally located in the SSC region have migrated to IRs, resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI-CAU, and trnL-CAA) was found within IR regions. The accD gene was found to be absent and the ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis based on the sequences of common CDS showed that the genus Corydalis is quite distantly related to the other genera of Papaveraceae, it provided a new clue for recent advocacy to establish a separate Fumariaceae family. Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships.
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Affiliation(s)
- Fengming Ren
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | | | - Ying Li
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
| | - Wei Zhuo
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | - Zhichao Xu
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
| | | | - Yan Liu
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | - Ranran Gao
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
| | - Jingyuan Song
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
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14
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Roguz K, Hill L, Roguz A, Zych M. Evolution of Bird and Insect Flower Traits in Fritillaria L. (Liliaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:656783. [PMID: 33868353 PMCID: PMC8044542 DOI: 10.3389/fpls.2021.656783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/03/2021] [Indexed: 05/27/2023]
Abstract
Pollinators are often perceived as a primary selective agent influencing flower traits such as colour, size, and nectar properties. The genus Fritillaria L. (Liliaceae), comprising approximately 150 species, is described as generally insect pollinated. However, there are at least three exceptions: two hummingbird-pollinated North American species and one passerine-pollinated Asian species. Despite this variation in pollination, little is known about flower traits that may accompany this shift in fritillaries. In this study, we aimed to assess the attractiveness of the floral traits for (new) pollinators and track the evolution of flowers traits in the context of a shift in the principal pollinator. Therefore, we studied 14 flower traits related to the pollination in 60 Fritillaria species and traced the evolutionary trajectory of these traits. We used a phylogenetic tree of the genus, based on five DNA markers (matK, rpl16, and rbcL, 18S, and ITS) to reconstruct the ancestral state of studied flower traits. The results show that in bird-pollinated species several new traits evolved. For example, flower colouration, nectar sugar, and amino acid concentration and composition fulfil the criteria of ornithophilous flowers, although flower traits do not exclude insect pollinators in bird-pollinated fritillaries. Interestingly, we recorded potential reversals from bird to insect pollination. Our analysis, showing a broad study of flower traits among closely related species in the context of pollinator shift, serves as a starting point for future work exploring the genetic and physiological mechanisms controlling flower traits in the genus Fritillaria.
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Affiliation(s)
- Katarzyna Roguz
- Botanic Garden, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | | | - Marcin Zych
- Botanic Garden, Faculty of Biology, University of Warsaw, Warsaw, Poland
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15
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Robinson R, Youngblood H, Iyer H, Bloom J, Lee TJ, Chang L, Lukowski Z, Zhi W, Sharma A, Sharma S. Diabetes Induced Alterations in Murine Vitreous Proteome Are Mitigated by IL-6 Trans-Signaling Inhibition. Invest Ophthalmol Vis Sci 2021; 61:2. [PMID: 32870245 PMCID: PMC7476668 DOI: 10.1167/iovs.61.11.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose Diabetic retinopathy (DR) is a microvascular complication caused by prolonged hyperglycemia and characterized by leaky retinal vasculature and ischemia-induced angiogenesis. Vitreous humor is a gel-like biofluid in the posterior segment of the eye between the lens and the retina. Disease-related changes are observed in the biochemical constituents of the vitreous, including proteins and macromolecules. Recently, we found that IL-6 trans-signaling plays a significant role in the vascular leakage and retinal pathology associated with DR. Therefore, in this study, comprehensive proteomic profiling of the murine vitreous was performed to identify diabetes-induced alterations and to determine effects of IL-6 trans-signaling inhibition on these changes. Methods Vitreous samples from mice were collected by evisceration, and proteomic analyses were performed using liquid chromatography–tandem mass spectrometry (LC-MS/MS). Results A total of 154 proteins were identified with high confidence in control mice and were considered to be characteristic of healthy murine vitreous fluid. The levels of 72 vitreous proteins were significantly altered in diabetic mice, including several members of heat shock proteins, 14-3-3 proteins, and tubulins. Alterations in 52 out of 72 proteins in diabetic mice were mitigated by IL-6 trans-signaling inhibition. Conclusions Proteomic analysis of murine vitreous fluid performed in this study provides important information about the changes caused by diabetes in the ocular microenvironment. These diabetes-induced alterations in the murine vitreous proteome were mitigated by IL-6 trans-signaling inhibition. These findings further support that IL-6 trans-signaling may be an important therapeutic target for the treatment of DR.
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Affiliation(s)
- Rebekah Robinson
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Hannah Youngblood
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Hersha Iyer
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Justin Bloom
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Luke Chang
- Department of Ophthalmology, Augusta University, Augusta, Georgia, United States
| | - Zachary Lukowski
- Department of Ophthalmology, Augusta University, Augusta, Georgia, United States
| | - Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States.,Department of Ophthalmology, Augusta University, Augusta, Georgia, United States.,Department of Population Health Sciences, Augusta University, Augusta, Georgia, United States.,Culver Vision Discovery Institute, Augusta University, Augusta, Georgia, United States
| | - Shruti Sharma
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States.,Department of Ophthalmology, Augusta University, Augusta, Georgia, United States.,Culver Vision Discovery Institute, Augusta University, Augusta, Georgia, United States
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16
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Wu JY, Ma XC, Ma L, Fang Y, Zhang YH, Liu LJ, Li XC, Zeng R, Sun WC. Complete chloroplast genome sequence and phylogenetic analysis of winter oil rapeseed ( Brassica rapa L.). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:723-731. [PMID: 33763561 PMCID: PMC7954489 DOI: 10.1080/23802359.2020.1860697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Winter oil rapeseed ‘18 R-1’ (Brassica rapa L.) is a new variety that can survive in northern China where the extreme low temperature is −20 °C to −32 °C. It is different from traditional B. rapa and Brassica napus. In this study, the complete chloroplast (cp) genome of ‘18 R-1’ was sequenced and analyzed to assess the genetic relationship. The size of cp genome is 153,494 bp, including one large single copy (LSC) region of 83,280 bp and one small single copy (SSC) region of 17,776 bp, separated by two inverted repeat (IR) regions of 26,219 bp. The GC content of the whole genome is 36.35%, while those of LSC, SSC, and IR are 34.12%, 29.20%, and 42.32%, respectively. The cp genome encodes 132 genes, including 87 protein-coding genes, eight rRNA genes, and 37 tRNA genes. In repeat structure analysis, 288 simple sequence repeats (SSRs) were identified. Cp genome of ‘18 R-1’ was closely related to Brassica chinensis, B. rapa and Brassica pekinesis.
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Affiliation(s)
- Jun Yan Wu
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Xue Cai Ma
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Li Ma
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Yan Fang
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Ya Hong Zhang
- Tianshui Institute of Agricultural Sciences, Tianshui Gansu, China
| | - Li Jun Liu
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Xue Cai Li
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Rui Zeng
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
| | - Wan Cang Sun
- College of Agronomy, Gansu Agricultural University/Rapeseed Engineering Research Center of Gansu Province, Lanzhou, China
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17
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Abdullah, Henriquez CL, Croat TB, Poczai P, Ahmed I. Mutational Dynamics of Aroid Chloroplast Genomes II. Front Genet 2021; 11:610838. [PMID: 33552129 PMCID: PMC7854696 DOI: 10.3389/fgene.2020.610838] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/16/2020] [Indexed: 01/30/2023] Open
Abstract
The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.
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Affiliation(s)
- Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | | | - Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
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18
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Gu L, Su T, An MT, Hu GX. The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1692. [PMID: 33276435 PMCID: PMC7760870 DOI: 10.3390/plants9121692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/18/2020] [Accepted: 11/28/2020] [Indexed: 12/03/2022]
Abstract
Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.
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Affiliation(s)
- Li Gu
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (L.G.); (T.S.)
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region Ministry of Education, Guizhou University, Guiyang 550025, China
- Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Ting Su
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (L.G.); (T.S.)
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region Ministry of Education, Guizhou University, Guiyang 550025, China
- Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Ming-Tai An
- College of Forestry, Guizhou University, Guiyang 550025, China;
| | - Guo-Xiong Hu
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (L.G.); (T.S.)
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region Ministry of Education, Guizhou University, Guiyang 550025, China
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Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae). Sci Rep 2020; 10:19781. [PMID: 33188288 PMCID: PMC7666119 DOI: 10.1038/s41598-020-76699-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
Pulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.
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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: 18] [Impact Index Per Article: 4.5] [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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21
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Liu Q, Li X, Li M, Xu W, Schwarzacher T, Heslop-Harrison JS. Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny. BMC PLANT BIOLOGY 2020; 20:406. [PMID: 32878602 PMCID: PMC7466839 DOI: 10.1186/s12870-020-02621-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 08/25/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Oat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena species, to examine the plastome evolutionary dynamics and analyze phylogenetic relationships between oat and its congeneric wild related species. RESULTS The chloroplast genomes of eleven Avena species (size range of 135,889-135,998 bp) share quadripartite structure, comprising of a large single copy (LSC; 80,014-80,132 bp), a small single copy (SSC; 12,575-12,679 bp) and a pair of inverted repeats (IRs; 21,603-21,614 bp). The plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs and 39 transfer RNAs. The nucleotide sequence diversities (Pi values) range from 0.0036 (rps19) to 0.0093 (rpl32) for ten most polymorphic genes and from 0.0084 (psbH-petB) to 0.0240 (petG-trnW-CCA) for ten most polymorphic intergenic regions. Gene selective pressure analysis shows that all protein-coding genes have been under purifying selection. The adjacent position relationships between tandem repeats, insertions/deletions and single nucleotide polymorphisms support the evolutionary importance of tandem repeats in causing plastome mutations in Avena. Phylogenomic analyses, based on the complete plastome sequences and the LSC intermolecular recombination sequences, support the monophyly of Avena with two clades in the genus. CONCLUSIONS Diversification of Avena plastomes is explained by the presence of highly diverse genes and intergenic regions, LSC intermolecular recombination, and the co-occurrence of tandem repeat and indels or single nucleotide polymorphisms. The study demonstrates that the A-genome diploid-polyploid lineage maintains two subclades derived from different maternal ancestors, with A. longiglumis as the first diverging species in clade I. These genome resources will be helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Avena and family Poaceae levels, and are potentially useful to exploit plastome variation in making hybrids for plant breeding.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoyu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Independent Researcher, Guangzhou, China
| | - Wenkui Xu
- Independent Researcher, Guangzhou, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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Naeem Z, Masud S, Hassan S, Naeem M. Molecular approach for identification of Catla catla using mitochondrial CO1 from Pakistan. Mitochondrial DNA B Resour 2020; 5:3000-3003. [PMID: 33458033 PMCID: PMC7782247 DOI: 10.1080/23802359.2020.1768913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 05/09/2020] [Indexed: 11/01/2022] Open
Abstract
DNA barcoding is a rapid, precise, and effective way of species identification. A short and standard target gene marker is used to create sequence profile of identified species. Specific tag or marker is used, which is derived from mitochondrial COI for identification. Effectiveness of this method axes the degree of divergence among species. Identification is necessary for their representation. In the present work, Catla catla was used to study by using Cytochrome C Oxidase 1.The genetic distances were computed, and Neighbor Joining tree was constructed based on the Kimura 2 Parameter method. GenBank and BOLD revealed definitive identity matches. Conspecific and congeneric K2P nucleotide divergence was estimated. Evolutionary tree was analyzed clearly by relating their species to phylogenetic tree, as same as species were bunched under same tree node, while species were differently clustered under distinct nodes. These findings conclude that the gene sequence may serve as a milestone for identification and phylogenetic history of related species at molecular level.
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Affiliation(s)
- Zara Naeem
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Samrah Masud
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Shoaib Hassan
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Naeem
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
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23
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Mehmood F, Abdullah, Ubaid Z, Shahzadi I, Ahmed I, Waheed MT, Poczai P, Mirza B. Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco ( Nicotiana rustica). PeerJ 2020; 8:e9552. [PMID: 32775052 PMCID: PMC7382938 DOI: 10.7717/peerj.9552] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323-25,369 bp each) separated by a large single-copy (LSC) region (86,510-86,716 bp) and a small single-copy (SSC) region (18,441-18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65-0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species.
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Affiliation(s)
- Furrukh Mehmood
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zartasha Ubaid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iram Shahzadi
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Mohammad Tahir Waheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Bushra Mirza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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24
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Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Zheng G, Wei L, Ma L, Wu Z, Gu C, Chen K. Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships. PLANT MOLECULAR BIOLOGY 2020; 102:659-676. [PMID: 31997112 DOI: 10.1007/s11103-020-00972-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/20/2020] [Indexed: 05/11/2023]
Abstract
Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed within Myrtales. The Lagerstroemia species used in this study originated in China and have high economic and ecological value. The shared interspecific morphological characteristics and intraspecific morphological variation resulting from hybridization among Lagerstroemia taxa have made resolving their classification problems and phylogenetic relationships difficult. Systematic comparative genomic analysis has been shown to resolve phylogenetic relationships. We sequenced and annotated 6 Lagerstroemia cp genomes (Lagerstroemia excelsa, Lagerstroemia limii, Lagerstroemia siamica, Lagerstroemia tomentosa, Lagerstroemia venusta, and Lagerstroemia calyculata) for the first time and combined them with previously published genomes for Lagerstroemia species. Bioinformatics was used to analyse the 13 cp genomes in terms of gene structure and organization, codon usage, contraction and expansion of inverted repeat regions, repeat structure, divergence hotspots, species pairwise Ka/Ks ratios and phylogenetic relationships. The length varied between 152,049 bp in Lagerstroemia subcostata and 152,521 bp in L. venusta. We selected seven divergence hotspots in the cp genomes that had the potential to act as plastid markers to distinguish Lagerstroemia species. The phylogenetic relationships within Myrtales inferred from the cp genomes of 13 Lagerstroemia species and 27 other Myrtales species were highly supported, which illustrated several novel relationships within Myrtales. Taken together, our results provide comprehensive chloroplast genomic resources, which can be used further for species identification and molecular breeding of Lagerstroemia species.
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Affiliation(s)
- Gang Zheng
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Lingling Wei
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- School of Humanities and social sciences, Beijing Forestry University, Beijing, 100083, China
| | - Li Ma
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Zhiqiang Wu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China.
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Kai Chen
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
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26
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Henriquez CL, Ahmed I, Carlsen MM, Zuluaga A, Croat TB, McKain MR. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae). PLANTA 2020; 251:72. [PMID: 32112137 DOI: 10.1007/s00425-020-03365-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/14/2020] [Indexed: 05/02/2023]
Abstract
This study provides broad insight into the chloroplast genomes of the subfamily Monsteroideae. The identified polymorphic regions may be suitable for designing unique and robust molecular markers for phylogenetic inference. Monsteroideae is the third largest subfamily (comprises 369 species) and one of the early diverging lineages of the monocot plant family Araceae. The phylogeny of this important subfamily is not well resolved at the species level due to scarcity of genomic resources and suitable molecular markers. Here, we report annotated chloroplast genome sequences of four Monsteroideae species: Spathiphyllum patulinervum, Stenospermation multiovulatum, Monstera adansonii, and Rhaphidophora amplissima. The quadripartite chloroplast genomes (size range 163,335-164,751 bp) consist of a pair of inverted repeats (25,270-25,931 bp), separating a small single copy region (21,448-22,346 bp) from a large single copy region (89,714-91,841 bp). The genomes contain 114 unique genes, including four rRNA genes, 80 protein-coding genes, and 30 tRNA genes. Gene features, amino acid frequencies, codon usage, GC contents, oligonucleotide repeats, and inverted repeats dynamics exhibit similarities among the four genomes. Higher rate of synonymous substitutions was observed as compared to non-synonymous substitutions in 76 protein-coding genes. Positive selection was observed in seven protein-coding genes, including psbK, ndhK, ndhD, rbcL, accD, rps8, and ycf2. Our included species of Araceae showed the monophyly in Monsteroideae and other subfamilies. We report 30 suitable polymorphic regions. The polymorphic regions identified here might be suitable for designing unique and robust markers for inferring the phylogeny and phylogeography among closely related species within the genus Spathiphyllum and among distantly related species within the subfamily Monsteroideae. The chloroplast genomes presented here are a valuable contribution towards understanding the molecular evolutionary dynamics in the family Araceae.
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Affiliation(s)
- Claudia L Henriquez
- University of California, Department of Ecology and Evolutionary Biology, Los Angeles, USA.
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, 45710, Pakistan
| | | | - Alejandro Zuluaga
- Departamento de Biología, Universidad del Valle, Calle 13, 100-00, Cali, Colombia
| | | | - Michael R McKain
- The University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, USA
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27
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Chen Q, Wu X, Zhang D. Comparison of the abilities of universal, super, and specific DNA barcodes to discriminate among the original species of Fritillariae cirrhosae bulbus and its adulterants. PLoS One 2020; 15:e0229181. [PMID: 32053689 PMCID: PMC7018091 DOI: 10.1371/journal.pone.0229181] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/02/2020] [Indexed: 11/18/2022] Open
Abstract
Fritillariae cirrhosae bulbus is a famous type of traditional Chinese medicine used for cough relief and eliminating phlegm. The medicine originates from dried bulbs of five species and one variety of Fritillaria. Recently, immature bulbs from other congeneric species, such as F. ussuriensis, have been sold as adulterants of Fritillariae cirrhosae bulbus in medicine markets owing to the high price and limited availability of the genuine medicine. However, it is difficult to accurately identify the bulbs from different original species of Fritillariae cirrhosae bulbus and its adulterants based on traditional methods, although such medicines have different prices and treatment efficacies. The present study adopted DNA barcoding to identify these different species and compared the discriminatory power of super, universal, and specific barcodes in Fritillaria. The results revealed that the super-barcode had strong discriminatory power (87.5%). Among universal barcodes, matK provided the best species resolution (87.5%), followed by ITS (62.5%), rbcL (62.5%), and trnH-psbA (25%). The combination of these four universal barcodes provided the highest discriminatory power (87.5%), which was equivalent to that of the super-barcode. Two plastid genes, ycf1 and psbM-psbD, had much better discriminatory power (both 87.5%) than did other plastid barcodes, and were suggested as potential specific barcodes for identifying Fritillaria species. Phylogenetic analyses indicated that F. cirrhosa was not a "good" species that was composed of multiple lineages, which might have affected the evaluation of the discriminatory ability. This study revealed that the complete plastid genome, as super barcode, was an efficient and reliable tool for identifying the original species of Fritillariae cirrhosae bulbus and its adulterants.
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Affiliation(s)
- Qi Chen
- College of Pharmacy and Chemistry, Dali University, Dali, China
| | - Xiaobo Wu
- College of Pharmacy and Chemistry, Dali University, Dali, China
| | - Dequan Zhang
- College of Pharmacy and Chemistry, Dali University, Dali, China
- Institute of Materia Medica, Dali University, Dali, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, China
- * E-mail:
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28
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Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution. PLANTS 2020; 9:plants9020133. [PMID: 31973113 PMCID: PMC7076684 DOI: 10.3390/plants9020133] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 01/15/2023]
Abstract
Fritillaria is a genus that has important medicinal and horticultural values. The study involved the most comprehensive chloroplast genome samples referring to Old and New World clades of Fritillaria for marker selection and phylogenetic studies. We reported and compared eleven newly sequenced whole-plastome sequences of Fritillaria which proved highly similar in overall size (151,652–152,434 bp), genome structure, gene content, and order. Comparing them with other species of Liliales (6 out of 10 families) indicated the same similarity but showed some structural variations due to the contraction or expansion of the inverted repeat (IR) regions. A/T mononucleotides, palindromic, and forward repeats were the most common types. Six hypervariable regions (rps16-trnQ, rbcL-accD, accD-psaI, psaJ-rpl33, petD-rpoA, and rpl32-trnL) were discovered based on 26 Fritillaria whole-plastomes to be potential molecular markers. Based on the plastome data that were collected from 26 Fritillaria and 21 Lilium species, a phylogenomic study was carried out with three Cardiocrinum species as outgroups. Fritillaria was sister to Lilium with a high support value, and the interspecies relationships within subgenus Fritillaria were resolved very well. The six hypervariable regions can be used as candidate DNA barcodes of Fritillaria and the phylogenomic framework can guide extensive genomic sampling for further phylogenetic analyses.
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29
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Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots. PLANTS 2019; 8:plants8110476. [PMID: 31698805 PMCID: PMC6918244 DOI: 10.3390/plants8110476] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/14/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.
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Zhong Y, Wang H, Wei Q, Cao R, Zhang H, He Y, Wang L. Combining DNA Barcoding and HPLC Fingerprints to Trace Species of an Important Traditional Chinese Medicine Fritillariae Bulbus. Molecules 2019; 24:molecules24183269. [PMID: 31500338 PMCID: PMC6766824 DOI: 10.3390/molecules24183269] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/01/2019] [Accepted: 09/04/2019] [Indexed: 12/23/2022] Open
Abstract
Fritillariae Bulbus is a precious Chinese herbal medicine that is grown at high elevation and used to relieve coughs, remove phlegm, and nourish the lungs. Historically, Fritillariae Bulbus has been divided into two odourless crude drugs: Fritillariae Cirrhosae Bulbus and Fritillariae Thunbergii Bulbus. However, now the Chinese Pharmacopoeia has described five Fritillariae Bulbus—the new additions include Fritillariae Pallidiflorae Bulbus, Fritillariae Ussuriensis Bulbus, and Fritillariae Hupehensis Bulbus. Because the morphology of dried Fritillariae Bulbus is similar, it is difficult to accurately identify the different types of Fritillariae Bulbus. In the current study, we develop a method combining DNA barcoding and high-performance liquid chromatography (HPLC) to help distinguish Fritillariae Cirrhosae Bulbus from other Fritillariae Bulbus and guarantee species traceability of the five types of Fritillariae Bulbus. We report on the validation of an integrated analysis method for plant species identification using DNA barcoding that is based on genetic distance, identification efficiency, inter- and intra-specific variation, calculated nearest distance, neighbour-joining tree and barcoding gap. Our results show that the DNA barcoding data successfully identified the five Fritillariae Bulbus by internal transcribed spacer region (ITS) and ITS2, with the ability to distinguish the species origin of these Fritillariae Bulbus. ITS2 can serve as a potentially useful DNA barcode for the Fritillaria species. Additionally, the effective chemical constituents are identified by HPLC combined with a chemical identification method to classify Fritillaria. The HPLC fingerprint data and HCA (hierarchical clustering analysis) show that Fritillariae Cirrhosae Bulbus is clearly different from Fritillariae Thunbergii Bulbus and Fritillariae Hupehensis Bulbus, but there is no difference between Fritillariae Cirrhosae Bulbus, Fritillariae Ussuriensis Bulbus, and Fritillariae Pallidiflorae Bulbus. These results show that DNA barcoding and HPLC fingerprinting can discriminate between the five Fritillariae Bulbus types and trace species to identify related species that are genetically similar.
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Affiliation(s)
- Yingchun Zhong
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Haiying Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Qianhe Wei
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Rui Cao
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hailong Zhang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yongzhi He
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Lizhi Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Chen Q, Wu X, Zhang D. Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes. PeerJ 2019; 7:e7480. [PMID: 31497389 PMCID: PMC6708372 DOI: 10.7717/peerj.7480] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/15/2019] [Indexed: 01/23/2023] Open
Abstract
Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.
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Affiliation(s)
- Qi Chen
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China
| | - Xiaobo Wu
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China.,Institute of Materia Medica, Dali University, Dali, Yunnan, China
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Khan A, Asaf S, Khan AL, Khan A, Al-Harrasi A, Al-Sudairy O, AbdulKareem NM, Al-Saady N, Al-Rawahi A. Complete chloroplast genomes of medicinally important Teucrium species and comparative analyses with related species from Lamiaceae. PeerJ 2019; 7:e7260. [PMID: 31328036 PMCID: PMC6625504 DOI: 10.7717/peerj.7260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/05/2019] [Indexed: 02/05/2023] Open
Abstract
Teucrium is one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes of T. stocksianum subsp. stenophyllum R.A.King (TSS), T. stocksianum subsp. stocksianum Boiss. (TS) and T. mascatense Boiss. (TM) through next-generation sequencing and compared them with the cp genomes of related species in Lamiaceae (Ajuga reptans L., Caryopteris mongholica Bunge, Lamium album L., Lamium galeobdolon (L.) Crantz, and Stachys byzantina K.Koch). The results revealed that the TSS, TS and TM cp genomes have sizes of 150,087, 150,076 and 150,499 bp, respectively. Similarly, the large single-copy (LSC) regions of TSS, TS and TM had sizes of 81,707, 81,682 and 82,075 bp, respectively. The gene contents and orders of these genomes were similar to those of other angiosperm species. However, various differences were observed at the inverted repeat (IR) junctions, and the extent of the IR expansion into ψrps19 was 58 bp, 23 bp and 61 bp in TSS, TS and TM, respectively. Similarly, in all genomes, the pbsA gene was present in the LSC at varying distances from the JLA (IRa-LSC) junction. Furthermore, 89, 72, and 92 repeats were identified in the TSS, TM and TS cp genomes, respectively. The highest number of simple sequence repeats was found in TSS (128), followed by TS (127) and TM (121). Pairwise alignments of the TSS cp genome with related cp genomes showed a high degree of synteny. However, relatively lower sequence identity was observed when various coding regions were compared to those of related cp genomes. The average pairwise divergence among the complete cp genomes showed that TSS was more divergent from TM (0.018) than from TS (0.006). The current study provides valuable genomic insight into the genus Teucrium and its subspecies that may be applied to a more comprehensive study.
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Affiliation(s)
- Arif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Adil Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Omar Al-Sudairy
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | | | | | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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Ren F, Wang Y, Xu Z, Li Y, Xin T, Zhou J, Qi Y, Wei X, Yao H, Song J. DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae. Ecol Evol 2019; 9:1934-1945. [PMID: 30847083 PMCID: PMC6392370 DOI: 10.1002/ece3.4886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/02/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya-Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA-trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P-distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia-recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well-supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.
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Affiliation(s)
- Feng‐Ming Ren
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Chongqing Institute of Medicinal Plant Cultivation, Research and Utilization on Characteristic Biological Resources of Sichuan and Chongqing Co‐construction LabChinese Medicine Breeding and Evaluation Engineering Technology Research Center of ChongqingChongqingChina
| | - Ying‐Wei Wang
- Beijing Botanical Garden, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Zhi‐Chao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Tian‐Yi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jian‐Guo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yao‐Dong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Xue‐Ping Wei
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jing‐Yuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
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