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Wang L, Huo Z, Xu W, Zhou P, Nan W, Guo H, Zhang Q, Yang P, Alolga RN, Yin X, Li P, Lu X. Comparative plastomes of eight subgenus Chamaesyce plants and system authentication of Euphorbiae Humifusae Herba. Food Chem 2024; 447:139039. [PMID: 38518619 DOI: 10.1016/j.foodchem.2024.139039] [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: 10/06/2023] [Revised: 02/22/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024]
Abstract
Euphorbiae Humifusae Herba (EHH) was provided with medicinal and edible uses, but frequently was adulterated with its closely related species. Hence, this study sought to identify EHH via an integrated approach comprising data from its morphological evaluation, HPLC analysis, comparative plastomes analysis and allele-specific PCR identification. First, the morphological characteristics of 8 subgenus Chamaesyce plants were summarized. Then, HPLC analysis showed that 18 batches of EHH were adulterated or unqualified. Furthermore, the plastomes of the 8 subg. Chamaesyce species were analyzed. Phylogenetic analysis revealed a sister relationship among the 8 subg. Chamaesyce species. The allele-specific PCR authentication was developed by the nucleotide polymorphisms (SNPs) and insertions or deletions (InDels) analysis. The results of allele-specific PCR showed that 27 batches of EHH were adulterated, indicating that the superior sensitivity of molecular authentication over the other methods used. This study provided a reference for rational use and phylogenetic research of EHH.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Ziting Huo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Wenbo Xu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Peina Zhou
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Wenxiang Nan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Huijun Guo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Qianwen Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Raphael N Alolga
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Xiaojian Yin
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China.
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, PR China; Medical Botanical Garden, China Pharmaceutical University, Nanjing 210009, China.
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2
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Hao Z, Zhang Z, Jiang J, Pan L, Zhang J, Cui X, Li Y, Li J, Luo L. Complete mitochondrial genome of Melia azedarach L., reveals two conformations generated by the repeat sequence mediated recombination. BMC PLANT BIOLOGY 2024; 24:645. [PMID: 38972991 PMCID: PMC11229266 DOI: 10.1186/s12870-024-05319-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/21/2024] [Indexed: 07/09/2024]
Abstract
Melia azedarach is a species of enormous value of pharmaceutical industries. Although the chloroplast genome of M. azedarach has been explored, the information of mitochondrial genome (Mt genome) remains surprisingly limited. In this study, we used a hybrid assembly strategy of BGI short-reads and Nanopore long-reads to assemble the Mt genome of M. azedarach. The Mt genome of M. azedarach is characterized by two circular chromosomes with 350,142 bp and 290,387 bp in length, respectively, which encodes 35 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A pair of direct repeats (R1 and R2) were associated with genome recombination, resulting in two conformations based on the Sanger sequencing and Oxford Nanopore sequencing. Comparative analysis identified 19 homologous fragments between Mt and chloroplast genome, with the longest fragment of 12,142 bp. The phylogenetic analysis based on PCGs were consist with the latest classification of the Angiosperm Phylogeny Group. Notably, a total of 356 potential RNA editing sites were predicted based on 35 PCGs, and the editing events lead to the formation of the stop codon in the rps10 gene and the start codons in the nad4L and atp9 genes, which were verified by PCR amplification and Sanger sequencing. Taken together, the exploration of M. azedarach gap-free Mt genome provides a new insight into the evolution research and complex mitogenome architecture.
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Affiliation(s)
- Zhigang Hao
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, 572025, China
| | - Zhiping Zhang
- Department of Pesticide Science, College of Plant Protection, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Juan Jiang
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
| | - Lei Pan
- CAIQ Center for Biosafety in Sanya, Sanya, Hainan, 572000, China
| | - Jinan Zhang
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Xiufen Cui
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Yingbin Li
- Department of Pesticide Science, College of Plant Protection, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jianqiang Li
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China.
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China.
| | - Laixin Luo
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China.
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China.
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3
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Liu L, Li H, Li J, Li X, Hu N, Sun J, Zhou W. Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis. BMC PLANT BIOLOGY 2024; 24:254. [PMID: 38594633 PMCID: PMC11003120 DOI: 10.1186/s12870-024-04979-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants. RESULTS The lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica's sister species is Caragana jubata, whereas C. turkestanica's closest relative is Caragana arborescens. CONCLUSIONS The present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.
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Affiliation(s)
- LiE Liu
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - HongYan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - JiaXin Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - XinJuan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Na Hu
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Wu Zhou
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China.
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Becker A, Bachelier JB, Carrive L, Conde E Silva N, Damerval C, Del Rio C, Deveaux Y, Di Stilio VS, Gong Y, Jabbour F, Kramer EM, Nadot S, Pabón-Mora N, Wang W. A cornucopia of diversity-Ranunculales as a model lineage. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1800-1822. [PMID: 38109712 DOI: 10.1093/jxb/erad492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
The Ranunculales are a hyperdiverse lineage in many aspects of their phenotype, including growth habit, floral and leaf morphology, reproductive mode, and specialized metabolism. Many Ranunculales species, such as opium poppy and goldenseal, have a high medicinal value. In addition, the order includes a large number of commercially important ornamental plants, such as columbines and larkspurs. The phylogenetic position of the order with respect to monocots and core eudicots and the diversity within this lineage make the Ranunculales an excellent group for studying evolutionary processes by comparative studies. Lately, the phylogeny of Ranunculales was revised, and genetic and genomic resources were developed for many species, allowing comparative analyses at the molecular scale. Here, we review the literature on the resources for genetic manipulation and genome sequencing, the recent phylogeny reconstruction of this order, and its fossil record. Further, we explain their habitat range and delve into the diversity in their floral morphology, focusing on perianth organ identity, floral symmetry, occurrences of spurs and nectaries, sexual and pollination systems, and fruit and dehiscence types. The Ranunculales order offers a wealth of opportunities for scientific exploration across various disciplines and scales, to gain novel insights into plant biology for researchers and plant enthusiasts alike.
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Affiliation(s)
- Annette Becker
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Giessen, Germany
| | - Julien B Bachelier
- Institute of Biology/Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Laetitia Carrive
- Université de Rennes, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Natalia Conde E Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Cédric Del Rio
- CR2P - Centre de Recherche en Paléontologie - Paris, MNHN - Sorbonne Université - CNRS, 43 Rue Buffon, 75005 Paris, France
| | - Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190 Gif-sur-Yvette, France
| | | | - Yan Gong
- Department of Organismic and Evolutionary Biology, Harvard University, MA, 02138, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, Paris, 75005, France
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, MA, 02138, USA
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie, Systématique et Evolution, Gif-sur-Yvette, France
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China and University of Chinese Academy of Sciences, Beijing, 100049China
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Xu KL, Zhang ZM, Fang WL, Wang YD, Jin HY, Wei F, Ma SC. Comparative analyses of complete chloroplast genomes reveal interspecific difference and intraspecific variation of Tripterygium genus. FRONTIERS IN PLANT SCIENCE 2024; 14:1288943. [PMID: 38264022 PMCID: PMC10803662 DOI: 10.3389/fpls.2023.1288943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024]
Abstract
The genus Tripterygium was of great medicinal value and attracted much attention on the taxonomic study using morphological and molecular methods. In this study, we assembled 12 chloroplast genomes of Tripterygium to reveal interspecific difference and intraspecific variation. The sequence length (156,692-157,061 bp) and structure of Tripterygium were conserved. Comparative analyses presented abundant variable regions for further study. Meanwhile, we determined the ndhB gene under positive selection through adaptive evolution analysis. And the phylogenetic analyses based on 15 chloroplast genomes supported the monophyly of Tripterygium hypoglaucum and the potential sister relationship between Tripterygium wilfordii and Tripterygium regelii. Molecular dating analysis indicated that the divergence time within Tripterygium was approximately 5.99 Ma (95% HPD = 3.11-8.68 Ma). The results in our study provided new insights into the taxonomy, evolution process, and phylogenetic construction of Tripterygium using complete plastid genomes.
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Affiliation(s)
- Kai-Ling Xu
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Zhong-Mou Zhang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wen-Liang Fang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Ya-Dan Wang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Hong-Yu Jin
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Feng Wei
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Shuang-Cheng Ma
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
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6
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Chen XH, Ding LN, Zong XY, Xu H, Wang WB, Ding R, Qu B. The complete chloroplast genome sequences of four Liparis species (Orchidaceae) and phylogenetic implications. Gene 2023; 888:147760. [PMID: 37661026 DOI: 10.1016/j.gene.2023.147760] [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: 06/08/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/05/2023]
Abstract
Liparis Richard (Malaxideae, Epidendroideae) is a large and diverse genus of the family Orchidaceae, the taxonomy of which is complicated and controversial. In this study, we sequenced, assembled and analyzed four complete chloroplast genomes of Liparis species including L. kumokiri, L. makinoana, L. pauliana, and L. viridiflora, and evaluated their phylogenetic relationships with related species for the first time. These four chloroplast genomes (size range 153,095 to 158,239 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 83,533-86,752 bp), a small single copy (SSC, 17,938-18,156 bp) and a pair of inverted repeats (IRs, 26,421-26,933 bp). The genomes contain 133 genes, including 87 protein coding genes, 38 tRNAs and 8 rRNA genes. The genome arrangements, gene contents, gene order, long repeats and simple sequence repeats were similar with small differences observed among these four chloroplast genomes. Five highly variable regions including ycf1, ndhA, ndhF, trnQ and trnK were identified from the comparative analysis with other nine related Liparis species, which had the potential to be used as DNA markers for species identification and phylogenetic studies of Liparis species. Phylogenetic analysis based on the complete chloroplast genome sequences strongly supported the polyphyly of Liparis and its further division into three branches. These results provided valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the Liparis genus.
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Affiliation(s)
- Xu-Hui Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Li-Na Ding
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Xiao-Yan Zong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Hua Xu
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, PR China
| | - Wei-Bin Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Rui Ding
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China.
| | - Bo Qu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China.
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7
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Yang J, Fan S, Guo M, Xie Z, Cheng Q, Gao P, Cheng C. DNA barcoding and comparative RNA-Seq analysis provide new insights into leaf formation using a novel resource of high-yielding Epimedium koreanum. FRONTIERS IN PLANT SCIENCE 2023; 14:1290836. [PMID: 38170141 PMCID: PMC10760978 DOI: 10.3389/fpls.2023.1290836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Epimedium koreanum Nakai, a well-known traditional Chinese medicinal herb, has been widely used to treat osteoporosis and sexual dysfunction for thousands of years. However, due to the decreasing population of East Asian natural resources, yearly output of Epimedium crude herb has been in low supply year by year. In this study, an unusual variety of E. koreanum was discovered in Dunhua, Jilin Province, the northernmost area where this variety was found containing 6 individuals, with three branches that had 27 leaflets, which is much more than the typical leaflet number of 9. Firstly, the novel E. koreanum varety was identified using DNA barcodes. Then, 1171 differentially expressed genes (DEGs) were discovered through parallel RNA-seq analysis between the newly discovered variety and wild type (WT) E. koreanum plant. Furthermore, the results of bioinformatics investigation revealed that 914 positively and 619 negatively correlated genes associated with the number of leaflets. Additionally, based on RNA-Seq and qRT-PCR analysis, two homologous hub TCP genes, which were commonly implicated in plant leaf development, and shown to be up regulated and down regulated in the discovered newly variety, respectively. Thus, our study discovered a novel wild resource for leaf yield rewarding medicinal Epimedium plant breeding, provided insights into the relationship between plant compound leaf formation and gene expression of TCPs transcription factors and other gene candidates, providing bases for creating high yield cultivated Epimedium variety by using further molecular selection and breeding techniques in the future.
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Affiliation(s)
- Jiaxin Yang
- Lushan Botanical Garden, Chinese Academic of Sciences, Jiujiang, China
| | - Siqing Fan
- Lushan Botanical Garden, Chinese Academic of Sciences, Jiujiang, China
| | - Min Guo
- Lushan Botanical Garden, Chinese Academic of Sciences, Jiujiang, China
| | - Zhaoqi Xie
- Lushan Botanical Garden, Chinese Academic of Sciences, Jiujiang, China
| | - Qiqing Cheng
- Lushan Botanical Garden, Chinese Academic of Sciences, Jiujiang, China
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
| | - Puxin Gao
- Lushan Botanical Garden, Chinese Academic of Sciences, Jiujiang, China
| | - Chunsong Cheng
- Lushan Botanical Garden, Chinese Academic of Sciences, Jiujiang, China
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, China
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8
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Zhang C, Meng R, Meng Y, Guo BL, Liu QR, Nie ZL. Parallel evolution, atavism, and extensive introgression explain the radiation of Epimedium sect. Diphyllon (Berberidaceae) in southern East Asia. FRONTIERS IN PLANT SCIENCE 2023; 14:1234148. [PMID: 37915504 PMCID: PMC10616310 DOI: 10.3389/fpls.2023.1234148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
East Asia is the richest region of plant biodiversity in the northern temperate zone, and its radiation provides key insights for understanding rapid speciation, including evolutionary patterns and processes. However, it is challenging to investigate the recent evolutionary radiation among plants because of the lack of genetic divergence, phenotypic convergence, and interspecific gene flow. Epimedium sect. Diphyllon is a rarely studied plant lineage endemic to East Asia, especially highly diversified in its southern part. In this study, we report a robust phylogenomic analysis based on genotyping-by-sequencing data of this lineage. The results revealed a clear biogeographic pattern for Epimedium sect. Diphyllon with recognition into two major clades corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms of East Asian Flora and rapid diversification of the extant species dated to the Pleistocene. Evolutionary radiation of Epimedium sect. Diphyllon is characterized by recent and predominant parallel evolution and atavism between the two subkingdom regions, with extensive reticulating hybridization within each region during the course of diversification in southern East Asia. A parallel-atavism-introgression hypothesis is referred to in explaining the radiation of plant diversity in southern East Asia, which represents a potential model for the rapid diversification of plants under global climate cooling in the late Tertiary. Our study advances our understanding of the evolutionary processes of plant radiation in East Asia as well as in other biodiversity hotspot regions.
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Affiliation(s)
- Cheng Zhang
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ran Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Bao-Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quan-Ru Liu
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ze-Long Nie
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
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9
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Sun Z, Wu Y, Fan P, Guo D, Zhang S, Song C. Assembly and analysis of the mitochondrial genome of Prunella vulgaris. FRONTIERS IN PLANT SCIENCE 2023; 14:1237822. [PMID: 37600185 PMCID: PMC10433383 DOI: 10.3389/fpls.2023.1237822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Prunella vulgaris (Lamiaceae) is widely distributed in Eurasia. Former studies have demonstrated that P. vulgaris has a wide range of pharmacological effects. Nevertheless, no complete P. vulgaris mitochondrial genome has been reported, which limits further understanding of the biology of P. vulgaris. Here, we assembled the first complete mitochondrial genome of P. vulgaris using a hybrid assembly strategy based on sequencing data from both Nanopore and Illumina platforms. Then, the mitochondrial genome of P. vulgaris was analyzed comprehensively in terms of gene content, codon preference, intercellular gene transfer, phylogeny, and RNA editing. The mitochondrial genome of P. vulgaris has two circular structures. It has a total length of 297, 777 bp, a GC content of 43.92%, and 29 unique protein-coding genes (PCGs). There are 76 simple sequence repeats (SSRs) in the mitochondrial genome, of which tetrameric accounts for a large percentage (43.4%). A comparative analysis between the mitochondrial and chloroplast genomes revealed that 36 homologous fragments exist in them, with a total length of 28, 895 bp. The phylogenetic analysis showed that P. vulgaris belongs to the Lamiales family Lamiaceae and P. vulgaris is closely related to Salvia miltiorrhiza. In addition, the mitochondrial genome sequences of seven species of Lamiaceae are unconservative in their alignments and undergo frequent genome reorganization. This work reports for the first time the complete mitochondrial genome of P. vulgaris, which provides useful genetic information for further Prunella studies.
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Affiliation(s)
- Zhihao Sun
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ya Wu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Pengyu Fan
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei, China
| | - Dengli Guo
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei, China
| | - Sanyin Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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10
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Jin YB, Liang XC, Cai JH, Wang K, Wang CY, Wang WH, Chen XL, Bao S. Mechanism of action of icaritin on uterine corpus endometrial carcinoma based on network pharmacology and experimental evaluation. Front Oncol 2023; 13:1205604. [PMID: 37538114 PMCID: PMC10394632 DOI: 10.3389/fonc.2023.1205604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023] Open
Abstract
Background Uterine corpus endometrial carcinoma (UCEC) belongs to a group of epithelial malignant tumors. Icaritin is the main active compound of Epimedii Folium. Icaritin has been utilized to induce UCEC cells to death. Methods We wished to identify potential targets for icaritin in the treatment of UCEC, as well as to provide a groundwork for future studies into its pharmacologic mechanism of action. Network pharmacology was employed to conduct investigations on icaritin. Target proteins were chosen from the components of icaritin for UCEC treatment. A protein-protein interaction (PPI) network was established using overlapping genes. Analyses of enrichment of function and signaling pathways were undertaken using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, to select "hub genes". Finally, experiments were carried out to ascertain the effect of icaritin on endometrial cancer (HEC-1-A) cells. Results We demonstrated that icaritin has bioactive components and putative targets that are therapeutically important. Icaritin treatment induced sustained activation of the phosphoinositide 3-kinase/protein kinase B (PI3K/Akt pathway) and inhibited growth of HEC-1-A cells. Conclusion Our data provide a rationale for preclinical and clinical evaluations of icaritin for UCEC therapy.
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Affiliation(s)
- Yan-Bin Jin
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Xiao-Chen Liang
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Jun-Hong Cai
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Kang Wang
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Chen-Yang Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wen-Hua Wang
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Xiu-Li Chen
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
| | - Shan Bao
- Department of Gynecology and Obstetrics, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
- Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Medical Laboratory Center, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, China
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Zhou Y, Shang XH, Xiao L, Wu ZD, Cao S, Yan HB. Comparative plastomes of Pueraria montana var. lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence. BMC Genomics 2023; 24:299. [PMID: 37268915 DOI: 10.1186/s12864-023-09356-8] [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: 06/24/2022] [Accepted: 05/05/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Pueraria montana var. lobata (kudzu) is an important food and medicinal crop in Asia. However, the phylogenetic relationships between Pueraria montana var. lobata and the other two varieties (P. montana var. thomsonii and P. montana var. montana) remain debated. Although there is increasing evidence showing that P. montana var. lobata adapts to various environments and is an invasive species in America, few studies have systematically investigated the role of the phylogenetic relationships and evolutionary patterns of plastomes between P. montana var. lobata and its closely related taxa. RESULTS 26 newly sequenced chloroplast genomes of Pueraria accessions resulted in assembled plastomes with sizes ranging from 153,360 bp to 153,551 bp. Each chloroplast genome contained 130 genes, including eight rRNA genes, 37 tRNA genes, and 85 protein-coding genes. For 24 newly sequenced accessions of these three varieties of P. montana, we detected three genes and ten noncoding regions with higher nucleotide diversity (π). After incorporated publically available chloroplast genomes of Pueraria and other legumes, 47 chloroplast genomes were used to construct phylogenetic trees, including seven P. montana var. lobata, 14 P. montana var. thomsonii and six P. montana var. montana. Phylogenetic analysis revealed that P. montana var. lobata and P. montana var. thomsonii formed a clade, while all sampled P. montana var. montana formed another cluster based on cp genomes, LSC, SSC and protein-coding genes. Twenty-six amino acid residues were identified under positive selection with the site model. We also detected six genes (accD, ndhB, ndhC, rpl2, rpoC2, and rps2) that account for among-site variation in selective constraint under the clade model between accessions of the Pueraria montana var. lobata clade and the Pueraria montana var. montana clade. CONCLUSION Our data provide novel comparative plastid genomic insights into conservative gene content and structure of cp genomes pertaining to P. montana var. lobata and the other two varieties, and reveal an important phylogenetic clue and plastid divergence among related taxa of P. montana come from loci that own moderate variation and underwent modest selection.
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Affiliation(s)
- Yun Zhou
- College of Pharmacy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xiao-Hong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Zheng-Dan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Hua-Bing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
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Jiang Y, Zhu C, Wang S, Wang F, Sun Z. Identification of three cultivated varieties of Scutellaria baicalensis using the complete chloroplast genome as a super-barcode. Sci Rep 2023; 13:5602. [PMID: 37019975 PMCID: PMC10075158 DOI: 10.1038/s41598-023-32493-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
Scutellaria baicalensis has been one of the most commonly used traditional Chinese medicinal plants in China for more than 2000 years. The three new varieties cultivated could not be distinguished by morphology before flowering. It will hinder the promotion of later varieties. Chloroplast DNA has been widely used in species identification. Moreover, previous studies have shown that complete chloroplast genome sequences have been suggested as super barcodes for identifying plants. Therefore, we sequenced and annotated the complete chloroplast genomes of three cultivated varieties. The chloroplast genomes of SBW, SBR, and SBP were 151,702 bp, 151,799 bp, and 151,876 bp, which contained 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The analysis of the repeat sequences, codon usage, and comparison of chloroplast genomes shared a high degree of conservation. However, the sliding window results show significant differences among the three cultivated varieties in matK-rps16 and petA-psbJ. And we found that the matK-rps16 sequence can be used as a barcode for the identification of three varieties. In addition, the complete chloroplast genome contains more variations and can be used as a super-barcode to identify these three cultivated varieties. Based on the protein-coding genes, the phylogenetic tree demonstrated that SBP was more closely related to SBW, in the three cultivated varieties. Interestingly, we found that S. baicalensis and S. rehderiana are closely related, which provides new ideas for the development of S. baicalensis. The divergence time analysis showed that the three cultivated varieties diverged at about 0.10 Mya. Overall, this study showed that the complete chloroplast genome could be used as a super-barcode to identify three cultivated varieties of S. baicalensis and provide biological information, and it also contributes to bioprospecting.
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Affiliation(s)
- Yuan Jiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chenghao Zhu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shangtao Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Fusheng Wang
- Dingxi Academy of Agricultural Sciences, Dingxi, China.
| | - Zhirong Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
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Wang C, Tian S, Tang Q, Zhou Z, Peng X, Cai X, Xu Y. Systematic Quality Evaluation of Epimedium wushanense T. S. Ying Based on Two Quality Control Standards: Total Flavonoid Glycosides and Epimedin C. Chem Biodivers 2023; 20:e202200579. [PMID: 36740574 DOI: 10.1002/cbdv.202200579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/28/2023] [Accepted: 02/03/2023] [Indexed: 02/07/2023]
Abstract
Two quality control standards, total flavonoid glycosides of Epimedii Folium and epimedin C of Epimedii Wushanensis Folium, were used to systematically evaluate the quality of Epimedium wushanense T. S. Ying, so as to provide reference for its germplasm screening and resource utilization. Seven representative populations of E. wushanense covering its main distribution areas were uniformly sampled during the flowering period. There were significant quality differences among the populations of E. wushanense. According to the quality standard of total flavonoid glycosides, all populations were superior to the quality standard of the Chinese Pharmacopoeia for Epimedii Folium, with more than 1.5 % total flavonoid glycosides. The variation ranges of epimedin A, epimedin B, epimedin C, icariin and total flavonoid glycosides were 0.40-0.76 %, 0.51-0.83 %, 1.70-9.31 %, 0.40-1.23 % and 3.05-10.61 %, respectively. According to the quality standard of epimedin C, all populations were better than the quality standard of the Chinese Pharmacopoeia for Epimedii Wushanensis Folium, with more than 1.0 % epimedin C. The variation range of epimedin C was 2.22-10.06 %. When comparing the results of the two methods, a trend of slightly lower mean values was found for total flavonoid glycosides, except for the HBXW population. The quality of E. wushanense was superior to both the quality standard of Epimedii Folium and Epimedii Wushanense Folium in the Chinese Pharmacopoeia. Epimedin C was the most abundant component. Among the investigated populations, HBXW and HBGK exhibited the highest quality, and may provide excellent genetic resources for standardized cultivation. In addition, the habitat of these populations can also serve a reference for cultivation conditions.
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Affiliation(s)
- Congying Wang
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Shuyun Tian
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Qin Tang
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Ziwei Zhou
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Xinheng Peng
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Xiaoxue Cai
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Yanqin Xu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
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Mao J, Liang Y, Wang X, Zhang D. Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization. BMC PLANT BIOLOGY 2023; 23:101. [PMID: 36800941 PMCID: PMC9940437 DOI: 10.1186/s12870-023-04088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with medicinal values. Gentiana cephalantha Franchet is a sister species to G. rigescens possessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences. RESULTS The plastid genomes were highly similar between G. rigescens and G. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp in G. rigescens and from 146,856 to 147,016 bp in G. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed that G. rigescens and G. cephalantha formed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports that G. rigescens and G. cephalantha are closely related, but independent species. However, hybridization was confirmed to occur frequently between G. rigescens and G. cephalantha in sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction of G. rigescens. CONCLUSION G. rigescens and G. cephalantha are recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species, G. rigescens faces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.
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Affiliation(s)
- Jiuyang Mao
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Yuze Liang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China.
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali, 671000, Yunnan, China.
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Bai X, Wang G, Ren Y, Su Y, Han J. Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome. FRONTIERS IN PLANT SCIENCE 2023; 14:1119041. [PMID: 36860895 PMCID: PMC9969298 DOI: 10.3389/fpls.2023.1119041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION The Aristolochia, as an important genus comprised of over 400 species, has attracted much interest because of its unique chemical and pharmacological properties. However, the intrageneric taxonomy and species identification within Aristolochia have long been difficult because of the complexity of their morphological variations and lack of high-resolution molecular markers. METHODS In this study, we sampled 11 species of Aristolochia collected from distinct habitats in China, and sequenced their complete chloroplast (cp) genomes. RESULTS The 11 cp genomes of Aristolochia ranged in size from 159,375bp (A. tagala) to 160,626 bp (A. tubiflora), each containing a large single-copy (LSC) region (88,914-90,251 bp), a small single-copy (SSC) region (19,311-19,917 bp), and a pair of inverted repeats (IR) (25,175-25,698 bp). These cp genomes contained 130-131 genes each, including 85 protein-coding genes (CDS), 8 ribosomal RNA genes, and 37-38 transfer RNA genes. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in Aristolochia species. A. littoralis had the highest number of repeats (168), while A. tagala had the lowest number (42). The total number of simple sequence repeats (SSRs) is at least 99 in A. kwangsiensis, and, at most, 161 in A. gigantea. Interestingly, we detected eleven highly mutational hotspot regions, including six gene regions (clpP, matK, ndhF, psbT, rps16, trnK-UUU) and five intergenic spacer regions (ccsA-ndhD, psbZ-trnG-GCC, rpl33-rps18, rps16-trnQ-UUG, trnS-GCU-trnG-UCC). The phylogenetic analysis based on the 72 protein-coding genes showed that 11 Aristolochia species were divided into two clades which strongly supported the generic segregates of the subgenus Aristolochia and Siphisia. DISCUSSION This research will provide the basis for the classification, identification, and phylogeny of medicinal plants of Aristolochiaceae.
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Jiang J, Ji Y, Li J, Zhang Y. Epimediumlongnanense (Berberidaceae), a new species from Gansu, China. PHYTOKEYS 2023; 219:97-106. [PMID: 37252453 PMCID: PMC10209716 DOI: 10.3897/phytokeys.219.94275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/27/2022] [Indexed: 05/31/2023]
Abstract
Epimediumlongnanense, a new species of Epimedium (Berberidaceae) from Longnan Prefecture, Gansu Province, China, is here proposed and illustrated. E.longnanense has large flowers with petals possessing long spur and obvious basal lamina, and thus should be grouped into series Davidianae. The species closely resembles E.flavum of ser. Davidianae in morphology. However, it can be easily distinguished by its elongated rhizome (vs. compact), trifoliolate leaves (vs. five leaflets, sometimes trifoliolate), pale pink or purplish-red inner sepals with 6-8 × 2-3 mm (vs. pale sulphur-yellow, ca. 11 × 4 mm).
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Affiliation(s)
- Jianhang Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaWuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
| | - Ying Ji
- Shangzhi Nature Studio of Shaanxi Tianyuan Chinese Herbal Medicine Development Co., Ltd., Mei County, Shaanxi Province, ChinaShangzhi Nature Studio of Shaanxi Tianyuan Chinese Herbal Medicine Development Co., Ltd.MeixianChina
| | - Jianqiang Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaWuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
| | - Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, ChinaWuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
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Yang Z, Ma W, Yang X, Wang L, Zhao T, Liang L, Wang G, Ma Q. Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales). BMC PLANT BIOLOGY 2022; 22:611. [PMID: 36566190 PMCID: PMC9789603 DOI: 10.1186/s12870-022-03991-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae. RESULTS All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (Pi > 0.02) and five noncoding regions (Pi > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution. CONCLUSIONS Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.
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Affiliation(s)
- Zhen Yang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Wenxu Ma
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Forest Botany and Tree Physiology, University of Goettingen, 37077, Goettingen, Germany
| | | | - Lujun Wang
- Anhui Academy of Forestry, Hefei, 230031, China
| | - Tiantian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Lisong Liang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Guixi Wang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Qinghua Ma
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China.
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China.
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China.
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Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences. Int J Mol Sci 2022; 23:ijms232012567. [PMID: 36293423 PMCID: PMC9604191 DOI: 10.3390/ijms232012567] [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: 09/23/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our daily lives, its genome information and phylogenetic relationships remain elusive. Thus, we performed the assembly and annotation of chloroplast genomes for 12 individuals from seven Dianthus species. On this basis, we carried out the first comprehensive and systematic analysis of the chloroplast genome sequence characteristics and the phylogenetic evolution of Dianthus. The chloroplast genome of 12 Dianthus individuals ranged from 149,192 bp to 149,800 bp, containing 124 to 126 functional genes. Sequence repetition analysis showed the number of simple sequence repeats (SSRs) ranged from 75 to 80, tandem repeats ranged from 23 to 41, and pair-dispersed repeats ranged from 28 to 43. Next, we calculated the synonymous nucleotide substitution rates (Ks) of all 76 protein coding genes to obtain the evolution rate of these coding genes in Dianthus species; rpl22 showed the highest Ks (0.0471), which suggested that it evolved the swiftest. By reconstructing the phylogenetic relationships within Dianthus and other species of Caryophyllales, 16 Dianthus individuals (12 individuals reported in this study and four individuals downloaded from NCBI) were divided into two strongly supported sister clades (Clade A and Clade B). The Clade A contained five species, namely D. caryophyllus, D. barbatus, D. gratianopolitanus, and two cultivars (‘HY’ and ‘WC’). The Clade B included four species, in which D. superbus was a sister branch with D. chinensis, D. longicalyx, and F1 ‘87M’ (the hybrid offspring F1 from D. chinensis and ‘HY’). Further, based on sequence divergence analysis and hypervariable region analysis, we selected several regions that had more divergent sequences, to develop DNA markers. Additionally, we found that one DNA marker can be used to differentiate Clade A and Clade B in Dianthus. Taken together, our results provide useful information for our understanding of Dianthus classification and chloroplast genome evolution.
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Wang J, Huang R, Liang Q, Zhang Y. The complete chloroplast genome of Epimedium muhuangense (Berberidaceae). Mitochondrial DNA B Resour 2022; 7:870-872. [PMID: 35602330 PMCID: PMC9116252 DOI: 10.1080/23802359.2022.2071650] [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: 10/14/2021] [Accepted: 01/27/2022] [Indexed: 10/29/2022] Open
Abstract
Epimedium muhuangense S. Z. He & Y. Y. Wang 2017, one of the rare unifoliolate species in the Epimedium genus of Berberidaceae, is distributed in the Guizhou province of China. In present research, we sequenced the complete chloroplast genome of E. muhuangense with Illumina sequencing technology. The whole genome was 157,264 bp in length, which consisted of a large single-copy region (LSC, 88,588 bp), a small single-copy region (SSC, 17,036 bp), and a pair of inverted repeat regions (IRa and IRb, 25,820 bp). A total of 112 unique genes were successfully annotated, consisting of 78 protein-encoding genes, 30 rRNA, and four tRNA. Phylogenetic analysis demonstrated that E. muhuangense is closely related to E. elachyphyllum.
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Affiliation(s)
- Jing Wang
- Department of Botany, College of Forestry, Jiangxi Agricultural University, Nanchang, People’s Republic of China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Ruoqi Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Department of Bioengineering, School of Life Sciences, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People’s Republic of China
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Tian S, Tang Q, Zhou Z, Li F, Peng X, Xu Y, Huang H. The complete chloroplast genome sequences of two ornamental Epimedium species (Berberidaceae). Mitochondrial DNA B Resour 2022; 7:878-880. [PMID: 35692709 PMCID: PMC9176344 DOI: 10.1080/23802359.2022.2077148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Shuyun Tian
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Qin Tang
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Ziwei Zhou
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Fengqin Li
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Xinheng Peng
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yanqin Xu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Hua Huang
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China
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Xu Y, Fu L, Huang X, Li F, Wang C, Hu S. The complete chloroplast genome of Epimedium jinchengshanense Y. J. Zhang & J. Q. Li (Berberidaceae), an ornamental and medicinal species. Mitochondrial DNA B Resour 2022; 7:428-430. [PMID: 35252577 PMCID: PMC8890517 DOI: 10.1080/23802359.2022.2044402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Epimedium jinchengshanense Y. J. Zhang & J. Q. Li 2014 is an important ornamental and medicinal herb, but of unclear taxonomy. In this study, the complete chloroplast genome of E. jinchengshanense was sequenced. The genome was 157,169 bp in length, with a large single-copy region of 88, 520 bp, a small single-copy region of 17,075 bp and 2 inverted repeat regions of 25, 787 bp. The genome consisted of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The GC contents were 38.78%. Phylogenetic analysis showed a close relationship between E. jinchengshanense and E. ilicifolium, which was explained by the morphological similarity of flowers and leaves of the two species.
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Affiliation(s)
- Yanqin Xu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, People’s Republic of China
| | - Limei Fu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, People’s Republic of China
| | - Xiaofang Huang
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, People’s Republic of China
| | - Fengqin Li
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, People’s Republic of China
| | - Congying Wang
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, People’s Republic of China
| | - Shengfu Hu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, People’s Republic of China
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Liu X, Zhang Y, Zhang C, Xu C, Qin W, Shen G, Guo B. The complete chloroplast genome of Epimedium platypetalum K. Mey. (Berberidaceae), a rare plant species from China. Mitochondrial DNA B Resour 2021; 6:3292-3294. [PMID: 34712815 PMCID: PMC8547863 DOI: 10.1080/23802359.2021.1974968] [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: 07/27/2021] [Accepted: 08/26/2021] [Indexed: 11/26/2022] Open
Abstract
Epimedium L. is an important medicinal herbaceous genus in the family Berberidaceae. Epimedium platypetalum K. Mey. is a plant species only narrowly distributed in the western part of China. Here, the complete chloroplast genome of Epimedium platypetalum was assembled. The chloroplast genome of E. platypetalum was 159,088 bp in length, with a total GC content of 38.79%. A total of 112 unique genes were identified, among which 78 are protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic results revealed that E. platypetalum formed a sister relationship with E. membranaceum K. Mey. Our findings provided valuable data for future research on phylogenetic relationship and germplasm exploration within the genus Epimedium.
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Affiliation(s)
- Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Yixin Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Weihan Qin
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
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