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Wang X, Guo L, Ding L, Medina L, Wang R, Li P. Comparative plastome analyses and evolutionary relationships of 25 East Asian species within the medicinal plant genus Scrophularia (Scrophulariaceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1439206. [PMID: 39301164 PMCID: PMC11411265 DOI: 10.3389/fpls.2024.1439206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/19/2024] [Indexed: 09/22/2024]
Abstract
Backgroud Scrophularia L., a genus of the Scrophulariaceae, is a group of important medicinal plants used for eliminating heat and detoxifying. East Asia has an abundance of potentially medicinal Scrophularia species, and it serves as a secondary diversity center of the genus. However, the genomic resources available for germplasm identification and pharmaceutical exploration of East Asian Scrophularia are insufficient, hindering its commercial and industrial development. Additionally, the interspecific relationships of most East Asian Scrophularia species remain unclear. Methods In this study, we sequenced the leaves of 25 East Asian species of the genus Scrophularia, assembled and annotated the complete chloroplast genomes, and subsequently performed comparative and phylogenetic analyses on these genomes. Results and discussion The conserved plastome length of these 25 species ranged from 151,582 bp to 153,239 bp, containing a total of 132 coding genes, including 18 duplicated genes and 114 unique genes. Through genome alignment of these 25 species, 38-53 repeated sequences and 7 shared SSRs were identified, along with regions with high nucleotide polymorphism (Pi), which could potentially serve as molecular markers for species identification. The genome structure, gene content, and arrangement showed conservation, while variations were observed in the IR boundary regions and IGS. Phylogenetic inferences based on whole plastomes or on coding sequences (CDS) only yielded congruent results. We categorized the 25 East Asian Scrophularia species into six distinct clades and further explored their interspecies relationships using morphological characteristics, such as flower color, the relative position of stamens and corolla, and plant height. This could lay a genetic basis for future resource development of Scrophularia in East Asia.
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Affiliation(s)
- Xia Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lei Guo
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lulu Ding
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Leopoldo Medina
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ruihong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Pan Li
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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Ahmed SS, Rahman MO. Deciphering the complete chloroplast genome sequence of Meconopsis torquata Prain: Insights into genome structure, comparative analysis and phylogenetic relationship. Heliyon 2024; 10:e36204. [PMID: 39224270 PMCID: PMC11367419 DOI: 10.1016/j.heliyon.2024.e36204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/22/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
In the present study, we have characterized the complete chloroplast (Cp) genome of Meconopsis torquata Prain (family Papaveraceae), revealing the plastome size of 153,290 bp, and a GC content of 38.72 %. The cp genome features the typical circular quadripartite structure found in flowering plants, including a pair of inverted repeat regions (25,816 bp), isolated by a small single-copy region (17,740 bp) and a large single-copy (83,918 bp). Genome annotation revealed 132 genes: 87 protein-coding genes, 37 tRNAs and eight rRNAs. This comparative study demonstrated that the genome structure, gene number and GC ratio are consistent with several other cp genomes of Meconopsis and Papaver genera. A total of 120 SSRs were detected in the plastome, the majority (111) of which were mononucleotide repeats. Among the longer repeats, palindromic sequences were most common, followed by forward, reverse, and complement repeats. The whole genome alignment revealed the conserved nature of the inverted repeat region over single-copy zones. Nucleotide diversity unveiled hypervariable sites (ycf1, rps16, accD, atpB and psbD) in both the small and large single-copy regions, which could be useful for designing molecular markers for taxonomic identification. Phylogenetic analysis revealed a close alliance of M. torquata with other Meconopsis species, such as M. pinnatifolia and M. paniculata, with strong bootstrap support. Molecular dating suggests that M. torquata originated during the Tortonian age of the Miocene epoch of the Cenozoic era. These findings provide valuable insights for biological research, especially in understanding the genetic and evolutionary divergence within the Papaveraceae family.
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Affiliation(s)
- Sheikh Sunzid Ahmed
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
| | - M. Oliur Rahman
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
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Li S, Tian C, Hu H, Yang Y, Ma H, Liu Q, Liu L, Li Z, Wu Z. Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species. Genes (Basel) 2024; 15:815. [PMID: 38927750 PMCID: PMC11202509 DOI: 10.3390/genes15060815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Bromus (Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced Bromus ciliatus, Bromus benekenii, Bromus riparius, and Bromus rubens chloroplast genomes and compared them with four previously described species. The genome sizes of Bromus species ranged from 136,934 bp (Bromus vulgaris) to 137,189 bp (Bromus ciliates, Bromus biebersteinii), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that Bromus is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of Bromus provides a scientific basis for species identification and phylogenetic studies.
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Affiliation(s)
- Shichao Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunyu Tian
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Haihong Hu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Yanting Yang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Huiling Ma
- Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China
| | - Qian Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Lemeng Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China; (S.L.)
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Xu ZL, Li BC, Huang LL, Lv LX, Luo Y, Xu WF, Yang RY. Two new cytochalasins from the endophytic fungus Xylaria sp. GDGJ-77B. Nat Prod Res 2024; 38:1503-1509. [PMID: 36469678 DOI: 10.1080/14786419.2022.2153362] [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: 09/23/2022] [Revised: 11/17/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022]
Abstract
Two new open-chain cytochalasins, xylarchalasins A and B (1 and 2), together with six known analogues (3-8), were isolated from the endophytic fungus Xylaria sp. GDGJ-77B from the Chinese medicinal plant Sophora tonkinensis. Their structures were elucidated on the basis of comprehensive spectroscopic analysis. Compound 2 displayed moderate antibacterial activities against Bacillus subtilis and Escherichia coli with MIC values of 25 and 12.5 μg/mL, respectively.
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Affiliation(s)
- Zhao-Long Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, P. R. China
- Guangxi Research Institute of Chemical Industry Co., Ltd., Nanning, P. R. China
| | - Ben-Chao Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, P. R. China
| | - Li-Li Huang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, P. R. China
| | - Liu-Xia Lv
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, P. R. China
| | - Yan Luo
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China
| | - Wei-Feng Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, P. R. China
| | - Rui-Yun Yang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, P. R. China
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Li BC, Lv LX, Huang LL, Zhou JT, Huang XS, Li J, Yang RY, Xu WF. Cycloaspeptide H, a cyclopentapeptide from the endophytic fungus Penicillium virgatum. Nat Prod Res 2024; 38:486-492. [PMID: 36190784 DOI: 10.1080/14786419.2022.2128346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/17/2022] [Indexed: 10/10/2022]
Abstract
One new cyclopentapeptide, cycloaspeptide H (1), featuring a serine residue, along with seven known compounds (2-8), was isolated from the endophytic fungus Penicillium virgatum GDGJ-227. The planar structure of 1 was elucidated by a comprehensive analysis of NMR and MS spectroscopic spectra, and the absolute configuration was determined by single-crystal X-ray diffraction (Cu Kα) analysis. Compounds 7 and 8 displayed antibacterial activities against Bacillus subtilis and Enterobacter aerogenes with MIC values ranging from 12.5 to 50 μg/mL.
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Affiliation(s)
- Ben-Chao Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P. R. China
- Guangxi Marine Environmental Monitoring Centre, Beihai, P. R. China
| | - Liu-Xia Lv
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P. R. China
| | - Li-Li Huang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P. R. China
| | - Jia-Tong Zhou
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P. R. China
| | - Xi-Shan Huang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P. R. China
| | - Jun Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P. R. China
| | - Rui-Yun Yang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P. R. China
| | - Wei-Feng Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P. R. China
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6
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Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [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: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
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Wen H, Su Y, Xie A, Lin C, Wei W. Characteristics and phylogenetic analysis of the complete chloroplast genome of Primulina hedyotidea. Mitochondrial DNA B Resour 2023; 8:1007-1011. [PMID: 37753244 PMCID: PMC10519256 DOI: 10.1080/23802359.2023.2238932] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/15/2023] [Indexed: 09/28/2023] Open
Abstract
Primulina hedyotidea (Woon Young Chun) Yin Zheng Wang 2011 is an important medicinal plant that has a long history of medicinal use in China. In this experiment, the whole chloroplast genome of P. hedyotidea was determined by next-generation sequencing technology. The total base length of P. hedyotidea was 153,297 bp, the GC content was 37.62%, the inverted repeat (IR) region length was 25,494 bp, the large single copy (LSC) region was 84,158 bp and the small single copy (SSC) region was 18,151 bp. In addition, the genome consisted of 80 protein-coding genes, 4 rRNA genes, and 28 tRNA genes, for a total of 112 genes. A phylogenetic tree was constructed to explore the evolutionary relationship between P. hedyotidea and other species. The findings of phylogenetic tree analysis show that Primulina huaijiensis and P. hedyotidea have a close relationship, and this study can help with species identification and phylogenetic analysis within Primulina and Gesneriaceae species.
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Affiliation(s)
- Haicheng Wen
- Guangxi University of Chinese Medicine, Guangxi, P.R. China
| | - Yongjing Su
- Guangxi University of Chinese Medicine, Guangxi, P.R. China
| | - Ao Xie
- Guangxi University of Chinese Medicine, Guangxi, P.R. China
| | - Chen Lin
- Guangxi University of Chinese Medicine, Guangxi, P.R. China
| | - Wei Wei
- Guangxi University of Chinese Medicine, Guangxi, P.R. China
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Kakkar RA, Haneen MA, Parida AC, Sharma G. The known, unknown, and the intriguing about members of a critically endangered traditional medicinal plant genus Aconitum. FRONTIERS IN PLANT SCIENCE 2023; 14:1139215. [PMID: 37575934 PMCID: PMC10421671 DOI: 10.3389/fpls.2023.1139215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/03/2023] [Indexed: 08/15/2023]
Abstract
Humanity will always be indebted to plants. In the ongoing scientific era, the 'Herbal Revolution' has helped discover several valuable medicinal plants and associated novel secondary metabolites from the diverse unexplored ecosystems, treating several diseases via phytotherapy. The Aconitum genus comprises several economically-important poisonous mountainous medicinal plant species whose unique biodiversity is on the verge of extinction due to illegal human intervention triggered habitat loss, over-harvesting, and unrestricted trading. Owing to its vast diversity of diterpene alkaloids, most species are extensively used to treat several ailments in rural parts of the world. Irrespective of this, many unexplored and intriguing prospects exist to understand and utilize this critical plant for human benefit. This systematic review tries to fill this gap by compiling information from the sporadically available literature known for ~300 Aconitum spp. regarding its nomenclature and classification, endangerment, plant morphology, ploidy, secondary metabolites, drug pharmacokinetics, conservation, and omics-based computational studies. We also depicted the disparity in the studied model organisms for this diverse genus. The absence of genomic/metagenomic data is becoming a limiting factor in understanding its plant physiology, metabolic pathways, and plant-microbes interactions, and therefore must be promoted. Additionally, government support and public participation are crucial in establishing conservation protocols to save this plant from endangerment.
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Affiliation(s)
- Richa Ashok Kakkar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Mariam Azeezuddin Haneen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | | | - Gaurav Sharma
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
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Niu T, Tian C, Yang Y, Liu Q, Liu L, Tao Q, Li Z, Wu Z. Complete Chloroplast Genome of Corethrodendron fruticosum (Papilionoideae: Fabaceae): Comparative and Phylogenetic Analysis. Genes (Basel) 2023; 14:1289. [PMID: 37372469 DOI: 10.3390/genes14061289] [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: 05/25/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Corethrodendron fruticosum is an endemic forage grasses in China with high ecological value. In this study, the complete chloroplast genome of C. fruticosum was sequenced using Illumina paired-end sequencing. The C. fruticosum chloroplast genome was 123,100 bp and comprised 105 genes, including 74 protein-coding genes, 4 rRNA-coding genes, and 27 tRNA-coding genes. The genome had a GC content of 34.53%, with 50 repetitive sequences and 63 simple repeat repetitive sequences that did not contain reverse repeats. The simple repeats included 45 single-nucleotide repeats, which accounted for the highest proportion and primarily comprised A/T repeats. A comparative analysis of C. fruticosum, C. multijugum, and four Hedysarum species revealed that the six genomes were highly conserved, with differentials primarily located in the conserved non-coding regions. Moreover, the accD and clpP genes in the coding regions exhibited high nucleotide variability. Accordingly, these genes may serve as molecular markers for the classification and phylogenetic analysis of Corethrodendron species. Phylogenetic analysis further revealed that C. fruticosum and C. multijugum appeared in different clades than the four Hedysarum species. The newly sequenced chloroplast genome provides further insights into the phylogenetic position of C. fruticosum, which is useful for the classification and identification of Corethrodendron.
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Affiliation(s)
- Tianxiu Niu
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China
| | - Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Yanting Yang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Qian Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Lemeng Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Qibo Tao
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot 010010, China
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An K, Zhou C, Feng L, Zhang Q, Pang Y, Li L, Bian F. Complete chloroplast genome and phylogenetic analysis of Anemone shikokiana. Mol Biol Rep 2023; 50:2095-2105. [PMID: 36542234 DOI: 10.1007/s11033-022-08204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Anemone shikokiana (Makino) Makino, disjunctly distributed in Shandong Peninsula of China and Shikoku Island of Japan, is a rare and endangered species. To provide genetic information and understand its phylogeny, we conducted research on the chloroplast (cp) genome of A. shikokiana. METHODS AND RESULTS The complete cp genome sequence of A. shikokiana was constructed in this study. The results showed that the cp genome of A. shikokiana has a typical quadripartite cyclic with a total length of 159,286 bp. In total, 111 unique genes were identified, including 78 protein-coding genes, 29 tRNA-coding genes and 4 rRNA-coding genes. A total of 37 long repeat sequences and 67 microsatellites were found in this cp genome. The cp genome of A. shikokiana was compared with eleven other Anemone cp genomes available from the Genbank database. We found some variations among the different genomes, especially in the LSC and SSC regions, and identified some regions as potential molecular markers such as ycf1, ndhE, ndhD, ndhF-trnL, ndhA and ndhF. The results of phylogenetic analysis suggested that A. narcissiflora was the closest relative of A. shikokiana. CONCLUSIONS The results filled the gap of cp genome sequence information of A. shikokiana, laying the foundation to explore the evolutionary relationships of A. shikokiana in future studies. It provided a valuable genetic resource for the molecular identification and phylogenetic study of Anemone.
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Affiliation(s)
- Kang An
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Chunxia Zhou
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Lei Feng
- Kunyu Mountain Forest Farm, Yantai, 264000, China
| | - Qing Zhang
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Yujuan Pang
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Lixia Li
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Fuhua Bian
- School of Life Sciences, Yantai University, Yantai, 264000, China.
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Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, Chen G, Ng WL, Islam MN, Punnarak P, Zheng H, Zhu X. A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea. FRONTIERS IN PLANT SCIENCE 2023; 13:1075353. [PMID: 36684775 PMCID: PMC9845719 DOI: 10.3389/fpls.2022.1075353] [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: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
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Affiliation(s)
- Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuchen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qianying Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Luzhen Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Md Nazrul Islam
- Forestry and Wood Technology Discipline, Khulna University, Khulna, Bangladesh
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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12
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Li X, Zhang Q, Weng G, Zhu M, Wang X. Analysis and characterization of the chloroplast genome of Stephania cepharantha Hayata. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2100719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Xinran Li
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| | - Qingyan Zhang
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| | - Guiying Weng
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| | - Miao Zhu
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| | - Xuying Wang
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
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13
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Yun S, Kim SC. Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae). BMC PLANT BIOLOGY 2022; 22:550. [PMID: 36443690 PMCID: PMC9706989 DOI: 10.1186/s12870-022-03946-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Saussurea is one of the most species-rich genera in the Cardueae, Asteraceae. There are approximately 40 Saussurea species distributed in Korea, with nearly 40% of them endemics. Infrageneric relationships remain uncertain due to insufficient resolutions and low statistical support. In this study, we sequenced the plastid genomes of five Korean endemic Saussurea (S. albifolia, S. calcicola, S. diamantica, S. grandicapitula, and S. seoulensis), and comparative analyses including two other endemics (S. chabyoungsanica and S. polylepis) were conducted. RESULTS The plastomes of Korean endemics were highly conserved in gene content, order, and numbers. Exceptionally, S. diamantica had mitochondrial DNA sequences including two tRNAs in SSC region. There were no significant differences of the type and numbers of SSRs among the seven Korean endemics except in S. seoulensis. Nine mutation hotspots with high nucleotide diversity value (Pi > 0.0033) were identified, and phylogenetic analysis suggested that those Korean endemic species most likely evolved several times from diverse lineages within the genus. Moreover, molecular dating estimated that the Korean endemic species diverged since the late Miocene. CONCLUSIONS This study provides insight into understanding the plastome evolution and evolutionary relationships of highly complex species of Saussurea in Korean peninsula.
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Affiliation(s)
- Seona Yun
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Korea
- Present Address: Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, One Forestry Drive, Syracuse, NY, 13210, USA
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Korea.
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14
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Huang S, Kang Z, Chen Z, Deng Y. Comparative Analysis of the Chloroplast Genome of Cardamine hupingshanensis and Phylogenetic Study of Cardamine. Genes (Basel) 2022; 13:2116. [PMID: 36421792 PMCID: PMC9690686 DOI: 10.3390/genes13112116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 05/04/2024] Open
Abstract
Cardamine hupingshanensis (K. M. Liu, L. B. Chen, H. F. Bai and L. H. Liu) is a perennial herbal species endemic to China with narrow distribution. It is known as an important plant for investigating the metabolism of selenium in plants because of its ability to accumulate selenium. However, the phylogenetic position of this particular species in Cardamine remains unclear. In this study, we reported the chloroplast genome (cp genome) for the species C. hupingshanensis and analyzed its position within Cardamine. The cp genome of C. hupingshanensis is 155,226 bp in length and exhibits a typical quadripartite structure: one large single copy region (LSC, 84,287 bp), one small single copy region (17,943 bp) and a pair of inverted repeat regions (IRs, 26,498 bp). Guanine-Cytosine (GC) content makes up 36.3% of the total content. The cp genome contains 111 unique genes, including 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. A total of 115 simple sequences repeats (SSRs) and 49 long repeats were identified in the genome. Comparative analyses among 17 Cardamine species identified the five most variable regions (trnH-GUG-psbA, ndhK-ndhC, trnW-CCA-trnP-UGG, rps11-rpl36 and rpl32-trnL-UAG), which could be used as molecular markers for the classification and phylogenetic analyses of various Cardamine species. Phylogenetic analyses based on 79 protein coding genes revealed that the species C. hupingshanensis is more closely related to the species C. circaeoides. This relationship is supported by their shared morphological characteristics.
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Affiliation(s)
- Sunan Huang
- Key Laboratory of Plant Resources Conservation & Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zujie Kang
- Management Bureau of Hunan Hupingshan National Nature Reserve, Shimen 415300, China
| | - Zhenfa Chen
- Management Bureau of Hunan Hupingshan National Nature Reserve, Shimen 415300, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation & Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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15
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Cai H, Gu X, Li Y, Ren Y, Yan S, Yang M. Cold Resistance of Euonymus japonicus Beihaidao Leaves and Its Chloroplast Genome Structure and Comparison with Celastraceae Species. PLANTS 2022; 11:plants11192449. [PMID: 36235317 PMCID: PMC9573587 DOI: 10.3390/plants11192449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022]
Abstract
Euonymus japonicus Beihaidao is one of the most economically important ornamental species of the Euonymus genus. There are approximately 97 genera and 1194 species of plants worldwide in this family (Celastraceae). Using E. japonicus Beihaidao, we conducted a preliminary study of the cold resistance of this species, evaluated its performance during winter, assembled and annotated its chloroplast genome, and performed a series of analyses to investigate its gene structure GC content, sequence alignment, and nucleic acid diversity. Our objectives were to understand the evolutionary relationships of the genus and to identify positive selection genes that may be related to adaptations to environmental change. The results indicated that E. japonicus Beihaidao leaves have certain cold resistance and can maintain their viability during wintering. Moreover, the chloroplast genome of E. japonicus Beihaidao is a typical double-linked ring tetrad structure, which is similar to that of the other four Euonymus species, E. hamiltonianus, E. phellomanus, E. schensianus, and E. szechuanensis, in terms of gene structure, gene species, gene number, and GC content. Compared to other Celastraceae species, the variation in the chloroplast genome sequence was lower, and the gene structure was more stable. The phylogenetic relationships of 37 species inferred that members of the Euonymus genus do not form a clade and that E. japonicus Beihaidao is closely related to E. japonicus and E. fortunei. A total of 11 functional positive selected genes were identified, which may have played an important role in the process of Celastraceae species adapting to environmental changes. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Celastraceae species.
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Affiliation(s)
- Hongyu Cai
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Xiaozheng Gu
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yongtan Li
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yachao Ren
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Shufang Yan
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang 050050, China
| | - Minsheng Yang
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
- Correspondence: ; Tel.: +86-0312-752-8715
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16
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Zhang Y, Guan YH, Pu CZ, Xi YJ, Tao AE, Xia CL. The complete chloroplast genome of Verbascum thapsus L. (Scrophulariaceae) and its phylogenetic affinities. Mitochondrial DNA B Resour 2022; 7:1583-1585. [PMID: 36082042 PMCID: PMC9448373 DOI: 10.1080/23802359.2022.2113749] [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: 11/15/2022] Open
Abstract
Verbascum thapsus L. has extensive pharmacological effects, including antioxidative and antineoplastic action, memory improvement and neuroprotection. However, its phylogenetic position is not established in Scrophulariaceae. In this study, we reported the complete chloroplast genome sequence of V. thapsus L. for the first time and investigate its phylogenetic relationship in Scrophulariaceae. The assembled chloroplast genome is a circular 153,338 bp sequence, including a large single copy (LSC) region of 84,627 bp, a small single copy (SSC) region of 17,829 bp and a pair of inverted repeats (IRs) of 25,441 bp. The genome contains 135 genes, including 86 protein coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic tree showed that V. thapsus is closely associated with V. chinense and V. phoeniceum.
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Affiliation(s)
- Yue Zhang
- College of Pharmacy, Dali University, Dali, China
| | - Yun-Hui Guan
- College of Pharmacy, Dali University, Dali, China
| | - Cheng-Zhao Pu
- College of Medicine, Lijiang Culture and Tourism College, Lijiang, China
| | - Yi-Jia Xi
- College of Medicine, Lijiang Culture and Tourism College, Lijiang, China
| | - Ai-en Tao
- College of Medicine, Lijiang Culture and Tourism College, Lijiang, China
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17
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Wei R, Li Q. The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications. Genes (Basel) 2022; 13:genes13081361. [PMID: 36011272 PMCID: PMC9407434 DOI: 10.3390/genes13081361] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Stemona parviflora is an endangered species, narrowly endemic to Hainan and Southwest Guangdong. The taxonomic classification of S. parviflora remains controversial. Moreover, studying endangered species is helpful for current management and conservation. In this study, the first complete chloroplast genome of S. parviflora was assembled and compared with other Stemona species. The chloroplast genome size of S. parviflora was 154,552 bp, consisting of 87 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and one pseudogene. The ψycf1 gene was lost in the cp genome of S. sessilifolia, but it was detected in four other species of Stemona. The inverted repeats (IR) regions have a relatively lower length variation compared with the large single copy (LSC) and small single copy (SSC) regions. Long repeat sequences and simple sequence repeat (SSR) were detected, and most SSR were distributed in the LSC region. Codon usage bias analyses revealed that the RSCU value of the genus Stemona has almost no difference. As with most angiosperm chloroplast genomes, protein-coding regions were more conservative than the inter-gene spacer. Seven genes (atpI, ccsA, cemA, matK, ndhA, petA, and rpoC1) were detected under positive selection in different Stemona species, which may result from adaptive evolution to different habitats. Phylogenetic analyses show the Stemona cluster in two main groups; S. parviflora were closest to S. tuberosa. A highly suitable region of S. parviflora was simulated by Maxent in this study; it is worth noting that the whole territory of Taiwan has changed to a low fitness area and below in the 2050 s, which may not be suitable for the introduction and cultivation of S. parviflora. In addition, limited by the dispersal capacity of S. parviflora, it is necessary to carry out artificial grafts to expand the survival areas of S. parviflora. Our results provide valuable information on characteristics of the chloroplast genome, phylogenetic relationships, and potential distribution range of the endangered species S. parviflora.
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Affiliation(s)
- Ran Wei
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
| | - Qiang Li
- Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Correspondence:
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18
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Yang MH, Xia CL, Guan YH, Zhang HZ, Chen XB, Wang Y. Sequencing and characterization of the chloroplast genome of Aconitum forrestii Stapf provide insights into phylogenetics in Aconitum. Mitochondrial DNA B Resour 2022; 7:1165-1167. [PMID: 35783038 PMCID: PMC9246018 DOI: 10.1080/23802359.2022.2088307] [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: 12/01/2022] Open
Abstract
Aconitum forrestii Stapf is an essential traditional Chinese medicine, and is beneficial in dispelling wind, removing dampness, warming, and relieving pain. However, its phylogenetic position of Aconitum is not accepted yet. In order to clarify the evolutionary relationship of A. forrestii, complete sequencing of chloroplast genome was carried out using Illumina sequencing technology. In total, the chloroplast genome was about 155,869 base pair (bp) in length and carried a typical tetrad structure that included a large single-copy, a small-single copy and two inverted repeat regions. A total of 132 genes were annotated, that included 85 protein -coding genes, 37 transfer RNA genes, eight ribosomal RNA genes, and two pseudogenes. The phylogenetic tree analysis indicated that Aconitum forrestii is closely related to Aconitum episcopale and Aconitum delavayi.
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Affiliation(s)
- Mei-hua Yang
- College of Pharmacy, Dali University, Dali, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, China
| | - Cong-long Xia
- College of Pharmacy, Dali University, Dali, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, China
| | - Yun-hui Guan
- College of Pharmacy, Dali University, Dali, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, China
| | - Hai-zhu Zhang
- College of Pharmacy, Dali University, Dali, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, China
| | - Xu-bing Chen
- College of Pharmacy, Dali University, Dali, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, China
| | - Ying Wang
- College of Pharmacy, Dali University, Dali, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, China
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19
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Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens. PLoS One 2022; 17:e0266546. [PMID: 35385539 PMCID: PMC8985940 DOI: 10.1371/journal.pone.0266546] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
Isodon rubescens (Hemsley) H. Hara (Lamiaceae) is a traditional Chinese medicine plant that has been used to treat various human diseases and conditions such as inflammation, respiratory and gastrointestinal bacterial infections, and malignant tumors. However, the contents of the main active components of I. rubescens from different origins differ significantly, which greatly affected its quality. Therefore, a molecular method to identify and classify I. rubescens is needed. Here, we report the DNA sequence of the chloroplast genome of I. rubescens collected from Lushan, Henan province. The genome is 152,642 bp in length and has a conserved structure that includes a pair of IR regions (25,726 bp), a LSC region (83,527 bp) and a SSC region (17,663 bp). The chloroplast genome contains 113 unique genes, four rRNA genes, 30 tRNA genes, and 79 protein-coding genes, 23 of which contain introns. The protein-coding genes account for a total of 24,412 codons, and most of them are A/T biased usage. We identified 32 simple sequence repeats (SSRs) and 48 long repeats. Furthermore, we developed valuable chloroplast molecular resources by comparing chloroplast genomes from three Isodon species, and both mVISTA and DnaSP analyses showed that rps16-trnQ, trnS-trnG, and ndhC-trnM are candidate regions that will allow the identification of intraspecific differences within I. rubescens. Also 14 candidate fragments can be used to identify interspecific differences between species in Isodon. A phylogenetic analysis of the complete chloroplast genomes of 24 species in subfamily Nepetoideae was performed using the maximum likelihood method, and shows that I. rubescens clustered closer to I. serra than I. lophanthoides. Interestingly, our analysis showed that I. rubescens (MW018469.1) from Xianyang, Shaanxi Province (IR-X), is closer to I. serra than to the other two I. rubescens accessions. These results strongly indicate that intraspecific diversity is present in I. rubescens. Therefore, our results provide further insight into the phylogenetic relationships and interspecific diversity of species in the genus Isodon.
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20
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Li Q. The Complete Chloroplast Genomes of Primula obconica Provide Insight That Neither Species nor Natural Section Represent Monophyletic Taxa in Primula (Primulaceae). Genes (Basel) 2022; 13:genes13040567. [PMID: 35456373 PMCID: PMC9030805 DOI: 10.3390/genes13040567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/30/2022] Open
Abstract
The genus Primula (Primulaceae) comprises more than 500 species, with 300 species distributed in China. The contradictory results between systematic analyses and morphology-based taxonomy make taxonomy studies difficult. Furthermore, frequent introgression between closely related species of Primula can result in non-monophyletic species. In this study, the complete chloroplast genome of sixteen Primula obconica subsp. obconica individuals were assembled and compared with 84 accessions of 74 species from 21 sections of the 24 sections of the genus in China. The plastome sizes of P. obconica subsp. obconica range from 153,584 bp to 154,028 bp. Genome-wide variations were detected, and 1915 high-quality SNPs and 346 InDels were found. Most SNPs were detected in downstream and upstream gene regions (45.549% and 41.91%). Two cultivated accessions, ZP1 and ZP2, were abundant with SSRs. Moreover, 12 SSRs shared by 9 accessions showed variations that may be used as molecular markers for population genetic studies. The phylogenetic tree showed that P. obconica subsp. obconica cluster into two independent clades. Two subspecies have highly recognizable morphological characteristics, isolated geographical distribution areas, and distinct phylogenetic relationships compared with P. obconica subsp. obconica. We elevate the two subspecies of P. obconica to separate species. Our phylogenetic tree is largely inconsistent with morphology-based taxonomy. Twenty-one sections of Primula were mainly divided into three clades. The monophyly of Sect. Auganthus, Sect. Minutissimae, Sect. Sikkimensis, Sect. Petiolares, and Sect. Ranunculoides are well supported in the phylogenetic tree. The Sect. Obconicolisteri, Sect. Monocarpicae, Sect. Carolinella, Sect. Cortusoides, Sect. Aleuritia, Sect. Denticulata, Sect. Proliferae Pax, and Sect. Crystallophlomis are not a monophyletic group. The possible explanations for non-monophyly may be hybridization, polyploidization, recent introgression, incorrect taxonomy, or chloroplast capture. Multiple genomic data and population genetic studies are therefore needed to reveal the evolutionary history of Primula. Our results provided valuable information for intraspecific variation and phylogenetic relationships within Primula.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
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21
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Tian C, Li X, Wu Z, Li Z, Hou X, Li FY. Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae). Front Genet 2021; 12:705482. [PMID: 34422006 PMCID: PMC8378255 DOI: 10.3389/fgene.2021.705482] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.
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Affiliation(s)
- Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiansong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Xiangyang Hou
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Lu M, Fang Z, Sheng F, Tong X, Han R. Characterization and phylogenetic analysis of the complete chloroplast genome of Juncus effusus L. Mitochondrial DNA B Resour 2021; 6:1612-1613. [PMID: 34027070 PMCID: PMC8118462 DOI: 10.1080/23802359.2021.1926357] [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: 11/02/2022] Open
Abstract
Juncus effusus L., a perennial herbaceous species of family Juncaceae, is distributed mainly in warm areas worldwide. We studied the complete chloroplast (cp) genome of J. effusus through next-generation sequencing technology. The whole cp genome contained 170,612 base pairs, with the GC ratio as 35.99%. The 70 genes annotated from the cp genome include 32 protein coding genes, eight rRNA genes and 30 tRNA genes. The genome’s large single-copy region (LSC) was 80,640 bp, with the small single-copy region (SSC) 64,718 bp, and inverted repeat (IR) 12,627 bp. Furthermore, a phylogenetic tree was generated to evaluate evolutionary relationship between J. effusus and relevant species. This study will be beneficial for the further understanding and application of J. effusus.
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Affiliation(s)
- Mengya Lu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Zhizheng Fang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Feihan Sheng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaohui Tong
- School of Life Sciences, Anhui University of Chinese Medicine, Hefei, China
| | - Rongchun Han
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
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Zhang W, Wang H, Dong J, Zhang T, Xiao H. Comparative chloroplast genomes and phylogenetic analysis of Aquilegia. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11412. [PMID: 33854846 PMCID: PMC8027367 DOI: 10.1002/aps3.11412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/07/2021] [Indexed: 05/25/2023]
Abstract
PREMISE Aquilegia is an ideal taxon for studying the evolution of adaptive radiation. Current phylogenies of Aquilegia based on different molecular markers are inconsistent, and therefore a clear and accurate phylogeny remains uncertain. Analyzing the chloroplast genome, with its simple structure and low recombination rate, may help solve this problem. METHODS Next-generation sequencing data were generated or downloaded for Aquilegia species, enabling their chloroplast genomes to be assembled. The assemblies were used to estimate the genome characteristics and infer the phylogeny of Aquilegia. RESULTS In this study, chloroplast genome sequences were assembled for Aquilegia species distributed across Asia, North America, and Europe. Three of the genes analyzed (petG, rpl36, and atpB) were shown to be under positive selection and may be related to adaptation. The phylogenetic tree of Aquilegia showed that its member species formed two clades with high support, North American and European species, with the Asian species being paraphyletic; A. parviflora and A. amurensis clustered with the North American species, while the remaining Asian species were found in the European clade. In addition, A. oxysepala var. kansuensis should be considered as a separate species rather than a variety. DISCUSSION The complete chloroplast genomes of these Aquilegia species provide new insights into the reconstruction of the phylogeny of related species and contribute to the further study of this genus.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Jianhua Dong
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
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Liao M, Gao XF, Zhang JY, Deng HN, Xu B. Comparative Chloroplast Genomics of Sophora Species: Evolution and Phylogenetic Relationships in the Early-Diverging Legume Subfamily Papilionoideae (Fabaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:778933. [PMID: 34975964 PMCID: PMC8716937 DOI: 10.3389/fpls.2021.778933] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/08/2021] [Indexed: 05/04/2023]
Abstract
The taxonomy and evolutionary history of Sophora L., a genus with high economic and medicinal value, remain uncertain due to the absence of genetic resource (especially in China) and low polymorphism of molecular markers. Our aim was to elucidate the molecular evolution and phylogenetic relationships in chloroplast genomes of Sophora species in the early-diverging legume subfamily Papilionoideae (Fabaceae). We reported nine Sophora chloroplast genome from China using Illumina sequencing. We performed a series of analyses with previously published genomes of Sophora species to investigate their genomic characteristics, identified simple sequence repeats, large repeat sequences, tandem repeats, and highly polymorphic loci. The genomes were 152,953-158,087 bp in length, and contained 111-113 unique genes, including 76-78 protein coding, 31 tRNA, and 4 rRNA. The expansion of inverted repeat boundary of Sophora resulted in rps12 entering into the LSC region and loss of trnT-CGU gene in some species. Also, we found an approximately 23 kb inversion between trnC-GCA and trnF-GAA within the genus. In addition, we identified seven highly polymorphic loci (pi (π) > 0.035) suitable for inferring the phylogeny of Sophora species. Among these, three regions also co-occurred with large repeat sequences and support use of repeats as a proxy for the identification of polymorphic loci. Based on whole chloroplast genome and protein-coding sequences data-set, a well-supported phylogenetic tree of Sophora and related taxa showed that this genus is monophyletic, but sect. Disamaea and sect. Sophora, are incongruent with traditional taxonomic classifications based on fruit morphology. Our finding provides significant genetic resources to support further investigation into the phylogenetic relationship and evolution of the genus Sophora.
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Affiliation(s)
- Min Liao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jun-Yi Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Heng-Ning Deng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- *Correspondence: Bo Xu,
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