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Wang X, Zhang Z, Shi Y, Man J, Huang Y, Zhang X, Liu S, He G, An K, Amu L, Chen W, Liu Z, Wang X, Wei S. Population identification and genetic diversity analysis of Fritillaria ussuriensis (Fritillaria) based on chloroplast genes atpF and petB. J Appl Genet 2024:10.1007/s13353-024-00874-z. [PMID: 38684618 DOI: 10.1007/s13353-024-00874-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024]
Abstract
The chloroplast genomes of five Fritillaria ussuriensis materials from different production areas were comparatively analyzed, atpF and petB were screened as specific DNA barcodes, and the population identification and genetic diversity of F. ussuriensis were analyzed based on them. The F. ussuriensis chloroplast genome showed a total length of 151 515-151 548 bp with a typical tetrad structure and encoded 130 genes. atpF and petB were used to amplify 183 samples from 13 populations, and they could identify 6 and 9 haplotypes, respectively. Joint analysis of the two sequences revealed 18 haplotypes, named H1-H18, with the most widely distributed and most abundant being H4. Ten haplotypes were unique for 7 populations that they could be used to distinguish from others. Haplotype diversity and nucleotide diversity were 0.99 and 2.09 × 10-3, respectively, indicating the genetic diversity was relatively rich. The results of the intermediary adjacency network showed that H5 was the oldest haplotype, and stellate radiation was centered around it, indicating that population expansion occurred in genuine production areas. This study lays a theoretical foundation for the population identification, genetic evolution, and breed selection of F. ussuriensis.
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Affiliation(s)
- Xin Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Zhifei Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Yue Shi
- School of Life and Science, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
- Engineering Research Center of Good Agricultural Practice for Chinese Crude Drugs, Ministry of Education, Beijing, 102488, People's Republic of China
| | - Jinhui Man
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Yuying Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Xiaoqin Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Shanhu Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Gaojie He
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Kelu An
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Laha Amu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Wenqin Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China
| | - Ziqi Liu
- Heilongjiang BCT Chinese Traditional Medicine Co.Ltd, Heilongjiang, 150600, People's Republic of China
| | - Xiaohui Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing Institute of Traditional Chinese Medicine,, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China.
- Engineering Research Center of Good Agricultural Practice for Chinese Crude Drugs, Ministry of Education, Beijing, 102488, People's Republic of China.
| | - Shengli Wei
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, People's Republic of China.
- Engineering Research Center of Good Agricultural Practice for Chinese Crude Drugs, Ministry of Education, Beijing, 102488, People's Republic of China.
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Choi TY, Lee SR. Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes. PLoS One 2024; 19:e0301346. [PMID: 38578735 PMCID: PMC10997070 DOI: 10.1371/journal.pone.0301346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, Chosun University, Gwangju, South Korea
| | - Soo-Rang Lee
- Department of Biology Education, Chosun University, Gwangju, South Korea
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Huang L, Xu Y, Valcárcel V, Lutz S, Wen J, Ren Z. Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae. BMC Genom Data 2024; 25:30. [PMID: 38491489 PMCID: PMC10943888 DOI: 10.1186/s12863-024-01200-6] [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: 11/17/2023] [Accepted: 01/30/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy. RESULTS The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship. CONCLUSIONS Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.
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Affiliation(s)
- Lan Huang
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Yujie Xu
- School of Geosciences, Qinghai Normal University, 810008, Xining, Qinghai, China
| | - Virginia Valcárcel
- Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidady Cambio Global (CIBC-UAM) , Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Sue Lutz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, 20013, Washington, DC, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, 20013, Washington, DC, USA.
| | - Zhumei Ren
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China.
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Zhang R, Xiang N, Qian C, Liu S, Zhao Y, Zhang G, Wei P, Li J, Yuan T. Comparative analysis of the organelle genomes of Aconitum carmichaelii revealed structural and sequence differences and phylogenetic relationships. BMC Genomics 2024; 25:260. [PMID: 38454328 PMCID: PMC10921738 DOI: 10.1186/s12864-024-10136-1] [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: 10/16/2023] [Accepted: 02/17/2024] [Indexed: 03/09/2024] Open
Abstract
In this study, we conducted an assembly and analysis of the organelle genomes of Aconitum carmichaelii. Our investigation encompassed the examination of organelle genome structures, gene transfer events, and the environmental selection pressures affecting A. carmichaelii. The results revealed distinct evolutionary patterns in the organelle genomes of A. carmichaelii. Especially, the plastome exhibited a more conserved structure but a higher nucleotide substitution rate (NSR), while the mitogenome displayed a more complex structure with a slower NSR. Through homology analysis, we identified several instances of unidirectional protein-coding genes (PCGs) transferring from the plastome to the mitogenome. However, we did not observe any events which genes moved from the mitogenome to the plastome. Additionally, we observed multiple transposable element (TE) fragments in the organelle genomes, with both organelles showing different preferences for the type of nuclear TE insertion. Divergence time estimation suggested that rapid differentiation occurred in Aconitum species approximately 7.96 million years ago (Mya). This divergence might be associated with the reduction in CO2 levels and the significant uplift of the Qinghai-Tibet Plateau (QTP) during the late Miocene. Selection pressure analysis indicated that the dN/dS values of both organelles were less than 1, suggested that organelle PCGs were subject to purification selection. However, we did not detect any positively selected genes (PSGs) in Subg. Aconitum and Subg. Lycoctonum. This observation further supports the idea that stronger negative selection pressure on organelle genes in Aconitum results in a more conserved amino acid sequence. In conclusion, this study contributes to a deeper understanding of organelle evolution in Aconitum species and provides a foundation for future research on the genetic mechanisms underlying the structure and function of the Aconitum plastome and mitogenome.
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Affiliation(s)
- Rongxiang Zhang
- School of Biological Science, Guizhou Education University, Guiyang, 550018, China
- Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, 550018, China
| | - Niyan Xiang
- School of Ecology and Environment, Tibet University, Lhasa, 850000, China
| | - Changjiang Qian
- School of Biological Science, Guizhou Education University, Guiyang, 550018, China
| | - Shuwen Liu
- School of Biological Science, Guizhou Education University, Guiyang, 550018, China
| | - Yuemei Zhao
- School of Biological Science, Guizhou Education University, Guiyang, 550018, China
| | - Guiyu Zhang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jianfeng Li
- School of Biological Science, Guizhou Education University, Guiyang, 550018, China.
- Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, 550018, China.
| | - Tao Yuan
- School of Ecology and Environment, Tibet University, Lhasa, 850000, China.
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Yang M, Liu J, Yang W, Li Z, Hai Y, Duan B, Zhang H, Yang X, Xia C. Analysis of codon usage patterns in 48 Aconitum species. BMC Genomics 2023; 24:703. [PMID: 37993787 PMCID: PMC10664653 DOI: 10.1186/s12864-023-09650-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/05/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The Aconitum genus is a crucial member of the Ranunculaceae family. There are 350 Aconitum species worldwide, with about 170 species found in China. These species are known for their various pharmacological effects and are commonly used to treat joint pain, cold abdominal pain, and other ailments. Codon usage bias (CUB) analysis contributes to evolutionary relationships and phylogeny. Based on protein-coding sequences (PCGs), we selected 48 species of Aconitum for CUB analysis. RESULTS The results revealed that Aconitum species had less than 50% GC content. Furthermore, the distribution of GC content was irregular and followed a trend of GC1 > GC2 > GC3, indicating a bias towards A/T bases. The relative synonymous codon usage (RSCU) heat map revealed the presence of conservative codons with slight variations within the genus. The effective number of codons (ENC)-Plot and the parity rule 2 (PR2)-bias plot analysis indicate that natural selection is the primary factor influencing the variation in codon usage. As a result, we screened various optimal codons and found that A/T bases were preferred as the last codon. Furthermore, our Maximum Likelihood (ML) analysis based on PCGs among 48 Aconitum species yielded results consistent with those obtained from complete chloroplast (cp.) genome data. This suggests that analyzing mutation in PCGs is an efficient method for demonstrating the phylogeny of species at the genus level. CONCLUSIONS The CUB analysis of 48 species of Aconitum was mainly influenced by natural selection. This study reveals the CUB pattern of Aconitum and lays the foundation for future genetic modification and phylogenetic analyses.
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Affiliation(s)
- Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Jiahao Liu
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Wanqing Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Zhen Li
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Yonglin Hai
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Haizhu Zhang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, Yunnan, 671000, China
| | - Xiaoli Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China.
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China.
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Yuan S, Nie C, Jia S, Liu T, Zhao J, Peng J, Kong W, Liu W, Gou W, Lei X, Xiong Y, Xiong Y, Yu Q, Ling Y, Ma X. Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1170004. [PMID: 37554563 PMCID: PMC10405828 DOI: 10.3389/fpls.2023.1170004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.
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Affiliation(s)
- Shuai Yuan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Cong Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianqi Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinghan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Weixia Kong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yao Ling
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Tiwari S, Acharya P, Solanki B, Sharma AK, Rawat S. A review on efforts for improvement in medicinally important chemical constituents in Aconitum through biotechnological interventions. 3 Biotech 2023; 13:190. [PMID: 37193333 PMCID: PMC10183062 DOI: 10.1007/s13205-023-03578-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/21/2023] [Indexed: 05/18/2023] Open
Abstract
The genus Aconitum belongs to the family Ranunculaceae, is endowed with more than 350 species on the earth. Medicinally important aconitine type of diterpenoid alkaloids are the characteristic compounds in most of the Aconitum species. The present review endeavored the major research carried out in the field of genetic resource characterization, pharmacological properties, phytochemistry, major factors influencing quantity, biosynthetic pathways and processing methods for recovery of active ingredients, variety improvement, propagation methods, and important metabolite production through cell/organ culture of various Aconitum species. More than 450 derivatives of aconitine-type C19 and C20-diterpenoid alkaloids along with a few other non-alkaloidal compounds, such as phenylpropanoids, flavonoids, terpenoids, and fatty acids, have been identified in the genus. A few Aconitum species and their common diterpenoid alkaloid compounds are also well characterized for analgesic, inflammatory and cytotoxic properties. However, the different isolated compound needs to be validated for supporting other traditional therapeutical uses of the plant species. Aconitine alkaloids shared common biosynthesis pathway, but their diversification mechanism remains unexplored in the genus. Furthermore, the process needs to be developed on secondary metabolite recovery, mass-scale propagation methods, and agro-technologies for maintaining the quality of products. Many species are losing their existence in nature due to over-exploitation or anthropogenic factors; thus, temporal monitoring of the population status in its habitat, and suitable management programs for ascertaining conservation needs to be developed.
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Affiliation(s)
- Sekhar Tiwari
- Department of Biotechnology, School of Sciences, P. P. Savani University, Surat, Gujarat India
| | - Puja Acharya
- Sikkim Regional Centre, G. B. Pant National Institute of Himalayan Environment, Pangthang, Gangtok, Sikkim India
| | - Bharat Solanki
- Department of Biochemistry, M. B. Patel Science College, Sardar Patel University, Anand, Gujarat India
| | - Anish Kumar Sharma
- Department of Biotechnology, School of Sciences, P. P. Savani University, Surat, Gujarat India
| | - Sandeep Rawat
- Sikkim Regional Centre, G. B. Pant National Institute of Himalayan Environment, Pangthang, Gangtok, Sikkim India
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Yanfei N, Tai S, Chunhua W, Jia D, Fazhong Y. Complete chloroplast genome sequences of the medicinal plant Aconitum transsectum (Ranunculaceae): comparative analysis and phylogenetic relationships. BMC Genomics 2023; 24:90. [PMID: 36855055 PMCID: PMC9976445 DOI: 10.1186/s12864-023-09180-0] [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: 06/22/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Aconitum transsectum Diels. (Ranunculaceae) is an important medicinal plant that is widely used in traditional Chinese medicine, but its morphological traits make it difficult to recognize from other Aconitum species. No research has sequenced the chloroplast genome of A.transsectum, despite the fact that phylogenetic analysis based on chloroplast genome sequences provides essential evidence for plant classification. RESULTS In this study, the chloroplast (cp) genome of A. transsectum was sequenced, assembled, and annotated. A. transsectum cp genome is a 155,872 bp tetrameric structure including a large single copy (LSC, 87,671 bp) and a small single copy (SSC, 18,891 bp) section, as well as a pair of inverted repeat sequences (IRa and IRb, 25,894 bp each). 131 genes are encoded by the complete cp genome, comprising 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The most favored codon in the A. transsectum cp genome is AUG, and 46 repeats and 241 SSRs were also identified. The A. transsectum cp genome is similar in size, gene composition, and IR expansion and contraction to the cp genomes of seven Ranunculaceae species. Phylogenetic analysis of cp genomes of 28 plants from the Ranunculaceae family shows that A. transsectum is most closely related to A. vilmorinianum, A. episcopale, and A. forrestii of Subgen. Aconitum. CONCLUSIONS Overall, this study provides complete cp genome resources for A. transsectum that will be beneficial for identifying potential.
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Affiliation(s)
- Niu Yanfei
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China ,grid.506261.60000 0001 0706 7839Yunnan Institute of Materia Medica, Kunming, 650111 China ,Yunnan Baiyao Group Chinese Medicinal Resources Division, Kunming, 650500 China
| | - Su Tai
- grid.506261.60000 0001 0706 7839Yunnan Institute of Materia Medica, Kunming, 650111 China
| | - Wu Chunhua
- Key Laboratory of State Forestry and Grassland Administration On Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Kunming, 650224, China. .,College of Chemical Engineering, Southwest Forestry University, Kunming, 650224, China.
| | - Deng Jia
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China
| | - Yang Fazhong
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China ,Key Laboratory of State Forestry and Grassland Administration On Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Kunming, 650224 China
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Zhou Z, Wang J, Pu T, Dong J, Guan Q, Qian J, Shi L, Duan B. Comparative analysis of medicinal plant Isodon rubescens and its common adulterants based on chloroplast genome sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1036277. [PMID: 36479509 PMCID: PMC9720329 DOI: 10.3389/fpls.2022.1036277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/26/2022] [Indexed: 06/03/2023]
Abstract
Isodon rubescens (Hemsley) H. Hara is the source of Donglingcao under the monograph Rabdosiae Rubescentis Herba in Chinese Pharmacopoeia. In the local marketplace, this medicine can be accidentally contaminated, deliberately substituted, or mixed with other related species. The contaminants of herbal products are a threat to consumer safety. Due to the scarcity of genetic information on Isodon plants, more molecular markers are needed to avoid misidentification. In the present study, the complete chloroplast (cp) genome of seven species of Isodon was sequenced, de novo assembled and characterized. The cp genomes of these species universally exhibited a conserved quadripartite structure, i.e., two inverted repeats (IRs) containing most of the ribosomal RNA genes and two unique regions (large single copy and small single copy). Moreover, the genome structure, codon usage, and repeat sequences were highly conserved and showed similarities among the seven species. Five highly variable regions (trnS-GCU-trnT-CGU, atpH-atpI, trnE-UUC-trnT-GGU, ndhC-trnM-CAU, and rps15-ycf1) might be potential molecular markers for identifying I. rubescens and its contaminants. These findings provide valuable information for further species identification, evolution, and phylogenetic research of Isodon.
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Affiliation(s)
- Zhongyu Zhou
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Tingting Pu
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jingjing Dong
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Qin Guan
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jun Qian
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
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10
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Zhang J, Li D, Zhong D, Zhou Q, Yin Y, Gao J, Peng C. Processed lateral root of Aconitum carmichaelii Debx.: A review of cardiotonic effects and cardiotoxicity on molecular mechanisms. Front Pharmacol 2022; 13:1026219. [PMID: 36324672 PMCID: PMC9618827 DOI: 10.3389/fphar.2022.1026219] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Fuzi, the lateral root of A. carmichaelii Debx., is a typical traditional herbal medicine with both poisonousness and effectiveness, and often used in the treatment of heart failure and other heart diseases. In this review, we searched domestic and foreign literature to sort out the molecular mechanisms of cardiotonic and cardiotoxicity of Fuzi, also including its components. The major bioactive components of Fuzi for cardiotonic are total alkaloids, polysaccharide and the water-soluble alkaloids, with specific mechanisms manifested in the inhibition of myocardial fibrosis, apoptosis and autophagy, and improvement of mitochondrial energy metabolism, which involves RAAS system, PI3K/AKT, JAK/STAT, AMPK/mTOR signaling pathway, etc. Diester-diterpenoid alkaloids in Fuzi can produce cardiotoxic effects by over-activating Na+ and Ca2+ ion channels, over-activating NLRP3/ASC/caspase-3 inflammatory pathway and mitochondria mediated apoptosis pathway. And three clinically used preparations containing Fuzi are also used as representatives to summarize their cardiac-strengthening molecular mechanisms. To sum up, Fuzi has shown valuable cardiotonic effects due to extensive basic and clinical studies, but its cardiotonic mechanisms have not been systematically sorted out. Therefore, it is a need for deeper investigation in the mechanisms of water-soluble alkaloids with low content but obvious therapeutic effect, as well as polysaccharide.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dan Li
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dan Zhong
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qinmei Zhou
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yanpeng Yin
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jihai Gao
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Jihai Gao, ; Cheng Peng,
| | - Cheng Peng
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Jihai Gao, ; Cheng Peng,
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11
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Guo H, Wang L, Xu W, Huo Z, Yang P, Zhang Q, Wang H, Li P, Lu X. The complete chloroplast genome sequence of Cyathula officinalis and comparative analysis with four related species. Gene 2022; 839:146728. [PMID: 35850203 DOI: 10.1016/j.gene.2022.146728] [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: 12/09/2021] [Revised: 06/14/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022]
Abstract
Cyathula officinalis is a medicinal and edible herb, which can remove blood stasis, stimulate menstrual flow, and ease joint movement. In this study, the complete chloroplast genome of Cyathula officinalis was sequenced, assembled, and analyzed. Compared with the chloroplast genomes of Cyathula capitata, Achyranthes bidentata, Achyranthes longifolianine and Achyranthes aspera, the basic characteristics, codon usage bias, repeat sequences, simple sequence repeats, and phylogenetic tree were analyzed. In addition, according to nucleotide diversity analysis and sequence alignment, DNA barcoding and allele-specific PCR primers were designed to identify and distinguish Cyathula officinalis from its fake drugs, which has effectively practical significance for the authentication of "Chuan Niuxi" crude drug in the market.
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Affiliation(s)
- Huijun Guo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Long Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Wenbo Xu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Ziting Huo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Qianwen Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Huiying Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China.
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China.
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12
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Zhang JY, Liao M, Cheng YH, Feng Y, Ju WB, Deng HN, Li X, Plenković-Moraj A, Xu B. Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:911702. [PMID: 35812969 PMCID: PMC9257239 DOI: 10.3389/fpls.2022.911702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The species in the genus Cypripedium (Orchidaceae) are considered endangered, mainly distributed in the temperate regions of the Northern Hemisphere, with high ornamental and economic value. Despite previous extensive studies based on both morphology and molecular data, species and sections relationships within Cypripedium remain controversial. Here, we employed two newly generated Cypripedium chloroplast genomes with five other published genomes to elucidate their genomic characteristics. The two genomes were 162,773-207,142 bp in length and contained 128-130 genes, including 82-84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We identified 2,192 simple sequence repeats, 786 large repeat sequences, and 7,929 variable loci. The increase of repeat sequences (simple sequence repeats and large repeat sequences) causes a significant amplification in the chloroplast genome size of Cypripedium. The expansion of the IR region led to the pseudogenization or loss of genes in the SSC region. In addition, we identified 12 highly polymorphic loci (Pi > 0.09) suitable for inferring the phylogeny of Cypripedium species. Based on data sets of whole chloroplast genomes (IRa excluded) and protein-coding sequences, a well-supported phylogenetic tree was reconstructed, strongly supporting the five subfamilies of Orchidaceae and the genus Cypripedium as monophyletic taxa. Our findings also supported that C. palangshanense belonged to sect. Palangshanensia rather than sect. Retinervia. This study also enriched the genomic resources of Cypripedium, which may help to promote the conservation efforts of these endangered species.
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Affiliation(s)
- Jun-Yi Zhang
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Min Liao
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & 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
| | - Yue-Hong Cheng
- Wolong National Natural Reserve Administration Bureau, Sichuan, China
| | - Yu Feng
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wen-Bing Ju
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & 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
| | - Heng-Ning Deng
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiong Li
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & 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
| | | | - Bo Xu
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & 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
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13
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Xia C, Wang M, Guan Y, Li J. Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships. Front Genet 2022; 13:878182. [PMID: 35711937 PMCID: PMC9194378 DOI: 10.3389/fgene.2022.878182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Aconitum is an important medicinal group of the Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. There are about 350 Aconitum species globally and about 170 species in China. It is challenging to identify the species in morphology, and the lack of molecular biology information hinders the identification and rational utilization of the germplasm of this genus. Therefore, it is necessary to increase the molecular data of Aconitum species. This paper acquired the complete chloroplast (CP) genome sequence of ten medicinal plants of Aconitum species from Yunnan by Illumina paired-end (PE) sequencing technology and compared it with other species in the same family and genus. These CP genomes exhibited typical circular quadripartite structure, and their sizes ranged from 155,475 (A. stylosum) to 155,921 bp (A. vilmoinianum), including a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRs). Their gene content, order, and GC content (38.1%) were similar. Moreover, their number of genes ranged from 129 (A. vilmoinianum) to 132 (A. ramulosum), including 83 to 85 protein-coding genes (PCGs), 37 tRNA genes (tRNAs), eight rRNA genes (rRNAs), and two pseudogenes. In addition, we performed repeated sequence analysis, genomic structure, and comparative analysis using 42 Aconitum chloroplast genomes, including ten Aconitum chloroplast genomes and other sequenced Aconitum species. A total of 48–79 simple sequence repeats (SSRs) and 17 to 77 long repeat sequences were identified. IR regions showed higher variability than the SSC region and LSC region. Seven mutational hotspots were screened out, including trnK-UUU-trnQ-UGG, psbD, ndhJ-ndhK, clpP, psbH-petB, ycf1, and trnA-UGC-trnI-GAU, respectively. The phylogenetic trees of ten Aconitum species and other Aconitum species revealed that the complete CP genome was beneficial in determining the complex phylogenetic relationships among Aconitum species. This study provides a potential molecular marker and genomic resource for phylogeny and species identification of Aconitum species and an important reference and basis for Ranunculaceae species identification and phylogeny.
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Affiliation(s)
- Conglong Xia
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, China.,College of Pharmacy, Dali University, Dali, China
| | - Manjiong Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, China
| | - Yunhui Guan
- College of Pharmacy, Dali University, Dali, China
| | - Jian Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, China.,College of Pharmacy, Dali University, Dali, China
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14
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Xia C, Wang M, Guan Y, Li Y, Li J. Comparative analysis of complete chloroplast genome of ethnodrug Aconitum episcopale and insight into its phylogenetic relationships. Sci Rep 2022; 12:9439. [PMID: 35676401 PMCID: PMC9178047 DOI: 10.1038/s41598-022-13524-3] [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: 08/29/2021] [Accepted: 05/10/2022] [Indexed: 11/22/2022] Open
Abstract
Aconitum episcopale Leveille is an important medicinal plant from the genus Aconitum L. of Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. According to the available data and Ethno folk applications, A. episcopale is the only Aconitum species that has detoxifying and antialcoholic property. It can detoxify opium, especially the poisoning of Aconitum plants. Aconitum species have been widely used for their medicinal properties, and it is important to be noted that many of the species of this plant are reported to be toxic also. Distinguishing the species of this plant based on the morphology is a tough task and there are also no significant differences in the chemical composition. Therefore, before application of this plant for medicinal usage, it is very important to identify the species which could be life-threatening and exclude them. In this paper, the complete chloroplast (cp) genome sequence of A. episcopale was acquired by Illumina paired-end (PE) sequencing technology and compared with other species in the same family and genus. Herein, we report the complete cp genome of A. episcopale. The whole circular cp genome of A. episcopale has been found to be of 155,827 bp in size and contains a large single-copy region (LSC) of 86,452 bp, a small single-copy region (SSC) of 16,939 bp, and two inverted repeat regions (IRs) of 26,218 bp. The A. episcopale cp genome was found to be comprised of 132 genes, including 85 protein-coding genes (PCGs), 37 transfer RNA genes (tRNAs), eight ribosomal RNA genes (rRNAs), and two pseudogenes. A total of 20 genes contained introns, of which 14 genes contained a single intron and two genes had two introns. The chloroplast genome of A. episcopale contained 64 codons encoding 20 amino acids, with the number of codons encoding corresponding amino acids ranging from 22 to 1068. The Met and Trp amino acids have only one codon, and other amino acids had 2–6 codons. A total of 64 simple sequence repeats (SSRs) were identified, among which mononucleotide sequences accounted for the most. Phylogenetic analysis showed that A. episcopale is closely related with A. delavayi. Cumulatively the results of this study provided an essential theoretical basis for the molecular identification and phylogeny of A. episcopale.
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15
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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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16
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Huo Z, Xu W, Guo H, Yang P, Zhang Q, Lu X, Wang L. The complete chloroplast genome of Persicaria perfoliata and comparative analysis with Four Medicinal Plants of Polygonaceae. Genome 2022; 65:377-389. [PMID: 35576612 DOI: 10.1139/gen-2021-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Polygonaceae is a large family of medicinal herbs that includes many species used as traditional Chinese medicine, such as Persicaria perfoliate. Here, we sequenced the complete cp genome of P. perfoliata using Illumina sequencing technology with the purpose to provide a method to facilitate accurate identification. After being annotated, the cp genome of P. perfoliata was compared with Fagopyrum tataricum, Persicaria chinensis, Fagopyrum dibotrys and Fallopia multiflora. The complete cp genome of P. perfoliata is 160,730 bp in length, containing a small single copy (SSC) region of 12,927 bp, a large single copy (LSC) region of 85,433 bp and a pair of inverted repeats (IR) regions of 62,370 bp. A total of 131 genes were annotated, including eight rRNA genes, 34 tRNA genes and 84 protein-coding genes. Forty-two simple sequence repeats and fifty-five repeat sequences were identified. Mutational hot spots analyses indicated that five genes (matK, ndhF, ccsA, cemA, rpl20) could be selected as candidates for molecular markers. Moreover, phylogenetic analysis showed that all the Polygonaceae species formed a monophyletic clade, and P. perfoliata showed the closest relationship with P. chinense. The study provides valuable molecular information to accurately identify P. perfoliata and assist in its development and application.
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Affiliation(s)
- Ziting Huo
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Wenbo Xu
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Huijun Guo
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Peng Yang
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Qianwen Zhang
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Xu Lu
- China Pharmaceutical University, 56651, Nanjing, China;
| | - Long Wang
- China Pharmaceutical University, 56651, Nanjing, China;
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Li Q, Xia M, Yu J, Chen S, Zhang F. Plastid genome insight to the taxonomic problem for Aconitum pendulum and A. flavum (Ranunculaceae). Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00969-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Han C, Ding R, Zong X, Zhang L, Chen X, Qu B. Structural characterization of Platanthera ussuriensis chloroplast genome and comparative analyses with other species of Orchidaceae. BMC Genomics 2022; 23:84. [PMID: 35086477 PMCID: PMC8796522 DOI: 10.1186/s12864-022-08319-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Tulotis has been classified into the genus Platanthera in the present taxonomic studies since the morphological characteristics of this genus is very similar to that of Platanthera. Platanthera ussuriensis, formerly named as Tulotis ussuriensis, is a small terrestrial orchid species and has been listed as wild plant under State protection (category II) in China. An improved understanding of the genomic information will enable future applications of conservation strategy as well as phylogenetic studies for this rare orchid species. The objective of this research was to characterize and compare the chloroplast genome of P. ussuriensis with other closely related species of Orchidaceae. RESULTS The chloroplast genome sequence of P. ussuriensis is 155,016 bp in length, which included a pair of inverted repeats (IRs) of 26,548 bp that separated a large single copy (LSC) region of 83,984 bp and a small single copy (SSC) region of 17,936 bp. The annotation contained a total of 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The simple sequence repeat (SSR) analysis showed that there were 104 SSRs in the chloroplast genome of P. ussuriensis. RNA editing sites recognition indicated 72 RNA editing events occurred, and all codon changes were C to T conversions. Comparative genomics showed that the chloroplast sequence of Platanthera related species were relatively conserved, while there were still some high variation regions that could be used as molecular markers. Moreover, Platanthera related species showed similar IR/SSC and IR/LSC borders. The phylogenetic analysis suggested that P. ussuriensis had a closer evolutionary relationship with P. japonica followed by the remaining Platanthera species. CONCLUSION Orchidaceae is a key group of biodiversity protection and also a hot spot group in the plant taxonomy and evolution studies due to their characteristics of high specialization and rapid evolution. This research determined the complete chloroplast genome of P. ussuriensis for the first time, and compared the sequence with other closely related orchid species. These results provide a foundation for future genomic and molecular evolution of the Orchidaceae species, and provide insights into the development of conservation strategy for Platanthera species.
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Affiliation(s)
- Chenyang Han
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Rui Ding
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110161, China
| | - Xiaoyan Zong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
| | - Lijie Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang, 110161, China
| | - Xuhui Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China.
| | - Bo Qu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China
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Sun J, Wang Y, Garran TA, Qiao P, Wang M, Yuan Q, Guo L, Huang L. Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources. Front Genet 2021; 12:721022. [PMID: 34603384 PMCID: PMC8479170 DOI: 10.3389/fgene.2021.721022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022] Open
Abstract
Leonurus cardiaca has a long history of use in western herbal medicine and is applied for the treatment of gynaecological conditions, anxiety, and heart diseases. Because of its botanical relationship to the primary Chinese species, L. japonicus, and extensive medical indications that go beyond the traditional indications for the Chinese species, it is a promising medicinal resource. Therefore, the features of genetic diversity and variability in the species have been prioritized. To explore these issues, we sequenced the chloroplast genomes of 22 accessions of L. cardiaca from different geographical locations worldwide using high-throughput sequencing. The results indicate that L. cardiaca has a typical quadripartite structure and range from 1,51,236 bp to 1,51,831 bp in size, forming eight haplotypes. The genomes all contain 114 distinct genes, including 80 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Comparative analysis showed abundant diversity of single nucleotide polymorphisms (SNPs), indels, simple sequence repeats (SSRs) in 22 accessions. Codon usage showed highly similar results for L. cardiaca species. The phylogenetic and network analysis indicated 22 accessions forming four clades that were partly related to the geographical distribution. In summary, our study highlights the advantage of chloroplast genome with large data sets in intraspecific diversity evaluation and provides a new tool to facilitate medicinal plant conservation and domestication.
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Affiliation(s)
- Jiahui Sun
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Thomas Avery Garran
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ping Qiao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Academician workstation, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Mengli Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qingjun Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Zhang M, Luo J, Su L, Ding Q, Yin X, Hou F, Gao J, Peng C. The complete chloroplast genome of Aconitum scaposum. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2149-2150. [PMID: 34250240 PMCID: PMC8245100 DOI: 10.1080/23802359.2021.1944380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aconitum scaposum Franch 1894 belongs to the Genus Aconitum and Subgenus Lycoctonum (Ranunculaceae). It is widely distributed in China and adjacent areas, used as herbal medicine and had highy toxic components. This species has little reasearch information, especially its chloroplast (cp) genome information being unclear. Therefore, with the method of high salt and low pH to extract the cp of A. scaposum, we sequenced and assembled the complete cp genome of A. scaposum using Illumina high-throughput sequencing platform. The results showed the cp genome of A. scaposum was 157 688 bp in length, including a pair of inverted repeated regions (IRa 26 156 bp and IRb 26 232 bp, respectively), large single copy region (LSC 69 309 bp) and small single copy region (SSC 16 917 bp). And cp genome of A. scaposum consisted of 145 unique genes, 8 ribosomal RNA (rRNA) genes and 38 transfer RNA (tRNA) genes, with GC content was 38%. Meanwhile, based on the cp complete genome, we performed the phylogenetic tree of 66 species with maximum likelihood (ML) method, respectively. Among them, we selected one Delphinium species as the outgroup and the bootstrap of each braches were greater than 90%. The results indicated that the phylogenetic relationship of A. scaposum was relatively closely related to A. scaposum var. vaginatum compared to other Aconitum species.
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Affiliation(s)
- Min Zhang
- Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiawei Luo
- Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lijun Su
- Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiaojiao Ding
- Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xianmei Yin
- Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Feixia Hou
- Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jihai Gao
- Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Cheng Peng
- Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Li J, Price M, Su DM, Zhang Z, Yu Y, Xie DF, Zhou SD, He XJ, Gao XF. Phylogeny and Comparative Analysis for the Plastid Genomes of Five Tulipa (Liliaceae). BIOMED RESEARCH INTERNATIONAL 2021; 2021:6648429. [PMID: 34239930 PMCID: PMC8235973 DOI: 10.1155/2021/6648429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/09/2021] [Indexed: 11/17/2022]
Abstract
Species of Tulipa (Liliaceae) are of great horticultural importance and are distributed across Europe, North Africa, and Asia. The Tien Shan Mountain is one of the primary diversity centres of Tulipa, but the molecular studies of Tulipa species from this location are lacking. In our study, we assembled four Tulipa plastid genomes from the Tien Shan Mountains, T. altaica, T. iliensis, T. patens, and T. thianschanica, combined with the plastid genome of T. sylvestris to compare against other Liliaceae plastid genomes. We focussed on the species diversity and evolution of their plastid genomes. The five Tulipa plastid genomes proved highly similar in overall size (151,691-152,088 bp), structure, gene order, and content. With comparative analysis, we chose 7 mononucleotide SSRs from the Tulipa species that could be used in further population studies. Phylogenetic analyses based on 24 plastid genomes robustly supported the monophyly of Tulipa and the sister relationship between Tulipa and Amana, Erythronium. T. iliensis, T. thianschanica, and T. altaica were clustered together, and T. patens was clustered with T. sylvestris, with our results clearly demonstrating the relationships between these five Tulipa species. Our results provide a more comprehensive understanding of the phylogenomics and comparative genomics of Tulipa.
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Affiliation(s)
- Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Dan-Mei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Zhen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan, China
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Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis. Sci Rep 2021; 11:11731. [PMID: 34083611 PMCID: PMC8175739 DOI: 10.1038/s41598-021-91071-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
Adrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla.
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Alanazi KM, Ali MA, Kim SY, Rahman MO, Farah MA, Alhemaid F, Elangbam M, Gurung AB, Lee J. The cp genome characterization of Adenium obesum: Gene content, repeat organization and phylogeny. Saudi J Biol Sci 2021; 28:3768-3775. [PMID: 34220230 PMCID: PMC8241589 DOI: 10.1016/j.sjbs.2021.03.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/01/2022] Open
Abstract
Adenium obesum (Forssk.) Roem. & Schult. belonging to the family Apocynaceae, is remarkable for its horticultural and ornamental values, poisonous nature, and medicinal uses. In order to have understanding of cp genome characterization of highly valued medicinal plant, and the evolutionary and systematic relationships, the complete plastome / chloroplast (cp) genome of A. obesum was sequenced. The assembled cp genome of A. obesum was found to be 154,437 bp, with an overall GC content of 38.1%. A total of 127 unique coding genes were annotated including 96 protein-coding genes, 28 tRNA genes, and 3 rRNA genes. The repeat structures were found to comprise of only mononucleotide repeats. The SSR loci are compososed of only A/T bases. The phylogenetic analysis of cp genomes revealed its proximity with Nerium oleander.
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Affiliation(s)
- Khalid Mashay Alanazi
- Genetics Laboratory, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Soo-Yong Kim
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - M Oliur Rahman
- Department of Botany, University of Dhaka, Dhaka 1000, Bangladesh
| | - Mohammad Abul Farah
- Genetics Laboratory, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fahad Alhemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Meena Elangbam
- Genetics Laboratory, Centre of Advanced Studies in Life Sciences, Manipur University, Canchipur 795 003, India
| | - Arun Bahadur Gurung
- Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong - 793022, Meghalaya, India
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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Wang Y, Wang S, Liu Y, Yuan Q, Sun J, Guo L. Chloroplast genome variation and phylogenetic relationships of Atractylodes species. BMC Genomics 2021; 22:103. [PMID: 33541261 PMCID: PMC7863269 DOI: 10.1186/s12864-021-07394-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07394-8.
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Affiliation(s)
- Yiheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qingjun Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jiahui Sun
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Guan Y, Wang P, Qie H, Huang Y, Yu W. The characterization and phylogenetic analysis of complete chloroplast genome in Morella cerifera (Myricaceae). Mitochondrial DNA B Resour 2021; 6:66-68. [PMID: 33521269 PMCID: PMC7819111 DOI: 10.1080/23802359.2020.1845997] [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
The first complete chloroplast genome of Morella cerifera was obtained by illumina platform sequencing technology in this study. The size of genome is 158,943 base pairs, consist of a pair of IRs 26,043 bp in length, the LSC region of 88,167 bp and SSC region of 18,690 bp. The genome has 112 unique genes, among which 79 protein-coding genes, 29 tRNAs, and 4 rRNAs. Phylogenetic analysis revealed that M. cerifera clustered with M. rubra within Myricaceae.
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Affiliation(s)
- Yuanlin Guan
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Hefei, China
| | - Pengkai Wang
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
- Suzhou Polytechnic Institute of Agriculture, Suzhou, China
| | - Hongli Qie
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
| | - Yinghong Huang
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
| | - Wensheng Yu
- Taihu Extension Center for Evergreen Fruit of Jiangsu Province, Suzhou, China
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Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae). Sci Rep 2020; 10:19781. [PMID: 33188288 PMCID: PMC7666119 DOI: 10.1038/s41598-020-76699-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
Pulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.
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The complete chloroplast genome of Amana baohuaensis (Liliaceae). Mitochondrial DNA B Resour 2020; 5:3665-3667. [PMID: 33367052 PMCID: PMC7646578 DOI: 10.1080/23802359.2020.1831989] [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] [Indexed: 11/18/2022] Open
Abstract
Amana baohuaensis is a new species that was just named in 2019. Here, we obtained the complete chloroplast (cp) genome of A. baohuaensis using the Illumina paired-end sequencing technology. The cp genome has a typical quadripartite structure with 150,757 bp in length, containing a large single-copy (LSC) region of 81,757 bp, a small single-copy (SSC) region of 16,962 bp, and two inverted repeat (IR) regions of 26,019 bp. The total GC content is 36.73%, of which, the GC content of LSC, SSC and IR regions are 34.63%, 30.11% and 42.20%, respectively. The cp genome of A. baohuaensis contains 111 unique genes, including 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. The Maximum Parsimony (MP) phylogenetic analysis suggested that A. baohuaensis had the closest relationship with A. wanzhensis, and all Amana species grouped together with high bootstrap support.
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Liu H, Hu H, Zhang S, Jin J, Liang X, Huang B, Wang L. The complete chloroplast genome of the rare species Epimedium tianmenshanensis and comparative analysis with related species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2075-2083. [PMID: 33088051 PMCID: PMC7548308 DOI: 10.1007/s12298-020-00882-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/30/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Epimedium tianmenshanensis is a rare perennial herb distributed in China, and it is also an important medicinal plant. Here, we used illumina paired-end sequencing technology to obtain the complete chloroplast genome of E. tianmenshanensis, and compared analysis with related species. The length of the complete chloroplast genome of E. tianmenshanensis is 156,956 bp, which is a relatively conserved quadripartite structure including a large single copy (LSC) region of 88,409 bp, a small single copy (SSC) region of 17,448 bp, and a pair of inverted repeat (IRa/IRb) regions of 25,550 bp. The whole genome contains 132 unique genes, including 85 protein-coding genes, 38 tRNA genes, eight rRNA genes and one pseudogene. 87 simple sequence repeats (SSRs) were identified, and most of them were found to be composed of A/T. In addition, 22,923 codons were detected in 78 protein-coding genes of E. tianmenshanensis, and the overall codon bias pattern in the genome tended to use A/U ending codons. Phylogenetic analysis demonstrated that all the Epimedium species formed a monophyletic clade, and E. tianmenshanensis had the closest relationship to E. dolichostemon. The results of this study provided useful molecular information about the evolution and molecular biology of E. tianmenshanensis.
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Affiliation(s)
- Hao Liu
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, 410013 China
| | - Haibo Hu
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000 China
| | - Shuihan Zhang
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, 410013 China
| | - Jian Jin
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, 410013 China
| | - Xuejuan Liang
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, 410013 China
| | - Bing Huang
- School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing, 211198 China
| | - Long Wang
- School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing, 211198 China
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Wang L, Lu G, Liu H, Huang L, Jiang W, Li P, Lu X. The complete chloroplast genome sequence of Gynostemma yixingense and comparative analysis with congeneric species. Genet Mol Biol 2020; 43:e20200092. [PMID: 33001132 PMCID: PMC7521087 DOI: 10.1590/1678-4685-gmb-2020-0092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/19/2020] [Indexed: 11/21/2022] Open
Abstract
Gynostemma yixingense, an important medicinal member of the Cucurbitaceae family, is an endemic herbaceous species distributed in East China. It is morphologically similar to the plants in the same genus, which resulted in some confusion in identification and application. Meanwhile, there are still some controversies in taxonomy. Herein, the complete chloroplast genome sequence of G. yixingense was obtained by Illumina paired-end sequencing technology and compared to other chloroplast genome sequences of congeneric species. The complete chloroplast genome of G. yixingense is 157,910 bp in length with 36.94% GC content and contains a large single-copy (LSC) region of 86,791 bp, a small single-copy (SSC) region of 18,635 bp and a pair of inverted repeat (IR) regions of 26,242 bp. The whole genome contains 133 unique genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. In addition, 74 simple sequence repeats (SSRs) were identified, most of which were A/T rich. The phylogenetic analysis indicated that G. yixingense had the closest relationship to G. laxiflorum. The result of this study provided an important theoretical basis for chloroplast genome and phylogenetic analysis of G. yixingense.
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Affiliation(s)
- Long Wang
- China Pharmaceutical University, School of Traditional Chinese Medicine, State Key Laboratory of Natural Medicines, Nanjing, China
| | - Gengyu Lu
- China Pharmaceutical University, School of Traditional Chinese Medicine, State Key Laboratory of Natural Medicines, Nanjing, China
| | - Hao Liu
- Hunan Academy of Chinese Medicine, Institute of Chinese Materia Medica, Changsha, China
| | - Lijin Huang
- China Pharmaceutical University, School of Traditional Chinese Medicine, State Key Laboratory of Natural Medicines, Nanjing, China
| | - Weimin Jiang
- Hengyang Normal University, College of Life Sciences and Environment, Hengyang, Hunan, China
| | - Ping Li
- China Pharmaceutical University, School of Traditional Chinese Medicine, State Key Laboratory of Natural Medicines, Nanjing, China
| | - Xu Lu
- China Pharmaceutical University, School of Traditional Chinese Medicine, State Key Laboratory of Natural Medicines, Nanjing, China
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Chloroplast genome characterization of Bupleurum dracaenoides, a critically endangered woody species endemic to China, with insights of Apioideae phylogeny. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Hishamuddin MS, Lee SY, Ng WL, Ramlee SI, Lamasudin DU, Mohamed R. Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships. Sci Rep 2020; 10:13034. [PMID: 32747724 PMCID: PMC7400740 DOI: 10.1038/s41598-020-70030-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/17/2020] [Indexed: 11/28/2022] Open
Abstract
Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.
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Affiliation(s)
- Muhammad Syahmi Hishamuddin
- Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Shiou Yih Lee
- Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900, Sepang, Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Dhilia Udie Lamasudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Rozi Mohamed
- Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Guo XL, Zheng HY, Price M, Zhou SD, He XJ. Phylogeny and Comparative Analysis of Chinese Chamaesium Species Revealed by the Complete Plastid Genome. PLANTS 2020; 9:plants9080965. [PMID: 32751647 PMCID: PMC7464574 DOI: 10.3390/plants9080965] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
Chamaesium H. Wolff (Apiaceae, Apioideae) is a small genus mainly distributed in the Hengduan Mountains and the Himalayas. Ten species of Chamaesium have been described and nine species are distributed in China. Recent advances in molecular phylogenetics have revolutionized our understanding of Chinese Chamaesium taxonomy and evolution. However, an accurate phylogenetic relationship in Chamaesium based on the second-generation sequencing technology remains poorly understood. Here, we newly assembled nine plastid genomes from the nine Chinese Chamaesium species and combined these genomes with eight other species from five genera to perform a phylogenic analysis by maximum likelihood (ML) using the complete plastid genome and analyzed genome structure, GC content, species pairwise Ka/Ks ratios and the simple sequence repeat (SSR) component. We found that the nine species’ plastid genomes ranged from 152,703 bp (C. thalictrifolium) to 155,712 bp (C. mallaeanum), and contained 133 genes, 34 SSR types and 585 SSR loci. We also found 20,953–21,115 codons from 53 coding sequence (CDS) regions, 38.4–38.7% GC content of the total genome and low Ka/Ks (0.27–0.43) ratios of 53 aligned CDS. These results will facilitate our further understanding of the evolution of the genus Chamaesium.
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Affiliation(s)
- Xian-Lin Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (X.-L.G.); (H.-Y.Z.)
| | - Hong-Yi Zheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (X.-L.G.); (H.-Y.Z.)
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China;
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (X.-L.G.); (H.-Y.Z.)
- Correspondence: (S.-D.Z.); (X.-J.H.)
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (X.-L.G.); (H.-Y.Z.)
- Correspondence: (S.-D.Z.); (X.-J.H.)
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Zavala-Páez M, Vieira LDN, de Baura VA, Balsanelli E, de Souza EM, Cevallos MC, Chase MW, Smidt EDC. Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae). FRONTIERS IN PLANT SCIENCE 2020; 11:799. [PMID: 32719690 PMCID: PMC7347972 DOI: 10.3389/fpls.2020.00799] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/19/2020] [Indexed: 05/23/2023]
Abstract
Pantropical Bulbophyllum, with ∼2,200 species, is one of the largest genera in Orchidaceae. Although phylogenetics and taxonomy of the ∼60 American species in the genus are generally well understood, some species complexes need more study to clearly delimit their component species and provide information about their evolutionary history. Previous research has suggested that the plastid genome includes phylogenetic markers capable of providing resolution at low taxonomic levels, and thus it could be an effective tool if these divergent regions can be identified. In this study, we sequenced the complete plastid genome of eight Bulbophyllum species, representing five of six Neotropical taxonomic sections. All plastomes conserve the typical quadripartite structure, and, although the general structure of plastid genomes is conserved, differences in ndh-gene composition and total length were detected. Total length was determined by contraction and expansion of the small single-copy region, a result of an independent loss of the seven ndh genes. Selection analyses indicated that protein-coding genes were generally well conserved, but in four genes, we identified 95 putative sites under positive selection. Furthermore, a total of 54 polymorphic simple sequence repeats were identified, for which we developed amplification primers. In addition, we propose 10 regions with potential to improve phylogenetic analyses of Neotropical Bulbophyllum species.
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Affiliation(s)
| | | | - Valter Antônio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Marco Cerna Cevallos
- Grupo de Investigación Nunkui Wakan, Universidad Politécnica Salesiana, Quito, Ecuador
| | - Mark W. Chase
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
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Li Q, Li X, Qieyang R, Nima C, Dongzhi D, Duojie, Guo X. Characterization of the complete chloroplast genome of the Tangut monkshood Aconitum tanguticum (Ranunculales: Ranunculaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2306-2307. [PMID: 33457769 PMCID: PMC7782905 DOI: 10.1080/23802359.2020.1773338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Tangut monkshood (Aconitum tanguticum) is a perennial herb with high medicinal values. Here, its chloroplast genome was assembled from Illumina sequencing reads. The circular genome is 157,114 bp long with an A + T-biased nucleotide composition, and comprises a pair of inverted repeat (IR) regions (26,255 bp), separated by a large single-copy (LSC) region (87,559 bp) and a small single-copy (SSC) region (17,045 bp). It encodes a total of 112 gene species, with 19 of them being completely or partially duplicated and 18 of them harboring one or two introns. Phylogenetic analysis recovered two major clades of the genus Aconitum.
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Affiliation(s)
- Qien Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Xianjia Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Rangzhong Qieyang
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Cairang Nima
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Duojie Dongzhi
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Duojie
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Xiao Guo
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
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He S, Yang Y, Li Z, Wang X, Guo Y, Wu H. Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment. PeerJ 2020; 8:e9132. [PMID: 32509453 PMCID: PMC7247528 DOI: 10.7717/peerj.9132] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/14/2020] [Indexed: 11/20/2022] Open
Abstract
The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.
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Affiliation(s)
- Shuilian He
- College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Yang Yang
- College of Science, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Ziwei Li
- College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Xuejiao Wang
- College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Yanbing Guo
- College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China
| | - Hongzhi Wu
- College of horticulture and landscape, Yunnan Agricultural University, Kunming, Yunnan, China
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Park S, An B, Park S. Recurrent gene duplication in the angiosperm tribe Delphinieae (Ranunculaceae) inferred from intracellular gene transfer events and heteroplasmic mutations in the plastid matK gene. Sci Rep 2020; 10:2720. [PMID: 32066766 PMCID: PMC7026143 DOI: 10.1038/s41598-020-59547-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/30/2020] [Indexed: 01/08/2023] Open
Abstract
The study of intracellular gene transfer may allow for the detection of interesting evolutionary processes such as ancient polyploidization. We compared 24 plastid genomes (plastomes) from tribe Delphinieae, one from tribe Nigelleae and one from tribe Ranunculeae, including five newly sequenced genomes. The functional transfers of the plastids rpl32 and rps16 to the nucleus in tribe Delphinieae were identified. Unexpectedly, we discovered multiple divergent copies of the nuclear-encoded plastid rpl32 in the genus Aconitum. Phylogenetic and synonymous substitution rate analyses revealed that the nuclear-encoded plastid rpl32 underwent two major duplication events. These ancient gene duplication events probably occurred via multiple polyploidization events in Aconitum between 11.9 and 24.7 Mya. Furthermore, our sequence rate analysis indicated that the eight plastid-encoded rpl subunits in Aconitum had a significantly accelerated evolutionary rate compared to those in other genera, suggesting that highly divergent paralogs targeted to the plastid may contribute to an elevated rate of evolution in plastid rpl genes. In addition, heteroplasmy of the plastid matK from two Aconitum species suggested the existence of potentially functional plastid maturases in its plastome. Our results provide insight into the evolutionary history of the tribe Delphinieae.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - Boram An
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
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Yang CJ, Zhang H, Bai YL, Yang TT. The complete chloroplast genome sequence of Thuja koraiensis from Changbai Mountain in China. Mitochondrial DNA B Resour 2020; 5:947-948. [PMID: 33366820 PMCID: PMC7748546 DOI: 10.1080/23802359.2020.1719918] [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: 11/05/2022] Open
Abstract
In this study, the complete chloroplast genome of Thuja koraiensis was sequenced and analyzed. The complete chloroplast genome of T. koraiensis was 130,027 bp in length, encoding a total of 116 genes, including 80 protein-coding genes, 32 tRNAs, and 4 rRNAs, with a CG content of 34.24%. The phylogenetic analysis of T. koraiensis was carried out to determine the position of Thujoideae in the phylogenetic evolution.
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Affiliation(s)
- Cheng Jun Yang
- Northeast Forestry University, Harbin, Heilongjiang, P. R. China
| | - Hang Zhang
- Northeast Forestry University, Harbin, Heilongjiang, P. R. China
| | - Yi Liang Bai
- Northeast Forestry University, Harbin, Heilongjiang, P. R. China
| | - Tian Tian Yang
- Northeast Forestry University, Harbin, Heilongjiang, P. R. China
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Cheng ZD, He J, Zhang YM, Yang CW, Ma XX, Li GD. The complete chloroplast genome sequence of Aconitum austroyunnanense W. T. Wang (Ranunculaceae): a medicinal plant endemic to China. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 5:248-249. [PMID: 33366507 PMCID: PMC7748539 DOI: 10.1080/23802359.2019.1700195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The complete chloroplast (cp) genome of Aconitum austroyunnanense W. T. Wang, a rare and endangered medicinal plant endemic to southwestern China, was sequenced to be 155,818 bp in length, including two inverted repeat (IR, 26,128 bp) regions, one large single-copy region (LSC) and one small single-copy region (SSC) of 86,555 bp and 17,007 bp, respectively. The cp genome has 131 annotated genes, including 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and a pseudogene (ycf1). The overall GC content of it is 38.1%. Phylogenetic analysis revealed that the cp genome of A. austroyunnanense is closely related to that of Aconitum hemsleyanum.
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Affiliation(s)
- Zi-Dan Cheng
- Faculty of Traditional Chinese Pharmacy, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Jun He
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ying-Min Zhang
- Faculty of Traditional Chinese Pharmacy, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Cong-Wei Yang
- Faculty of Traditional Chinese Pharmacy, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Xiao-Xia Ma
- Faculty of Traditional Chinese Pharmacy, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Guo-Dong Li
- Faculty of Traditional Chinese Pharmacy, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
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Lee SR, Kim K, Lee BY, Lim CE. Complete chloroplast genomes of all six Hosta species occurring in Korea: molecular structures, comparative, and phylogenetic analyses. BMC Genomics 2019; 20:833. [PMID: 31706273 PMCID: PMC6842461 DOI: 10.1186/s12864-019-6215-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/22/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia. Due to considerable morphological variability, the genus has been well recognized as a group with taxonomic problems. Chloroplast is a cytoplasmic organelle with its own genome, which is the most commonly used for phylogenetic and genetic diversity analyses for land plants. To understand the genomic architecture of Hosta chloroplasts and examine the level of nucleotide and size variation, we newly sequenced four (H. clausa, H. jonesii, H. minor, and H. venusta) and analyzed six Hosta species (including the four, H. capitata and H. yingeri) distributed throughout South Korea. RESULTS The average size of complete chloroplast genomes for the Hosta taxa was 156,642 bp with a maximum size difference of ~ 300 bp. The overall gene content and organization across the six Hosta were nearly identical with a few exceptions. There was a single tRNA gene deletion in H. jonesii and four genes were pseudogenized in three taxa (H. capitata, H. minor, and H. jonesii). We did not find major structural variation, but there were a minor expansion and contractions in IR region for three species (H. capitata, H. minor, and H. venusta). Sequence variations were higher in non-coding regions than in coding regions. Four genic and intergenic regions including two coding genes (psbA and ndhD) exhibited the largest sequence divergence showing potential as phylogenetic markers. We found compositional codon usage bias toward A/T at the third position. The Hosta plastomes had a comparable number of dispersed and tandem repeats (simple sequence repeats) to the ones identified in other angiosperm taxa. The phylogeny of 20 Agavoideae (Asparagaceae) taxa including the six Hosta species inferred from complete plastome data showed well resolved monophyletic clades for closely related taxa with high node supports. CONCLUSIONS Our study provides detailed information on the chloroplast genome of the Hosta taxa. We identified nucleotide diversity hotspots and characterized types of repeats, which can be used for developing molecular markers applicable in various research area.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biological Science, Texas Tech University, Lubbock, TX USA
| | - Kyeonghee Kim
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 South Korea
| | - Byoung-Yoon Lee
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 South Korea
| | - Chae Eun Lim
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 South Korea
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40
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Kim Y, Yi JS, Min J, Xi H, Kim DY, Son J, Park J, Jeon JI. The complete chloroplast genome of Aconitum coreanum (H. Lév.) Rapaics (Ranunculaceae). Mitochondrial DNA B Resour 2019; 4:3404-3406. [PMID: 33366014 PMCID: PMC7707295 DOI: 10.1080/23802359.2019.1674213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/23/2019] [Indexed: 11/29/2022] Open
Abstract
Aconitum coreanum (H. Lév.) Rapaics listed in the Korean Red List is a medicinal herb. We presented complete chloroplast genome, which is 157,024 bp long and has four subregions: 87,637 bp of large single-copy and 16,901 bp of small single-copy regions, which are separated by two 26,243 bp inverted repeat regions including 132 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast is 38.0%. Phylogenetic trees show that A. coreanum occupied a basal position at subgenus Aconitum clade and two A. coreanum isolated from midwestern and eastern regions of Korea are clustered together.
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Affiliation(s)
- Yongsung Kim
- InfoBoss Co., Ltd., Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Jae-Sun Yi
- Shingu Botanic Garden, Seongnam-si, The Republic of Korea
- Department of Environmental Horticulture, University of Seoul, Seoul, The Republic of Korea
| | - Juhyeon Min
- InfoBoss Co., Ltd., Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Hong Xi
- InfoBoss Co., Ltd., Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Da Yeon Kim
- Shingu Botanic Garden, Seongnam-si, The Republic of Korea
- Department of Environmental Horticulture, University of Seoul, Seoul, The Republic of Korea
| | - Janghyuk Son
- InfoBoss Co., Ltd., Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, The Republic of Korea
- InfoBoss Research Center, Seoul, The Republic of Korea
| | - Jeong-Ill Jeon
- Shingu Botanic Garden, Seongnam-si, The Republic of Korea
- Department of Horticulture Design, Shingu College, Seongnam-si, The Republic of Korea
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Ge Y, Dong X, Wu B, Wang N, Chen D, Chen H, Zou M, Xu Z, Tan L, Zhan R. Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships. PLoS One 2019; 14:e0221827. [PMID: 31532782 PMCID: PMC6750585 DOI: 10.1371/journal.pone.0221827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/15/2019] [Indexed: 11/19/2022] Open
Abstract
Chloroplasts significantly influence species phylogenies because of their maternal inheritance and the moderate evolutionary rate of their genomes. Avocado, which is a member of the family Lauraceae, has received considerable attention from botanists, likely because of its position as a basal angiosperm. However, there is relatively little avocado genomic information currently available. In this study, six complete avocado chloroplast genomes from three ecological races were assembled to examine the sequence diversity among the three avocado ecological races. A comparative genomic analysis revealed that 515 simple sequence repeat loci and 176 repeats belonging to four other types were polymorphic across the six chloroplast genomes. Three highly variable regions (trnC-GCA-petN, petN-psbM, and petA-psbJ) were identified as highly informative markers. A phylogenetic analysis based on 79 common protein-coding genes indicated that the six examined avocado accessions from three ecological races form a monophyletic clade. The other three genera belonging to the Persea group clustered to form a sister clade with a high bootstrap value. These chloroplast genomes provide important genetic information for future attempts at identifying avocado races and for the related biological research.
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Affiliation(s)
- Yu Ge
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiangshu Dong
- College of Agriculture, Yunnan University, Yunnan, China
| | - Bin Wu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Nan Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Di Chen
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Haihong Chen
- College of Agriculture, Guangxi Vocational and Technical College, Nanning, China
| | - Minghong Zou
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Zining Xu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lin Tan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- * E-mail: (LT); (RZ)
| | - Rulin Zhan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- * E-mail: (LT); (RZ)
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Rapid identification of Aconitum plants based on loop-mediated isothermal amplification assay. BMC Res Notes 2019; 12:408. [PMID: 31307543 PMCID: PMC6631447 DOI: 10.1186/s13104-019-4463-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/11/2019] [Indexed: 12/25/2022] Open
Abstract
Objective Aconitum plants (Ranunculaceae) exhibit toxicity, and accidental ingestion of the plants has been reported in Japan. Identifying the cause of poisoning is important for emergency medical treatment, and a rapid and simple detection technique is required for the identification of poisoning cause. In the present study, we developed a rapid and simple method for detecting Aconitum plant DNA using a loop-mediated isothermal amplification (LAMP) assay. Results Specific LAMP primers for Aconitum plants were designed based on the trnL–trnF intergenic spacer region. Using the LAMP primers, the LAMP assay included an initiation reaction of 10 min followed by amplification for 20 min at the isothermal reaction temperature of 65 °C. The LAMP reaction was demonstrated to be specific and highly sensitive to Aconitum plants, given that the assay can be used for 1 pg of purified DNA. Using raw extracted DNA as template, the entire detection procedure from DNA extraction to final detection required only 30 min. Moreover, the protocol identified samples containing approximately 5 mg of Aconitum plants cooked and digested with artificial gastric juice. The currently proposed protocol exhibits good potential as a screening method of Aconitum plant poisoning for emergency medical care. Electronic supplementary material The online version of this article (10.1186/s13104-019-4463-1) contains supplementary material, which is available to authorized users.
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Gao B, Yuan L, Tang T, Hou J, Pan K, Wei N. The complete chloroplast genome sequence of Alpinia oxyphylla Miq. and comparison analysis within the Zingiberaceae family. PLoS One 2019; 14:e0218817. [PMID: 31233551 PMCID: PMC6590956 DOI: 10.1371/journal.pone.0218817] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/10/2019] [Indexed: 11/18/2022] Open
Abstract
Alpinia oxyphylla Miq. (A. oxyphylla) is an important edible and traditional herbal medicine. In this study, the complete chloroplast genome of A. oxyphylla was sequenced, analysed, and compared to five species in the Zingiberaceae family. The size of the A. oxyphylla chloroplast genome was 161351 bp, which consisted of a large single-copy (LSC, 87248 bp) and small single-copy (SSC, 16175 bp) region separated by a pair of inverted repeats (IRa and IRb, 28964 bp each). The genome encoded 132 unique genes, including 87 protein-coding genes, 37 tRNAs and four rRNAs. The GC content of the genome was 36.17%. A total of 53 simple sequence repeats (SSRs) and 80 long repeats were identified in the A. oxyphylla chloroplast genome. The chloroplast genome of A. oxyphylla shared the highest sequence similarity of >90% with the chloroplast genome of A. zerumbet, and six chloroplast genomes in the Zingiberaceae family were compared by using CGView Comparison Tool (CCT). According to the phylogenetic tree, the Zingiberaceae family is divided into two categories, which coincide with the classification of the characteristics of sun-like and shade-like in plants. Our results reveal the phototrophic component of NADH-dehydrogenase (ndhB and ndhC), photosystem II (psbZ) and ATP synthase (atpE, atpF) exhibit adaptive evolution under different environments, and the strength of light is an important trigger for the adaptations at the chloroplast level.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of R&D on Tropical Herbs, Hainan Medical University, Haikou, China
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Lin Yuan
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Tianle Tang
- Environmental Science, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou, China
| | - Jie Hou
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Kun Pan
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Na Wei
- Hainan Provincial Key Laboratory of R&D on Tropical Herbs, Hainan Medical University, Haikou, China
- School of Pharmacy, Hainan Medical University, Haikou, China
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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus. Molecules 2018; 23:molecules23102426. [PMID: 30248930 PMCID: PMC6222381 DOI: 10.3390/molecules23102426] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023] Open
Abstract
We sequenced and analyzed the complete chloroplast genome of Aster tataricus (family Asteraceae), a Chinese herb used medicinally to relieve coughs and reduce sputum. The A. tataricus chloroplast genome was 152,992 bp in size, and harbored a pair of inverted repeat regions (IRa and IRb, each 24,850 bp) divided into a large single-copy (LSC, 84,698 bp) and a small single-copy (SSC, 18,250 bp) region. Our annotation revealed that the A. tataricus chloroplast genome contained 115 genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. In addition, 70 simple sequence repeats (SSRs) were detected in the A. tataricus chloroplast genome, including mononucleotides (36), dinucleotides (1), trinucleotides (23), tetranucleotides (1), pentanucleotides (8), and hexanucleotides (1). Comparative chloroplast genome analysis of three Aster species indicated that a higher similarity was preserved in the IR regions than in the LSC and SSC regions, and that the differences in the degree of preservation were slighter between A. tataricus and A. altaicus than between A. tataricus and A. spathulifolius. Phylogenetic analysis revealed that A. tataricus was more closely related to A. altaicus than to A. spathulifolius. Our findings offer valuable information for future research on Aster species identification and selective breeding.
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