1
|
Song C, Zhu J, Li H. Complete chloroplast genomes of eight Delphinium taxa (Ranunculaceae) endemic to Xinjiang, China: insights into genome structure, comparative analysis, and phylogenetic relationships. BMC PLANT BIOLOGY 2024; 24:600. [PMID: 38926811 PMCID: PMC11201361 DOI: 10.1186/s12870-024-05279-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Delphinium L. represents a taxonomically intricate genus of significant phylogenetic and economic importance in Ranunculaceae. Despite the existence of few chloroplast genome datasets, a comprehensive understanding of genome structures and selective pressures within the genus remains unknown. Furthermore, several taxa in this genus are exclusively found in Xinjiang, China, a region renowned for its distribution and diversity of Chinese and Central Asian Delphinium species. Therefore, investigating the features of chloroplast genomes in this area will provide valuable insights into the evolutionary processes and phylogenetic relationships of the genus. RESULTS In this study, the eight newly completed chloroplast genomes are examined, ranging in length from 153,979 bp to 154,284 bp. Alongside these, analysing six previously reported taxa re-annotated in Delphinium, 111 unique genes are identified across all samples. Genome structure, distributions of simple sequence repeats and short dispersed repeats, as well as gene content are similar among these Delphinium taxa. Nine hypervariable intergenic spacers and protein coding regions, including ndhF-trnL(TAG), rpl16-intron, rpl33, rps15, rps18, trnK(TTT)-trnQ(TTG), trnP(TGG)-psaJ, trnT(GGT)-psbD and ycf1, are identified among 13 perennial Delphinium. Selective pressure and codon usage bias of all the plastid genes are performed within 14 Delphinium taxa. Phylogenetic analysis based on 14 Delphinium plastomes, alongside two Aconitum (Ranunculaceae) species serving as outgroup taxa, reveals the monophyletic nature of Delphinium. Our findings further discern Delphinium into two distinct clades: perennial species (clade I) and annual species (clade II). In addition, compared with the nrDNA ITS topology, cytological data and morphological characters, D. mollifolium and D. maackianum showed potential involvement in hybridization or polyploidization processes. Excluding these two species, the perennial Delphinium (clade I) exhibits a stronger consistency with the morphology-based system that utilized seed morphology. CONCLUSION This study represents the first comprehensive analysis of plastomic variations among Delphinium taxa, based on the examination of 14 complete plastomes. The chloroplast genome structure of Delphinium is similar to other angiosperms and possesses the typical quadripartite structure with the conserved genome arrangement and gene features. In addition, the variation of non-coding regions is larger than coding regions of the chloroplast genome. Through DNA sequence divergence across Delphinium plastomes and subsequent phylogenomic analyses ndhF-trnL(TAG) and ycf1 are identified as promising molecular markers. These highly variable loci held significant potential for future phylogenetic and phylogeographic studies on Delphinium. Our phylogenomic analyses based on the whole plastomes, concatenation of 132 unique intergenic spacer regions, concatenation of 77 unique protein-coding genes and nrDNA ITS, all support the monophyly of Delphinium and perennial taxa clusters together into one clade within this genus. These findings provide crucial data for systematic, phylogenomic and evolutionary research in the genus for future studies.
Collapse
Affiliation(s)
- Chunfeng Song
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat- Sen), Nanjing, 210014, Jiangsu, China
| | - Junwen Zhu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat- Sen), Nanjing, 210014, Jiangsu, China
| | - Huimin Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat- Sen), Nanjing, 210014, Jiangsu, China.
| |
Collapse
|
2
|
Lubna, Asaf S, Khan I, Jan R, Asif S, Bilal S, Kim KM, Al-Harrasi A. Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome. Sci Rep 2024; 14:14509. [PMID: 38914674 PMCID: PMC11196742 DOI: 10.1038/s41598-024-65073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising four sections: the Large Single-Copy (LSC) (85,538 bp), the Small Single-Copy (SSC) (17,984 bp), and two Inverted Repeat (IR) regions (25,299 bp). A comparative study of N. sativa's plastome with ten other species from various genera in the Ranunculaceae family reveals substantial structural variations. The contraction of the inverted repeat region in N. sativa influences the boundaries of single-copy regions, resulting in a shorter plastome size than other species. When comparing the plastome of N. sativa with those of its related species, significant divergence is observed, particularly except for N. damascena. Among these, the plastome of A. glaucifolium displays the highest average pairwise sequence divergence (0.2851) with N. sativa, followed by A. raddeana (0.2290) and A. coerulea (0.1222). Furthermore, the study identified 12 distinct hotspot regions characterized by elevated Pi values (> 0.1). These regions include trnH-GUG-psbA, matK-trnQ-UUG, psbK-trnR-UCU, atpF-atpI, rpoB-psbD, ycf3-ndhJ, ndhC-cemA, petA-psaJ, trnN-GUU-ndhF, trnV-GAC-rps12, ycf2-trnI-CAU, and ndhA-ycf1. Approximately, 24 tandem and 48 palindromic and forward repeats were detected in N. sativa plastome. The analysis revealed 32 microsatellites with the majority being mononucleotide repeats. In the N. sativa plastome, phenylalanine had the highest number of codons (1982 codons), while alanine was the least common amino acid with 260 codons. A phylogenetic tree, constructed using protein-coding genes, revealed a distinct monophyletic clade comprising N. sativa and N. damascene, closely aligned with the Cimicifugeae tribe and exhibiting robust support. This plastome provides valuable genetic information for precise species identification, phylogenetic resolution, and evolutionary studies of N. sativa.
Collapse
Affiliation(s)
- Lubna
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Ibrahim Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman.
| |
Collapse
|
3
|
Xue H, Xing Y, Bian C, Hou W, Men W, Zheng H, Yang Y, Ying X, Kang T, Xu L. Comparative analysis of chloroplast genomes of Pulsatilla species reveals evolutionary and taxonomic status of newly discovered endangered species Pulsatilla saxatilis. BMC PLANT BIOLOGY 2024; 24:293. [PMID: 38632540 PMCID: PMC11022354 DOI: 10.1186/s12870-024-04940-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Pulsatilla saxatilis, a new species of the genus Pulsatilla has been discovered. The morphological information of this species has been well described, but its chloroplast genome characteristics and comparison with species of the same genus remain to be reported. RESULTS Our results showed that the total length of chloroplast (cp.) genome of P. saxatilis is 162,659 bp, with a GC content of 37.5%. The cp. genome contains 134 genes, including 90 known protein-coding genes, 36 tRNA genes, and 8 rRNA genes. P. saxatilis demonstrated similar characteristics to other species of genus Pulsatilla. Herein, we compared cp. genomes of 10 species, including P. saxatilis, and found that the cp. genomes of the genus Pulsatilla are extremely similar, with a length of 162,322-163,851 bp. Furthermore, The SSRs of Pulsatilla ranged from 10 to 22 bp in length. Among the four structural regions of the cp. genome, most long repeats and SSRs were detected in the LSC region, followed by that in the SSC region, and least in IRA/ IRB regions. The most common types of long repeats were forward and palindromic repeats, followed by reverse repeats, and only a few complementary repeats were found in 10 cp. genomes. We also analyzed nucleotide diversity and identified ccsA_ndhD, rps16_trnK-UUU, ccsA, and rbcL, which could be used as potential molecular markers for identification of Pulsatilla species. The results of the phylogenetic tree constructed by connecting the sequences of high variation regions were consistent with those of the cp. gene phylogenetic tree, and the species more closely related to P. saxatilis was identified as the P. campanella. CONCLUSION It was determined that the closest species to P. saxatilis is P. campanella, which is the same as the conclusion based on pollen grain characteristics, but different from the P. chinensis determined based on morphological characteristics. By revealing information on the chloroplast characteristics, development, and evolution of the cp. genome and the potential molecular markers, this study provides effective molecular data regarding the evolution, genetic diversity, and species identification of the genus Pulsatilla.
Collapse
Affiliation(s)
- Hefei Xue
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde, 067000, China
| | - Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
- State Key Laboratory of Dao-di Herbs, Beijing, 100700, China
| | - Che Bian
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Wenjuan Hou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Wenxiao Men
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Han Zheng
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- State Key Laboratory of Dao-di Herbs, Beijing, 100700, China
| | - Yanyun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China.
| | - Xixiang Ying
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Tingguo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China.
| |
Collapse
|
4
|
Liu L, Li H, Li J, Li X, Hu N, Wang H, Zhou W. Chloroplast genome analyses of Caragana arborescens and Caragana opulens. BMC Genom Data 2024; 25:16. [PMID: 38336648 PMCID: PMC10854190 DOI: 10.1186/s12863-024-01202-4] [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: 06/08/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Numerous species within the genus Caragana have high ecological and medicinal value. However, species identification based on morphological characteristics is quite complicated in the genus. To address this issue, we analyzed complete plastid genome data for the genus. RESULTS We obtained chloroplast genomes of two species, Caragana arborescens and Caragana opulens, using Illumina sequencing technology, with lengths of 129,473 bp and 132,815 bp, respectively. The absence of inverted repeat sequences in the two species indicated that they could be assigned to the inverted repeat-lacking clade (IRLC). The genomes included 111 distinct genes (4 rRNA genes, 31 tRNA genes, and 76 protein-coding genes). In addition, 16 genes containing introns were identified in the two genomes, the majority of which contained a single intron. Repeat analyses revealed 129 and 229 repeats in C. arborescens and C. opulens, respectively. C. arborescens and C. opulens genomes contained 277 and 265 simple sequence repeats, respectively. The two Caragana species exhibited similar codon usage patterns. rpl20-clpP, rps19-rpl2, and rpl23-ycf2 showed the highest nucleotide diversity (pi). In an analysis of sequence divergence, certain intergenic regions (matK-rbcL, psbM-petN, atpA-psbI, petA-psbL, psbE-petL, and rps7-rps12) were highly variable. A phylogenetic analysis showed that C. arborescens and C. opulens were related and clustered together with four other Caragana species. The genera Astragalus and Caragana were relatively closely related. CONCLUSIONS The present study provides valuable information about the chloroplast genomes of C. arborescens and C. opulens and lays a foundation for future phylogenetic research and molecular marker development.
Collapse
Affiliation(s)
- LiE Liu
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Hongyan Li
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Jiaxin Li
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Xinjuan Li
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Na Hu
- Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Honglun Wang
- Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Wu Zhou
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China.
| |
Collapse
|
5
|
Bian C, Xing YP, Xue HF, Hou WJ, Yang YY, Xu L, Kang TG. The complete chloroplast genome of Pulsatilla chinensis f. alba D. K. Zang (Ranunculaceae, Pulsatilla Miller). Mitochondrial DNA B Resour 2024; 9:233-236. [PMID: 38313466 PMCID: PMC10836482 DOI: 10.1080/23802359.2023.2294894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/09/2023] [Indexed: 02/06/2024] Open
Abstract
Pulsatilla chinensis f. alba D. K. Zang 1993 is a forma of Pulsatilla chinensis (Bge.) Regel, the root of P. chinensis is traditional Chinese medicine called Pulsatillae radix. The biggest difference between P. chinensis f. alba and P. chinensis is that P. chinensis f. alba sepals is white. The complete chloroplast genome of P. chinensis f. alba was sequenced using the Illumina NovaSeq platform for the first time. The lengths of the genome, large single-copy (LSC), small single-copy (SSC), two inverted repeats (IRs), and GC content were 163,654 bp, 82,355 bp, 19,069 bp, 31,115 bp, and 37.2%, respectively. It had 134 genes, including 90 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The maximum-likelihood tree indicated that P. chinensis f. alba had a closer relationship with P. chinensis. This study would provide a theoretical basis for the further study of Pulsatilla plants genetics phylogenetic research.
Collapse
Affiliation(s)
- Che Bian
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yan-Ping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - He-Fei Xue
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Wen-Juan Hou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yan-Yun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Ting-Guo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| |
Collapse
|
6
|
Li Z, Duan B, Zhou Z, Fang H, Yang M, Xia C, Zhou Y, Wang J. Comparative analysis of medicinal plants Scutellaria baicalensis and common adulterants based on chloroplast genome sequencing. BMC Genomics 2024; 25:39. [PMID: 38191291 PMCID: PMC10773089 DOI: 10.1186/s12864-023-09920-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/17/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Scutellaria baicalensis Georgi has been extensively used as a medicinal herb in China for over 2000 years. They may be intentionally or inadvertently substituted or blended with comparable species in the local market, threatening clinical medication safety. Molecular markers are effective tools to prevent misidentification and eliminate doping and falsification among Scutellaria plants. This study screened four highly variable regions to identify Scutellaria and its adulterants. In addition, a phylogenetic analysis was performed using the complete cp genome combined with published Scutellaria species samples. Moreover, a comparative analysis of the cp genomes was conducted to investigate the cp genome evolution of S. baicalensis. RESULTS The complete cp genome of five species of Scutellaria was sequenced for the first time, and four previously published Scutellaria species were re-sequenced. They all exhibited a conserved quadripartite structure in their cp genomes, including two distinct regions, namely a small and large single copy region, respectively, and two inverted repeats encompassing the majority of ribosomal RNA genes. Furthermore, the nine species exhibited high conservation from aspects of the genome structure, codon usage, repeat sequences, and gene content. Four highly variable regions (matK-rps16, ndhC-trnV-UAC, psbE-petL, and rps16-trnQ-UUG) may function as potential molecular markers for differentiating S. baicalensis from its adulterants. Additionally, the monophyly of Scutellaria was ascertained and could be reclassified into two subgenera, subgenus Anaspis and subgenus Scutellaria, as evidenced by the phylogenetic analyses on sequences of cp genome and shared protein-coding sequences. According to the molecular clock analysis, it has been inferred that the divergence of Scutellaria occurred at approximately 4.0 Mya during the Pliocene Epoch. CONCLUSION Our study provides an invaluable theoretical basis for further Scutellaria species identification, phylogenetics, and evolution analysis.
Collapse
Affiliation(s)
- Zhen Li
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Zhongyu Zhou
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, 133002, China
| | - Hui Fang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Ying Zhou
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- Institute of Caulis Dendrobii of Longling County, Baoshan, 678300, China.
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| |
Collapse
|
7
|
Alshegaihi RM. The complete chloroplast genome of the halophyte flowering plant Suaeda monoica from Jeddah, Saudi Arabia. Mol Biol Rep 2024; 51:60. [PMID: 38165474 DOI: 10.1007/s11033-023-09069-x] [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: 06/27/2023] [Accepted: 10/11/2023] [Indexed: 01/03/2024]
Abstract
The complete chloroplast genome (plastome) of the annual flowering halophyte herb Suaeda monoica Forssk. ex J. F. Gmel. family (Amaranthaceae) that grows in Jeddah, Saudi Arabia, was identified for the first time in this study. Suaeda monoica is a medicinal plant species whose taxonomic classification remains controversial. Further, studying the species is useful for current conservation and management efforts. In the current study, the full chloroplast genome S. monoica was reassembled using whole-genome next-generation sequencing and compared with the previously published chloroplast genomes of Suaeda species. The chloroplast genome size of Suaeda monoica was 151,789 bp, with a single large copy of 83,404 bp, a small single copy of 18,007 bp and two inverted repeats regions of 25,189 bp. GC content in the whole genome was 36.4%. The cp genome included 87 genes that coded for proteins, 37 genes coding for tRNA, 8 genes coding for rRNA and one non-coding pseudogene. Five chloroplast genome features were compared between S. monoica and S. japonica, S. glauca, S. salsa, S. malacosperma and S. physophora. Among Suaeda genus and equal to most angiosperms chloroplast genomes, the RSCU values were conservative. Two pseudogenes (accD and ycf1), rpl16 intron and ndhF-rpl32 intergenic spacer, were highlighted as suitable DNA barcodes for different Suaeda species. Phylogenetic analyses show Suaeda cluster into three main groups; one in which S. monoica was closer to S. salsa. The obtained result provided valuable information on the characteristics of the S. monoica chloroplast genome and the phylogenetic relationships.
Collapse
Affiliation(s)
- Rana M Alshegaihi
- Department of Biological Sciences, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia.
| |
Collapse
|
8
|
Mi Y, Xue Z, Qu S, Yin Y, Huang J, Kou R, Wang X, Luo S, Li W, Tang Y. The economic burden of coronary heart disease in mainland China. Public Health 2023; 224:140-151. [PMID: 37797560 DOI: 10.1016/j.puhe.2023.08.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/06/2023] [Accepted: 08/25/2023] [Indexed: 10/07/2023]
Abstract
OBJECTIVES The aim of this study was to systematically evaluate the current economic burden of coronary heart disease (CHD) in mainland China and provide a reference for the formulation of policies to reduce the economic burden of CHD. STUDY DESIGN A systematic literature review was conducted of empirical studies on the economic burden of CHD over the past 20 years. METHODS PubMed, Web of Science, Embase, China Knowledge Resource Integrated Database and the WANFANG database were comprehensively searched for relevant articles published between 1 January 2000 and 22 December 2021. Content analysis was used to extract the data, and Stata 17.0 software was used for analysis. The median values were used to describe trends. RESULTS A total of 35 studies were included in this review. The annual median per-capita hospitalisation expense and the average expense per hospitalisation were $3544.40 ($891.64-$18,371.46) and $5407.34 ($1139.93-$8277.55), respectively. The median ratio on medical consumables expenses, drug expenses, medical examination expenses and treatment expenses were 41.59% (12.40%-63.73%), 26.90% (7.30%-60.00%), 9.45% (1.65%-33.40%) and 10.10% (2.36%-66.00%), respectively. The median per-capita hospitalisation expense in the eastern, central and western regions were $9374.45 ($2056.13-$18,371.46), $4751.5 ($2951.95-$8768.93) and $3251.25 ($891.64-$13,986.38), respectively. The median average expense per hospitalisation in the eastern and central regions were $6177.15 ($1679.15-$8277.55) and $1285.49 ($1239.93-$2197.36), respectively. The median average length of stay in the eastern, central and western regions were 9.3 days, 15.2 days and 16.1 days, respectively. CONCLUSIONS The economic burden of CHD is more severe in mainland China than in developed countries, especially in terms of the direct economic burden. In terms of the types of direct medical expenses, a proportion of medical examination expenses, treatment expenses and drug expenses were lowest in the eastern region, but medical consumables expenses were the highest in this region. This study provides guidance for the formulation of policies to reduce the economic burden of CHD in mainland China.
Collapse
Affiliation(s)
- Y Mi
- School of Public Health, Weifang Medical University, Weifang, PR China
| | - Z Xue
- School of Public Health, Weifang Medical University, Weifang, PR China
| | - S Qu
- School of Public Health, Weifang Medical University, Weifang, PR China
| | - Y Yin
- Qingdao Stomatological Hospital, Qingdao, PR China
| | - J Huang
- School of Public Health, Weifang Medical University, Weifang, PR China
| | - R Kou
- School of Public Health, Weifang Medical University, Weifang, PR China
| | - X Wang
- Personnel Department, Weifang Medical University, Weifang, PR China
| | - S Luo
- School of Management, Weifang Medical University, Weifang, PR China
| | - W Li
- School of Public Health, Weifang Medical University, Weifang, PR China.
| | - Y Tang
- School of Public Health, Weifang Medical University, Weifang, PR China.
| |
Collapse
|
9
|
Yuan Y, Sheng P, Ma B, Xue B, Shen M, Zhang L, Li D, Hou J, Ren J, Liu J, Yan BC, Jiang Y. Elucidation of the mechanism of Yiqi Tongluo Granule against cerebral ischemia/reperfusion injury based on a combined strategy of network pharmacology, multi-omics and molecular biology. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 118:154934. [PMID: 37393828 DOI: 10.1016/j.phymed.2023.154934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 06/10/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Ischemic stroke is caused by local lesions of the central nervous system and is a severe cerebrovascular disease. A traditional Chinese medicine, Yiqi Tongluo Granule (YQTL), shows valuable therapeutic effects. However, the substances and mechanisms remain unclear. PURPOSE We combined network pharmacology, multi-omics, and molecular biology to elucidate the mechanisms by which YQTL protects against CIRI. STUDY DESIGN We innovatively created a combined strategy of network pharmacology, transcriptomics, proteomics and molecular biology to study the active ingredients and mechanisms of YQTL. We performed a network pharmacology study of active ingredients absorbed by the brain to explore the targets, biological processes and pathways of YQTL against CIRI. We also conducted further mechanistic analyses at the gene and protein levels using transcriptomics, proteomics, and molecular biology techniques. RESULTS YQTL significantly decreased the infarction volume percentage and improved the neurological function of mice with CIRI, inhibited hippocampal neuronal death, and suppressed apoptosis. Fifteen active ingredients of YQTL were detected in the brains of rats. Network pharmacology combined with multi-omics revealed that the 15 ingredients regulated 19 pathways via 82 targets. Further analysis suggested that YQTL protected against CIRI via the PI3K-Akt signaling pathway, MAPK signaling pathway, and cAMP signaling pathway. CONCLUSION We confirmed that YQTL protected against CIRI by inhibiting nerve cell apoptosis enhanced by the PI3K-Akt signaling pathway.
Collapse
Affiliation(s)
- Yue Yuan
- Institute for Chinese Materia Medica, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of TCM Pharmacology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100730, China
| | - Peng Sheng
- Department of Neurology, Medical College, Institute of Translational Medicine, Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225001, China
| | - Bo Ma
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Materia Medica, Beijing 100730, China
| | - Bingjie Xue
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Mengmeng Shen
- Department of Neurology, Medical College, Institute of Translational Medicine, Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225001, China
| | - Ling Zhang
- Department of Neurology, Medical College, Institute of Translational Medicine, Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225001, China
| | - Dan Li
- Shineway Pharmaceutical Group Co., Ltd., Shijiazhuang 051430, China
| | - Jincai Hou
- Shineway Pharmaceutical Group Co., Ltd., Shijiazhuang 051430, China
| | - Junguo Ren
- Beijing Key Laboratory of TCM Pharmacology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100730, China
| | - Jianxun Liu
- Beijing Key Laboratory of TCM Pharmacology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100730, China.
| | - Bing Chun Yan
- Department of Neurology, Medical College, Institute of Translational Medicine, Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225001, China.
| | - Yunyao Jiang
- Institute for Chinese Materia Medica, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
10
|
Kim KR, Park SY, Kim H, Hong JM, Kim SY, Yu JN. Complete Chloroplast Genome Determination of Ranunculus sceleratus from Republic of Korea (Ranunculaceae) and Comparative Chloroplast Genomes of the Members of the Ranunculus Genus. Genes (Basel) 2023; 14:1149. [PMID: 37372329 DOI: 10.3390/genes14061149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed among Ranunculus species. The chloroplast genome was assembled from Illumina HiSeq 2500 sequencing raw data. The genome was 156,329 bp and had a typical quadripartite structure comprising a small single-copy region, a large single-copy region, and two inverted repeats. Fifty-three simple sequence repeats were identified in the four quadrant structural regions. The region between the ndhC and trnV-UAC genes could be useful as a genetic marker to distinguish between R. sceleratus populations from Republic of Korea and China. The Ranunculus species formed a single lineage. To differentiate between Ranunculus species, we identified 16 hotspot regions and confirmed their potential using specific barcodes based on phylogenetic tree and BLAST-based analyses. The ndhE, ndhF, rpl23, atpF, rps4, and rpoA genes had a high posterior probability of codon sites in positive selection, while the amino acid site varied between Ranunculus species and other genera. Comparison of the Ranunculus genomes provides useful information regarding species identification and evolution that could guide future phylogenetic analyses.
Collapse
Affiliation(s)
- Kang-Rae Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - So Young Park
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Heesoo Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Jeong Min Hong
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Sun-Yu Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Jeong-Nam Yu
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| |
Collapse
|
11
|
An K, Zhou C, Feng L, Zhang Q, Pang Y, Li L, Bian F. Complete chloroplast genome and phylogenetic analysis of Anemone shikokiana. Mol Biol Rep 2023; 50:2095-2105. [PMID: 36542234 DOI: 10.1007/s11033-022-08204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Anemone shikokiana (Makino) Makino, disjunctly distributed in Shandong Peninsula of China and Shikoku Island of Japan, is a rare and endangered species. To provide genetic information and understand its phylogeny, we conducted research on the chloroplast (cp) genome of A. shikokiana. METHODS AND RESULTS The complete cp genome sequence of A. shikokiana was constructed in this study. The results showed that the cp genome of A. shikokiana has a typical quadripartite cyclic with a total length of 159,286 bp. In total, 111 unique genes were identified, including 78 protein-coding genes, 29 tRNA-coding genes and 4 rRNA-coding genes. A total of 37 long repeat sequences and 67 microsatellites were found in this cp genome. The cp genome of A. shikokiana was compared with eleven other Anemone cp genomes available from the Genbank database. We found some variations among the different genomes, especially in the LSC and SSC regions, and identified some regions as potential molecular markers such as ycf1, ndhE, ndhD, ndhF-trnL, ndhA and ndhF. The results of phylogenetic analysis suggested that A. narcissiflora was the closest relative of A. shikokiana. CONCLUSIONS The results filled the gap of cp genome sequence information of A. shikokiana, laying the foundation to explore the evolutionary relationships of A. shikokiana in future studies. It provided a valuable genetic resource for the molecular identification and phylogenetic study of Anemone.
Collapse
Affiliation(s)
- Kang An
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Chunxia Zhou
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Lei Feng
- Kunyu Mountain Forest Farm, Yantai, 264000, China
| | - Qing Zhang
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Yujuan Pang
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Lixia Li
- School of Life Sciences, Yantai University, Yantai, 264000, China
| | - Fuhua Bian
- School of Life Sciences, Yantai University, Yantai, 264000, China.
| |
Collapse
|
12
|
Szandar K, Jakub S, Paukszto Ł, Krawczyk K, Szczecińska M. Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?-A Case Study of Pulsatilla patens (L.) Mill. Genes (Basel) 2022; 14:genes14010067. [PMID: 36672808 PMCID: PMC9859050 DOI: 10.3390/genes14010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD-ccsA, rps4-rps16, and trnL(UAG)-ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes-11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset.
Collapse
Affiliation(s)
- Kamil Szandar
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Sawicki Jakub
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
- Correspondence:
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Monika Szczecińska
- Department of Ecology and Environmental Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727 Olsztyn, Poland
| |
Collapse
|
13
|
Lan Z, Shi Y, Yin Q, Gao R, Liu C, Wang W, Tian X, Liu J, Nong Y, Xiang L, Wu L. Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species. FRONTIERS IN PLANT SCIENCE 2022; 13:1049209. [PMID: 36479523 PMCID: PMC9720176 DOI: 10.3389/fpls.2022.1049209] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Artemisia Linn. is a large genus within the family Asteraceae that includes several important medicinal plants. Because of their similar morphology and chemical composition, traditional identification methods often fail to distinguish them. Therefore, developing an effective identification method for Artemisia species is an urgent requirement. In this study, we analyzed 15 chloroplast (cp) genomes, including 12 newly sequenced genomes, from 5 Artemisia species. The cp genomes from the five Artemisia species had a typical quadripartite structure and were highly conserved across species. They had varying lengths of 151,132-151,178 bp, and their gene content and codon preferences were similar. Mutation hotspot analysis identified four highly variable regions, which can potentially be used as molecular markers to identify Artemisia species. Phylogenetic analysis showed that the five Artemisia species investigated in this study were sister branches to each other, and individuals of each species formed a monophyletic clade. This study shows that the cp genome can provide distinguishing features to help identify closely related Artemisia species and has the potential to serve as a universal super barcode for plant identification.
Collapse
Affiliation(s)
- Zhaohui Lan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qinggang Yin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ranran Gao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chunlian Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Wenting Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xufang Tian
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Jiawei Liu
- Department of product development, Hubei Aiaitie Health Technology Co., LTD, Huanggang, China
| | - Yiying Nong
- Department of product development, Hubei Aiaitie Health Technology Co., LTD, Huanggang, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
14
|
Xing YP, Song YY, Yang YY, Bian C, Men WX, Xue HF, Xu L, Kang TG. The complete chloroplast genome of Dictamnus dasycarpus Turcz. (Rutaceae). Mitochondrial DNA B Resour 2022; 7:1516-1518. [PMID: 36034535 PMCID: PMC9415454 DOI: 10.1080/23802359.2022.2109439] [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: 12/02/2022] Open
Abstract
Dictamnus dasycarpus Turcz. 1842 is a medicinal plant of China. Its dry root bark is called BAIXIANPI, which is a common traditional Chinese medicine. Here, we report the complete chloroplast genome of D. dasycarpus. The length of the genome, large single-copy (LSC), small single-copy (SSC), inverted repeat (IR), and GC content was 157,056 bp, 84,497 bp, 18,487 bp, 27,036 bp, and 38.5%, respectively. A total of 132 genes were annotated, including 87 protein coding, eight rRNA, and 37 tRNA genes. Interestingly, 15 genes contained single intron while two others contained two introns. The phylogenetic tree showed the two D. dasycarpus (D. albus) clustered in a clade, which was sister to clade formed by the species of Melicope, Tetradium, Phellodendron, and Zanthoxylum.
Collapse
Affiliation(s)
- Yan-ping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yue-yue Song
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yan-yun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Che Bian
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Wen-xiao Men
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - He-fei Xue
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Ting-guo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| |
Collapse
|
15
|
Wei R, Li Q. The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications. Genes (Basel) 2022; 13:genes13081361. [PMID: 36011272 PMCID: PMC9407434 DOI: 10.3390/genes13081361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Stemona parviflora is an endangered species, narrowly endemic to Hainan and Southwest Guangdong. The taxonomic classification of S. parviflora remains controversial. Moreover, studying endangered species is helpful for current management and conservation. In this study, the first complete chloroplast genome of S. parviflora was assembled and compared with other Stemona species. The chloroplast genome size of S. parviflora was 154,552 bp, consisting of 87 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and one pseudogene. The ψycf1 gene was lost in the cp genome of S. sessilifolia, but it was detected in four other species of Stemona. The inverted repeats (IR) regions have a relatively lower length variation compared with the large single copy (LSC) and small single copy (SSC) regions. Long repeat sequences and simple sequence repeat (SSR) were detected, and most SSR were distributed in the LSC region. Codon usage bias analyses revealed that the RSCU value of the genus Stemona has almost no difference. As with most angiosperm chloroplast genomes, protein-coding regions were more conservative than the inter-gene spacer. Seven genes (atpI, ccsA, cemA, matK, ndhA, petA, and rpoC1) were detected under positive selection in different Stemona species, which may result from adaptive evolution to different habitats. Phylogenetic analyses show the Stemona cluster in two main groups; S. parviflora were closest to S. tuberosa. A highly suitable region of S. parviflora was simulated by Maxent in this study; it is worth noting that the whole territory of Taiwan has changed to a low fitness area and below in the 2050 s, which may not be suitable for the introduction and cultivation of S. parviflora. In addition, limited by the dispersal capacity of S. parviflora, it is necessary to carry out artificial grafts to expand the survival areas of S. parviflora. Our results provide valuable information on characteristics of the chloroplast genome, phylogenetic relationships, and potential distribution range of the endangered species S. parviflora.
Collapse
Affiliation(s)
- Ran Wei
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
| | - Qiang Li
- Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Correspondence:
| |
Collapse
|
16
|
Mlinarec J, Boštjančić LL, Malenica N, Jurković A, Boland T, Yakovlev SS, Besendorfer V. Structure and Methylation of 35S rDNA in Allopolyploids Anemone multifida (2 n = 4 x = 32, BBDD) and Anemone baldensis (2 n = 6 x = 48, AABBDD) and Their Parental Species Show Evidence of Nucleolar Dominance. FRONTIERS IN PLANT SCIENCE 2022; 13:908218. [PMID: 35874014 PMCID: PMC9296772 DOI: 10.3389/fpls.2022.908218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/07/2022] [Indexed: 05/26/2023]
Abstract
Transcriptional silencing of 35S rDNA loci inherited from one parental species is occurring relatively frequently in allopolyploids. However, molecular mechanisms by which it is selected for transcriptional silencing remain unclear. We applied NGS, silver staining and bisulfite sequencing to study the structure, expression and methylation landscape of 35S rDNA in two allopolyploids of common origin, allotetraploid Anemone multifida (2n = 4x = 32, genome composition BBDD) and allohexaploid A. baldensis (2n = 6x = 48, AABBDD), and their genome donors, A. sylvestris (2n = 16, AA), A. cylindrica (2n = 16, BB) and A. parviflora (2n = 16, DD). The size of the recovered 35S rDNA units varied from 10,489 bp in A. cylindrica to 12,084 bp in A. sylvestris. Anemone showed an organization typical of most ribosomal 35S rDNA composed of NTS, ETS, rRNA genes, TTS and TIS with structural features of plant IGS sequences and all functional elements needed for rRNA gene activity. The NTS was more variable than the ETS and consisted of SRs which are highly variable among Anemone. Five to six CpG-rich islands were found within the ETS. CpG island located adjacent to the transcription initiation site (TIS) was highly variable regarding the sequence size and methylation level and exhibited in most of the species lower levels of methylation than CpG islands located adjacent to the 18S rRNA gene. Our results uncover hypomethylation of A. sylvestris- and A. parviflora-derived 35S rDNA units in allopolyploids A. multifida and A. baldensis. Hypomethylation of A. parviflora-derived 35S rDNA was more prominent in A. baldensis than in A. multifida. We showed that A. baldensis underwent coupled A. sylvestris-derived 35S rDNA array expansion and A. parviflora-derived 35S rDNA copy number decrease that was accompanied by lower methylation level of A. sylvestris-derived 35S rDNA units in comparison to A. parviflora-derived 35S rDNA units. These observations suggest that in A. baldensis nucleolar dominance is directed toward A. sylvestris-derived chromosomes. This work broadens our current knowledge of the 35S rDNA organization in Anemone and provides evidence of the progenitor-specific 35S rDNA methylation in nucleolar dominance.
Collapse
Affiliation(s)
| | - Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
- Department of Computer Science, ICube, UMR 7357, CNRS, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, Strasbourg, France
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Todd Boland
- Memorial University of Newfoundland’s Botanical Gardens, St. John’s, NL, Canada
| | - Sonja Siljak Yakovlev
- CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| |
Collapse
|
17
|
Choi KS, Ha YH, Gil HY, Choi K, Kim DK, Oh SH. Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. PLANTS (BASEL, SWITZERLAND) 2021; 10:397. [PMID: 33669616 PMCID: PMC7922562 DOI: 10.3390/plants10020397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
Previous studies on the chloroplast genome in Clematis focused on the chloroplast structure within Anemoneae. The chloroplast genomes of Cleamtis were sequenced to provide information for studies on phylogeny and evolution. Two Korean endemic Clematis chloroplast genomes (Clematis brachyura and C. trichotoma) range from 159,170 to 159,532 bp, containing 134 identical genes. Comparing the coding and non-coding regions among 12 Clematis species revealed divergent sites, with carination occurring in the petD-rpoA region. Comparing other Clematis chloroplast genomes suggested that Clematis has two inversions (trnH-rps16 and rps4), reposition (trnL-ndhC), and inverted repeat (IR) region expansion. For phylogenetic analysis, 71 protein-coding genes were aligned from 36 Ranunculaceae chloroplast genomes. Anemoneae (Anemoclema, Pulsatilla, Anemone, and Clematis) clades were monophyletic and well-supported by the bootstrap value (100%). Based on 70 chloroplast protein-coding genes, we compared nonsynonymous (dN) and synonymous (dS) substitution rates among Clematis, Anemoneae (excluding Clematis), and other Ranunculaceae species. The average synonymoussubstitution rates (dS)of large single copy (LSC), small single copy (SSC), and IR genes in Anemoneae and Clematis were significantly higher than those of other Ranunculaceae species, but not the nonsynonymous substitution rates (dN). This study provides fundamental information on plastid genome evolution in the Ranunculaceae.
Collapse
Affiliation(s)
- Kyoung Su Choi
- Institute of Natural Science, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea;
- Department of Life Sciences, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea
| | - Young-Ho Ha
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
- Department of Life Science, Gachon University, Seongnam-si, Gyeonggi-do 13120, Korea
| | - Hee-Young Gil
- DMZ Botanic Garden, Korea National Arboretum, 916-70, Punchbowl-ro, Haean-myeon, Yanggu, Gangwon-do 24564, Korea;
| | - Kyung Choi
- Research Planning and Coordination Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea;
| | - Dong-Kap Kim
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
| | - Seung-Hwan Oh
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
| |
Collapse
|
18
|
Zhuang W, Shu X, Zhang M, Wang T, Zhang F, Wang N, Wang Z. Characterization of the complete chloroplast genome of Populus deltoides Zhonglin 2025. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3723-3724. [PMID: 33367076 PMCID: PMC7671709 DOI: 10.1080/23802359.2020.1833773] [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: 11/18/2022]
Abstract
The complete chloroplast genome of Populus deltoides was characterized by reference-based assembly using whole-genome sequencing data. The total chloroplast genome size of Populus deltoides included a pair of inverted repeat regions (IRs) of 27,649 bp each, a small single-copy region (SSC) of 16,563 bp, and large single-copy region (LSC) of 85,096 bp, which was 156,957 bp in length. A total of 109 genes were predicted from the chloroplast genome, including 83 protein-coding genes, 22 tRNA genes, and four rRNA genes. The GC content of chloroplast genome for Populus deltoides was 36.68%. The phylogenetic analysis based on the reported chloroplast genomes of Populus showed that the chloroplast of the Populus deltoides is most closely related to the Populus fremontii. The complete chloroplast genome of Populus deltoides provides new insights into Populus evolutionary and genomic studies.
Collapse
Affiliation(s)
- Weibing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Xiaochun Shu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Ming Zhang
- Jiangsu Forest Resources Inspect Center, Nanjing, PR China
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Fengjiao Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Ning Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Zhong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| |
Collapse
|
19
|
Wang SJ, Zhang TT, Xu L, Yang YY, Xie M, Kang TG. The complete chloroplast genome of Ligusticum jeholense (Umbelliferae, Ligusticum L.). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3025-3027. [PMID: 33458043 PMCID: PMC7781892 DOI: 10.1080/23802359.2020.1797560] [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: 10/28/2022]
Abstract
Ligusticum jeholense is an important medicinal plant. Chloroplast genome information is helpful for the development of molecular markers and the study of plant phylogeny. In this study, we report the complete chloroplast genome sequence of L. jeholense. The genome sequence is 148,493 bp in size (GenBank accession number MN652885), with 37.25% GC contents. There are 127 genes in the genome, including 83 known protein-coding genes (PCGs), 36 transfer RNAs (tRNAs), and 8 ribosomal RNAs (rRNAs). The maximum-likelihood method are used to construct phylogenetic tree of 32 species. These data will provide certain theoretical basis for plant genetics research.
Collapse
Affiliation(s)
- Shi-Jie Wang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Ting-Ting Zhang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yan-Yun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Ming Xie
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Ting-Guo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| |
Collapse
|