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Zhang Z, Shi X, Tian H, Qiu J, Ma H, Tan D. Complete Chloroplast Genome of Megacarpaea megalocarpa and Comparative Analysis with Related Species from Brassicaceae. Genes (Basel) 2024; 15:886. [PMID: 39062665 PMCID: PMC11276580 DOI: 10.3390/genes15070886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Megacarpaea megalocarpa, a perennial herbaceous species belonging to the Brassicaceae family, has potential medicinal value. We isolated and characterized the chloroplast (cp) genome of M. megalocarpa and compared it with closely related species. The chloroplast genome displayed a typical quadripartite structure, spanning 154,877 bp, with an overall guanine-cytosine (GC) content of 36.20%. Additionally, this genome contained 129 genes, 105 simple sequence repeats (SSRs), and 48 long repeat sequences. Significantly, the ycf1 gene exhibited a high degree of polymorphism at the small single copy (SSC) region and the inverted repeat a (IRa) boundary. Despite this polymorphism, relative synonymous codon usage (RSCU) values were found to be similar across species, and no large segment rearrangements or inversions were detected. The large single copy (LSC) and SSC regions showed higher sequence variations and nucleotide polymorphisms compared to the IR region. Thirteen distinct hotspot regions were identified as potential molecular markers. Our selection pressure analysis revealed that the protein-coding gene rpl20 is subjected to different selection pressures in various species. Phylogenetic analysis positioned M. megalocarpa within the expanded lineage II of the Brassicaceae family. The estimated divergence time suggests that M. megalocarpa diverged approximately 4.97 million years ago. In summary, this study provides crucial baseline information for the molecular identification, phylogenetic relationships, conservation efforts, and utilization of wild resources in Megacarpaea.
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Affiliation(s)
| | | | | | | | | | - Dunyan Tan
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (Z.Z.); (X.S.); (H.T.); (J.Q.); (H.M.)
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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.
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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.
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Yang Y, Liu JF, Jiang XF. A chromosome-level genome assembly of Chinese quince ( Pseudocydonia sinensis). FRONTIERS IN PLANT SCIENCE 2024; 15:1368861. [PMID: 38887462 PMCID: PMC11180997 DOI: 10.3389/fpls.2024.1368861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024]
Abstract
Introduction Pseudocydonia sinensis, also known as Chinese quince, is a perennial shrub or small tree highly valued for its edibility and medicinal properties. Method This study presents the first chromosome-level genome assembly of P. sinensis, achieved using HiFi sequencing and Hi-C scaffolding technology. Results The assembly resulted in a high-quality genome of 576.39 Mb in size. The genome was anchored to 17 pseudo-chromosomes, with a contig N50 of 27.6 Mb and a scaffold N50 of 33.8 Mb. Comprehensive assessment using BUSCO, CEGMA and BWA tools indicates the high completeness and accuracy of the genome assembly. Our analysis identified 116 species-specific genes, 1196 expanded genes and 1109 contracted genes. Additionally, the distribution of 4DTv values suggests that the most recent duplication event occurred before the divergence of P. sinensis from both Chaenomeles pinnatifida and Pyrus pyrifolia. Discussion The assembly of this high-quality genome provides a valuable platform for the genetic breeding and cultivation of P. sinensis, as well as for the comparison of the genetic complexity of P. sinensis with other important crops in the Rosaceae family.
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Affiliation(s)
- Ying Yang
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
| | - Jin Feng Liu
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
| | - Xian Feng Jiang
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yunnan, China
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Liu R, Mu Z, Du X, Zhong G, Wang X. Chloroplast Genome Sequences and Phylogenetic Analysis of Eight Newly Sequenced Caryophyllaceae Species. J AOAC Int 2024; 107:345-353. [PMID: 38039156 DOI: 10.1093/jaoacint/qsad129] [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: 08/29/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND Caryophyllaceae is a big family composed of many economic and medicinal species. However, the phylogeny of the family is insufficient and genome data are lacking for many species. OBJECTIVE Using next-generation sequencing (NGS) to acquire the chloroplast (cp) genomes of Eremogone acicularis (F.N.Williams) Ikonn., E. brevipetala (Tsui & L.H.Zhou) Sadeghian & Zarre, E. bryophylla (Fernald) Pusalkar & D.K.Singh, E. kansuensis (Maxim.) Dillenb. & Kadereit, Shivparvatia glanduligera (Edgew.) Pusalkar & D.K.Singh, Silene atsaensis (Marq.) Bocquet, S. caespitella Williams, and S. lhassana (Williams) Majumdar. METHODS Bioinformatic software was used to conduct the comparative genome and phylogeny analysis of these cp genomes. RESULTS The eight cp genomes were 132 188-151 919 bp in length, containing 130-132 genes. A/T was dominant in simple sequence repeats (SSRs). Forward repeats and palindromic repeats were the most frequent in long terminal repeats (LTRs). Compared with the four species of Eremogone Fenzl, the inverted repeat (IR) boundaries of S. caespitella, S. atsaensis, S. lhassana, and Sh. glanduligera were significantly expanded. Four and one mutational hotspots were identified in the large single copy (LSC) region and small single copy (SSC) region, respectively. The ratio of nonsynonymous substitution to synonymous substitution (Ka/Ks ratio) showed these cp genomes may have undergone strong purifying selection. In the phylogenetic trees, both Silene L. and Eremogone were monophyletic groups. However, Sh. glanduligera was closely related to Amaranthus hypochondriacus. CONCLUSION These results have provided new evidence and useful information for species identification, evolution, and genetic research on the Caryophyllaceae. HIGHLIGHTS In this study, eight newly sequenced cp genomes of Caryophyllaceae species were reported for the first time.
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Affiliation(s)
- Rongpeng Liu
- Jiangxi University of Chinese Medicine, Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, No. 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
| | - Zejing Mu
- Jiangxi University of Chinese Medicine, Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, No. 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
| | - Xiaolang Du
- Jiangxi University of Chinese Medicine, Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, No. 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
| | - Guoyue Zhong
- Jiangxi University of Chinese Medicine, Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, No. 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
| | - Xiaoyun Wang
- Jiangxi University of Chinese Medicine, Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, No. 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
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Chen XH, Ding LN, Zong XY, Xu H, Wang WB, Ding R, Qu B. The complete chloroplast genome sequences of four Liparis species (Orchidaceae) and phylogenetic implications. Gene 2023; 888:147760. [PMID: 37661026 DOI: 10.1016/j.gene.2023.147760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/05/2023]
Abstract
Liparis Richard (Malaxideae, Epidendroideae) is a large and diverse genus of the family Orchidaceae, the taxonomy of which is complicated and controversial. In this study, we sequenced, assembled and analyzed four complete chloroplast genomes of Liparis species including L. kumokiri, L. makinoana, L. pauliana, and L. viridiflora, and evaluated their phylogenetic relationships with related species for the first time. These four chloroplast genomes (size range 153,095 to 158,239 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 83,533-86,752 bp), a small single copy (SSC, 17,938-18,156 bp) and a pair of inverted repeats (IRs, 26,421-26,933 bp). The genomes contain 133 genes, including 87 protein coding genes, 38 tRNAs and 8 rRNA genes. The genome arrangements, gene contents, gene order, long repeats and simple sequence repeats were similar with small differences observed among these four chloroplast genomes. Five highly variable regions including ycf1, ndhA, ndhF, trnQ and trnK were identified from the comparative analysis with other nine related Liparis species, which had the potential to be used as DNA markers for species identification and phylogenetic studies of Liparis species. Phylogenetic analysis based on the complete chloroplast genome sequences strongly supported the polyphyly of Liparis and its further division into three branches. These results provided valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the Liparis genus.
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Affiliation(s)
- Xu-Hui Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Li-Na Ding
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Xiao-Yan Zong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Hua Xu
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, PR China
| | - Wei-Bin Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Rui Ding
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China.
| | - Bo Qu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China.
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Li J, Du Y, Xie L, Jin X, Zhang Z, Yang M. Comparative plastome genomics and phylogenetic relationships of the genus Trollius. FRONTIERS IN PLANT SCIENCE 2023; 14:1293091. [PMID: 38046610 PMCID: PMC10690957 DOI: 10.3389/fpls.2023.1293091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Trollius, a genus in the Ranunculaceae family, has significant medicinal and ornamental value. It is widely distributed in China with 16 different species accepted. However, due to the lack of enough samples and information sites, the molecular phylogenetic relationships of Trollius have been unresolved till now. Here we sequenced, assembled and annotated the plastomes of 16 Trollius species to investigate their genomic characteristics, inverted repeat (IR) boundaries, sequence repeats, and hypervariable loci. In addition, the phylogenetic relationships of this genus was reconstructed based on the whole plastomes and the protein-coding sequences data-sets. The plastomes of Trollius ranged between 159,597 bp and 160,202 bp in length, and contained 113 unique genes, including 79 protein coding, 30 tRNA, and 4 rRNA. The IR boundaries were relatively conserved within the genus Trollius. 959 simple sequence repeats and 657 long sequence repeats were detected in the Trollius plastomes. We identified 12 highly polymorphic loci (Pi > 0.0115) that can be used as plastid markers in molecular identification and phylogenetic investigation of the genus. Besides, Trollius was a monophyletic group with the earliest divergence clade being Trollius lilacinus Bunge, and the remaining species were divided into two strongly-supported clades. The phylogeny in our study supported the traditional classification systems based on the color of sepal, but not the previous classification system based on the types and relative lengths of the nectaries, and distribution. The genomic resources provided in our study can be used in the taxonomy of the genus Trollius, promoting the development and utilization of this genus.
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Affiliation(s)
- Jiaxin Li
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Yan Du
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhirong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meiqing Yang
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
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Yan M, Dong S, Gong Q, Xu Q, Ge Y. Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny. Sci Rep 2023; 13:16495. [PMID: 37779129 PMCID: PMC10543443 DOI: 10.1038/s41598-023-43638-1] [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: 02/28/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.
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Affiliation(s)
- Meixiu Yan
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qiuyi Gong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qin Xu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
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Yoon WS, Kim CK, Kim YK. The First Complete Chloroplast Genome of Campanula carpatica: Genome Characterization and Phylogenetic Diversity. Genes (Basel) 2023; 14:1597. [PMID: 37628648 PMCID: PMC10454809 DOI: 10.3390/genes14081597] [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: 07/06/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Campanula carpatica is an ornamental flowering plant belonging to the family Campanulaceae. The complete chloroplast genome of C. carpatica was obtained using Illumina HiSeq X and Oxford Nanopore (Nanopore GridION) platforms. The chloroplast genome exhibited a typical circular structure with a total length of 169,341 bp, comprising a large single-copy region of 102,323 bp, a small single-copy region of 7744 bp, and a pair of inverted repeats (IRa/IRb) of 29,637 bp each. Out of a total 120 genes, 76 were protein-coding genes, 36 were transfer RNA genes, and eight were ribosomal RNA genes. The genomic characteristics of C. carpatica are similar to those of other Campanula species in terms of repetitive sequences, sequence divergence, and contraction/expansion events in the inverted repeat regions. A phylogenetic analysis of 63 shared genes in 16 plant species revealed that Campanula zangezura is the closest relative of C. carpatica. Phylogenetic analysis indicated that C. carpatica was within the Campanula clade, and C. pallida occupied the outermost position of that clade.
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Affiliation(s)
- Won-Sub Yoon
- Department of Mechanical Design Engineering, Wonkwang University, Iksan 54538, Republic of Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju 54874, Republic of Korea;
| | - Yong-Kab Kim
- Department of Information Communication Engineering, Wonkwang University, Iksan 54538, Republic of Korea
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Cao P, Huang Y, Zong M, Xu Z. De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers. Genes (Basel) 2023; 14:526. [PMID: 36833452 PMCID: PMC9957484 DOI: 10.3390/genes14020526] [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: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
As a valuable Chinese traditional medicinal species, Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of C. speciosa was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The C. speciosa mitochondrial genome was found to have two circular chromosomes as its major conformation, with a total length of 436,464 bp and 45.2% GC content. The mitochondrial genome contained 54 genes, including 33 unique protein-coding genes, 18 tRNAs, and 3 rRNA genes. Seven pairs of repeat sequences involving recombination events were analyzed. Both the repeat pairs, R1 and R2, played significant roles in mediating the major and minor conformations. In total, 18 MTPTs were identified, 6 of which were complete tRNA genes. There were 454 RNA editing sites in the 33 protein-coding sequences predicted by the PREPACT3 program. A phylogenetic analysis based on 22 species of mitochondrial genomes was constructed and indicated highly conserved PCG sequences. Synteny analyses showed extensive genomic rearrangements in the mitochondrial genome of C. speciosa and closely related species. This work is the first to report the C. speciosa mitochondrial genome, which is of great significance for conducting additional genetic studies on this organism.
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Affiliation(s)
- Pei Cao
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuan Huang
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Mei Zong
- College of Life Sciences, Anqing Normal University, Anqing 246133, China
| | - Zilong Xu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Tang C, Chen X, Deng Y, Geng L, Ma J, Wei X. Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships. BMC PLANT BIOLOGY 2022; 22:495. [PMID: 36273120 PMCID: PMC9587547 DOI: 10.1186/s12870-022-03858-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Sorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections. RESULTS The 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny. CONCLUSION Phylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.
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Affiliation(s)
- Chenqian Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Liyang Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianhui Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xueyan Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Kim SH, Kwon JH, Cho KH, Jun JH, Shin IS. The complete chloroplast genome of Korean cultivar 'Harmony' ( Prunus salicina × Prunus armeniaca). Mitochondrial DNA B Resour 2022; 7:1820-1822. [PMID: 36278123 PMCID: PMC9586692 DOI: 10.1080/23802359.2022.2132839] [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: 11/21/2022] Open
Abstract
Prunus Linnaeus 1753 species include many economically important fruit crops, of which plumcot is generated by inter-species crossing between Prunus salicina Lindley 1830 × Prunus armeniaca Linnaeus 1753. In this study, the complete chloroplast genome of Korean plumcot cultivar 'Harmony' was characterized through the de novo assembly of Nanopore and Illumina sequencing data. The chloroplast genome is a circular molecule of 157,916 bp length with 36.75% GC content and has a total of 113 genes including 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Phylogenetic analysis with protein-coding sequences of chloroplast genome revealed that 'Harmony' showed closer to P. salicina than P. armeniaca.
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Affiliation(s)
- Se Hee Kim
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju, Republic of Korea,CONTACT Se Hee Kim Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju-gun, Jeollabuk-do55365, Republic of Korea
| | - Jung-hyun Kwon
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju, Republic of Korea
| | - Kang Hee Cho
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju, Republic of Korea
| | - Ji Hae Jun
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju, Republic of Korea
| | - Il Sheob Shin
- Pear Research Institute, National Institute of Horticultural and Herbal Science, Naju, Republic of Korea
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12
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Contreras-Díaz R, Carevic FS, Huanca-Mamani W, Oses R, Arias-Aburto M, Navarrete-Fuentes M. Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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13
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La-Rostami F, Wax N, Druschka M, Adams E, Albert C, Fischer M. In Vitro CRISPR-Cpf1 Assay for Differentiation of Fine and Bulk Cocoa ( Theobroma cacao L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8819-8826. [PMID: 35786882 DOI: 10.1021/acs.jafc.2c02537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cocoa cultivation is dominated by the clone "Colleción Castro Naranjal 51" (CCN-51). In contrast, CCN-51 is the expensive and aromatic fine cocoa "Arriba Nacional" from Ecuador. The differences in the overall quality of the beans and in the prices show that it is necessary to develop a rapid and accurate method to distinguish these varieties and prevent food fraud. To this end, we used a CRISPR-Cpf1 assay suitable for AT-rich targets such as the chloroplast genome (cpGenome). SNPs in cocoa plastid genomes were selected to replace the canonical PAM sequence of Cpf1 (5'-TTTV-3'). We developed two assay systems to digest both Arriba and CCN-51. The results were tested qualitatively by agarose gel electrophoresis and quantitatively by capillary gel electrophoresis. Using the assay described here, we were able to reliably detect admixtures of 5% CCN-51 (P < 0.01) and 10% Arriba (P < 0.05). The application to processed cocoa products was also successful.
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Affiliation(s)
- Farshad La-Rostami
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Nils Wax
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Michael Druschka
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Elena Adams
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Chenyang Albert
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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14
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Xia X, Peng J, Yang L, Zhao X, Duan A, Wang D. Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus. Life (Basel) 2022; 12:life12060848. [PMID: 35743879 PMCID: PMC9224849 DOI: 10.3390/life12060848] [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: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/30/2022] Open
Abstract
The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89−104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.
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Affiliation(s)
- Xi Xia
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Jingyu Peng
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100089, China;
| | - Lin Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Xueli Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Anan Duan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Dawei Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
- Correspondence: ; Tel.: +86-138-8891-5161
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15
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Zhao D, Liu Z, Zhou T, Wu Z, Zhang Y, Xiao C. The complete chloroplast genome of Bletilla ochracea Schltr., a medicinal plant with yellow flowers. Mitochondrial DNA B Resour 2022; 7:1053-1055. [PMID: 35756447 PMCID: PMC9225769 DOI: 10.1080/23802359.2021.1992316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Dan Zhao
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhishang Liu
- Administration center of Nonggang National Nature Reserves, Longzhou, China
| | - Tao Zhou
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhikun Wu
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yongping Zhang
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chenghong Xiao
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
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16
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Zhang M, Chen N. Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity. BMC Genomics 2022; 23:327. [PMID: 35477350 PMCID: PMC9044688 DOI: 10.1186/s12864-022-08532-6] [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: 12/12/2021] [Accepted: 04/04/2022] [Indexed: 11/22/2022] Open
Abstract
The cosmopolitan Thalassionema species are often dominant components of the plankton diatom flora and sediment diatom assemblages in all but the Polar regions, making important ecological contribution to primary productivity. Historical studies concentrated on their indicative function for the marine environment based primarily on morphological features and essentially ignored their genomic information, hindering in-depth investigation on Thalassionema biodiversity. In this project, we constructed the complete chloroplast genomes (cpDNAs) of seven Thalassionema strains representing three different species, which were also the first cpDNAs constructed for any species in the order Thalassionematales that includes 35 reported species and varieties. The sizes of these Thalassionema cpDNAs, which showed typical quadripartite structures, varied from 124,127 bp to 140,121 bp. Comparative analysis revealed that Thalassionema cpDNAs possess conserved gene content inter-species and intra-species, along with several gene losses and transfers. Besides, their cpDNAs also have expanded inverted repeat regions (IRs) and preserve large intergenic spacers compared to other diatom cpDNAs. In addition, substantial genome rearrangements were discovered not only among different Thalassionema species but also among strains of a same species T. frauenfeldii, suggesting much higher diversity than previous reports. In addition to confirming the phylogenetic position of Thalassionema species, this study also estimated their emergence time at approximately 38 Mya. The availability of the Thalassionema species cpDNAs not only helps understand the Thalassionema species, but also facilitates phylogenetic analysis of diatoms.
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Affiliation(s)
- Mengjia Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, 10039, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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17
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Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens. PLoS One 2022; 17:e0266546. [PMID: 35385539 PMCID: PMC8985940 DOI: 10.1371/journal.pone.0266546] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
Isodon rubescens (Hemsley) H. Hara (Lamiaceae) is a traditional Chinese medicine plant that has been used to treat various human diseases and conditions such as inflammation, respiratory and gastrointestinal bacterial infections, and malignant tumors. However, the contents of the main active components of I. rubescens from different origins differ significantly, which greatly affected its quality. Therefore, a molecular method to identify and classify I. rubescens is needed. Here, we report the DNA sequence of the chloroplast genome of I. rubescens collected from Lushan, Henan province. The genome is 152,642 bp in length and has a conserved structure that includes a pair of IR regions (25,726 bp), a LSC region (83,527 bp) and a SSC region (17,663 bp). The chloroplast genome contains 113 unique genes, four rRNA genes, 30 tRNA genes, and 79 protein-coding genes, 23 of which contain introns. The protein-coding genes account for a total of 24,412 codons, and most of them are A/T biased usage. We identified 32 simple sequence repeats (SSRs) and 48 long repeats. Furthermore, we developed valuable chloroplast molecular resources by comparing chloroplast genomes from three Isodon species, and both mVISTA and DnaSP analyses showed that rps16-trnQ, trnS-trnG, and ndhC-trnM are candidate regions that will allow the identification of intraspecific differences within I. rubescens. Also 14 candidate fragments can be used to identify interspecific differences between species in Isodon. A phylogenetic analysis of the complete chloroplast genomes of 24 species in subfamily Nepetoideae was performed using the maximum likelihood method, and shows that I. rubescens clustered closer to I. serra than I. lophanthoides. Interestingly, our analysis showed that I. rubescens (MW018469.1) from Xianyang, Shaanxi Province (IR-X), is closer to I. serra than to the other two I. rubescens accessions. These results strongly indicate that intraspecific diversity is present in I. rubescens. Therefore, our results provide further insight into the phylogenetic relationships and interspecific diversity of species in the genus Isodon.
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He X, Dong S, Gao C, Wang Q, Zhou M, Cheng R. The complete chloroplast genome of Carpesium abrotanoides L. (Asteraceae): structural organization, comparative analysis, mutational hotspots and phylogenetic implications within the tribe Inuleae. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Zhai M, Jia XD, Zhang JY, Guo ZR, Xuan JP. Characterization of the complete chloroplast genome of Carya laciniosa (F.Michx.) G.Don (Juglandaceae). Mitochondrial DNA B Resour 2022; 6:1261-1262. [PMID: 35141403 PMCID: PMC8820796 DOI: 10.1080/23802359.2021.1906178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Carya laciniosa (F.Michx.) G.Don is a slow-growing valuable tree in the family Juglandaceae. In this research, we first reported the chloroplast genome sequence of C. laciniosa. The chloroplast genome was a circular form with 160,832 bp in size, comprising four subregions: a large single-copy (LSC) region of 90,065 bp, a small single-copy (SSC) region of 18,791 bp, and two copies of inverted repeats (IRs; IRa and IRb) of 25,988 bp each. A total of 132 genes were annotated in the chloroplast genome of C. laciniosa, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome was 36.14%. Phylogenetic analysis suggested that C. laciniosa was closely related to C. ovata.
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Affiliation(s)
- Min Zhai
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, PR China.,Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, PR China
| | - Xiao-Dong Jia
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, PR China.,Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, PR China
| | - Ji-Yu Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, PR China.,Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, PR China
| | - Zhong-Ren Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, PR China.,Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, PR China
| | - Ji-Ping Xuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, PR China.,Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, PR China
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20
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Wang S, Ding S, Deng R, Shi W, Zhang H. The complete chloroplast genome of Callianthe picta (Malvaceae). Mitochondrial DNA B Resour 2022; 7:10-11. [PMID: 34912955 PMCID: PMC8667874 DOI: 10.1080/23802359.2021.2005487] [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: 12/04/2022] Open
Abstract
Callianthe picta likes a warm and humid climate, is resistant to barrenness, and is easy to reproduce. Its petals and leaves can promote blood circulation and remove blood stasis, and can also be used to relax the muscles and collaterals. In this study, we sequenced the complete chloroplast genome sequence of C. picta to investigate its phylogenetic relationship in the family Abutilon. The complete chloroplast size of C. picta is 160,398 bp, including a large single-copy (LSC) region of 89,088 bp, a small single-copy (SSC) region of 20,138 bp, a pair of invert repeats (IRs) regions of 25,586 bp. The GC content of the whole complete chloroplast genome is 37.0%. We annotated 128 genes in the genome in detail, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that C. picta was closely related to Abutilon theophrati.
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Affiliation(s)
- Sujie Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Shujin Ding
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Glassland Administration, Southwest Forestry University, Kunming, China
| | - Ruyou Deng
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Glassland Administration, Southwest Forestry University, Kunming, China
| | - Wanyuan Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
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21
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Pascual-Díaz JP, Garcia S, Vitales D. Plastome Diversity and Phylogenomic Relationships in Asteraceae. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122699. [PMID: 34961169 PMCID: PMC8705268 DOI: 10.3390/plants10122699] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae-as well as in the sister family Calyceraceae-lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family's phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.
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Affiliation(s)
- Joan Pere Pascual-Díaz
- Institut Botànic de Barcelona (IBB-CSIC), Passeig del Migdia s/n, 08038 Barcelona, Spain;
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC), Passeig del Migdia s/n, 08038 Barcelona, Spain;
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB-CSIC), Passeig del Migdia s/n, 08038 Barcelona, Spain;
- Laboratori de Botànica–Unitat Associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
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22
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Dong S, Ying Z, Yu S, Wang Q, Liao G, Ge Y, Cheng R. Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships. BMC Genomics 2021; 22:880. [PMID: 34872502 PMCID: PMC8647421 DOI: 10.1186/s12864-021-08193-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 11/16/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. RESULTS The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy. CONCLUSIONS Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.
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Affiliation(s)
- Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zhiqi Ying
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Shuisheng Yu
- The Administration Bureau of Zhejiang Jiulongshan National Nature Reserve, Suichang, Zhejiang Province, People's Republic of China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Guanghui Liao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China.
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Ulaszewski B, Jankowska-Wróblewska S, Świło K, Burczyk J. Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112534. [PMID: 34834899 PMCID: PMC8618278 DOI: 10.3390/plants10112534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Several genera formerly contained within the genus Sorbus L. sensu lato have been proposed as separate taxa, including Aria, Chamaemespilus and Torminalis. However, molecular evidence for such distinctions are rather scarce. We assembled the complete chloroplast genome of Sorbus aucuparia, another representative of Sorbus s.s., and performed detailed comparisons with the available genomes of Aria edulis, Chamaemespilus alpina and Torminalis glaberrima. Additionally, using 110 complete chloroplast genomes of the Maleae representatives, we constructed the phylogenetic tree of the tribe using Maximum Likelihood methods. The chloroplast genome of S. aucuparia was found to be similar to other species within Maleae. The phylogenetic tree of the Maleae tribe indicated that A. edulis, C. alpina and T. glaberrima formed a concise group belonging to a different clade (related to Malus) than the one including Sorbus s.s. (related to Pyrus). However, Aria and Chamaemespilus appeared to be more closely related to each other than to Torminalis. Our results provide additional support for considering Aria, Chamaemespilus and Torminalis as separate genera different from Sorbus s.s.
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Xie C, An W, Liu S, Huang Y, Yang Z, Lin J, Zheng X. Comparative genomic study on the complete plastomes of four officinal Ardisia species in China. Sci Rep 2021; 11:22239. [PMID: 34782652 PMCID: PMC8594775 DOI: 10.1038/s41598-021-01561-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 10/21/2021] [Indexed: 11/23/2022] Open
Abstract
Ardisia Sw. (Primulaceae) is naturally distributed in tropical and subtropical areas. Most of them possess edible and medicinal values and are popular in clinical and daily use in China. However, ambiguous species delineation and genetic information limit the development and utilization of this genus. In this study, the chloroplast genomes of four Ardisia species, namely A. gigantifolia Stapf, A. crenata Sims, A. villosa Roxb. and A. mamillata Hance, were sequenced, annotated, and analyzed comparatively. All the four chloroplast genomes possess a typical quadripartite structure, and each of the genomes is about 156 Kb in size. The structure and gene content of the Ardisia plastomes were conservative and showed low sequence divergence. Furthermore, we identified five mutation hotspots as candidate DNA barcodes for Ardisia, namely, trnT-psbD, ndhF-rpl32, rpl32-ccsA, ccsA-ndhD and ycf1. Phylogenetic analysis based on the whole-chloroplast genomes data showed that Ardisia was sister to Tapeinosperma Hook. f. In addition, the results revealed a great topological profile of Ardisia's with strong support values, which matches their geographical distribution patterns. Summarily, our results provide useful information for investigations on taxonomic differences, molecular identification, and phylogenetic relationships of Ardisia plants.
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Affiliation(s)
- Chunzhu Xie
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Wenli An
- grid.411866.c0000 0000 8848 7685School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Shanshan Liu
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Yuying Huang
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Zerui Yang
- grid.411866.c0000 0000 8848 7685School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Ji Lin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong, China.
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong, China.
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Su N, Liu BB, Wang JR, Tong RC, Ren C, Chang ZY, Zhao L, Potter D, Wen J. On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology. FRONTIERS IN PLANT SCIENCE 2021; 12:743643. [PMID: 34707629 PMCID: PMC8542774 DOI: 10.3389/fpls.2021.743643] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 05/23/2023]
Abstract
The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.
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Affiliation(s)
- Na Su
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Bin-bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
| | - Jun-ru Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Ru-chang Tong
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhao-yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, Davis, CA, United States
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
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Chen J, Zang Y, Shang S, Liang S, Zhu M, Wang Y, Tang X. Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass. FRONTIERS IN PLANT SCIENCE 2021; 12:741152. [PMID: 34630493 PMCID: PMC8495015 DOI: 10.3389/fpls.2021.741152] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/23/2021] [Indexed: 05/29/2023]
Abstract
Seagrasses are marine flowering plants found in tropical and sub-tropical areas that live in coastal regions between the sea and land. All seagrass species evolved from terrestrial monocotyledons, providing the opportunity to study plant adaptation to sea environments. Here, we sequenced the chloroplast genomes (cpGenomes) of three Zostera species, then analyzed and compared their cpGenome structures and sequence variations. We also performed a phylogenetic analysis using published seagrass chloroplasts and calculated the selection pressure of 17 species within seagrasses and nine terrestrial monocotyledons, as well as estimated the number of shared genes of eight seagrasses. The cpGenomes of Zosteraceae species ranged in size from 143,877 bp (Zostera marina) to 152,726 bp (Phyllospadix iwatensis), which were conserved and displayed similar structures and gene orders. Additionally, we found 17 variable hotspot regions as candidate DNA barcodes for Zosteraceae species, which will be helpful for studying the phylogenetic relationships and interspecies differences between seagrass species. Interestingly, nine genes had positive selection sites, including two ATP subunit genes (atpA and atpF), two ribosome subunit genes (rps4 and rpl20), two DNA-dependent RNA polymerase genes (rpoC1 and rpoC2), as well as accD, clpP, and ycf2. These gene regions may have played key roles in the seagrass adaptation to diverse environments. The Branch model analysis showed that seagrasses had a higher rate of evolution than terrestrial monocotyledons, suggesting that seagrasses experienced greater environmental pressure. Moreover, a branch-site model identified positively selected sites (PSSs) in ccsA, suggesting their involvement in the adaptation to sea environments. These findings are valuable for further investigations on Zosteraceae cpGenomes and will serve as an excellent resource for future studies on seagrass adaptation to sea environments.
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Affiliation(s)
- Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Shuai Shang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Shuo Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiling Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 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: 8] [Impact Index Per Article: 2.7] [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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Fang L, Wang Y, Guo CL, Wang XY. The complete chloroplast genome sequence of Strobilanthes tonkinensis Lindau. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1786-1787. [PMID: 34104775 PMCID: PMC8168735 DOI: 10.1080/23802359.2021.1934144] [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: 10/29/2022]
Abstract
Strobilanthes tonkinensis Lindau is a member of the family Acanthaceae, which was originated from Yunnan province of China and is used as tea and health promotion. Here, we reported the complete chloroplast genome sequence of S. tonkinensis using Illumina high-throughput sequencing approach. The size of the chloroplast genome is 144,765 bp in length, containing a pair of inverted repeats (IRs, 17,362 bp) that are separated by the large single-copy (LSC, 92,248 bp), and small single-copy (SSC, 17,793 bp) regions. A total of 129 genes were identified, including 37 tRNA genes, 8 rRNA genes, and 84 protein-coding genes. The overall GC content is 38.21%. Phylogenetic analysis indicated that S. tonkinensis is closely related to Strobilanthes cusia and Strobilanthes bantonensis.
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Affiliation(s)
- Liu Fang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ying Wang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Cui-Ling Guo
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xing-Ya Wang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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The Comparative Analyses of Six Complete Chloroplast Genomes of Morphologically Diverse Chenopodium album L. (Amaranthaceae) Collected in Korea. Int J Genomics 2021; 2021:6643444. [PMID: 33996994 PMCID: PMC8096589 DOI: 10.1155/2021/6643444] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/09/2021] [Indexed: 01/16/2023] Open
Abstract
Chenopodium album sensu stricto belonging to C. album aggregate is an annual cosmopolitan weed displaying the diversity of morphologies. We completed the six chloroplast genomes of C. album s. str. collected in Korea to understand the relationship between the diversity of chloroplast genomes and their morphological variations. All six C. album chloroplast genomes have a typical quadripartite structure with length ranging from 151,906 bp to 152,199 bp, similar to the previously sequenced C. album chloroplast genome (NC_034950). In total, 56 single nucleotide polymorphisms (SNPs) and 26 insertion and deletion (INDEL) regions (308 bp in total) were identified from the six chloroplast genomes, presenting a low level of intraspecific variations in comparison to the other angiosperm species. 376 normal simple sequence repeats were identified in all seven C. album chloroplast genomes. The phylogenetic analysis based on all available complete Amaranthaceae chloroplast genomes presents phylogenetic positions of six C. album samples as well as correlation with one of C. album morphological features. Our results provide the way to investigate intraspecific features of C. album chloroplast genomes and also the insights of understanding various intraspecific characteristics including morphological features.
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Wang CY, Luo JH, He HL, Wang Q. The complete chloroplast genome of Callicarpa bodinieri (Lamiales, Lamiaceae), an ornamental and medicinal plant from Chongqing, China. Mitochondrial DNA B Resour 2021; 6:1229-1230. [PMID: 33796788 PMCID: PMC7995876 DOI: 10.1080/23802359.2021.1875932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Plants classified to the genus Callicarpa L. have important medicinal and ornamental value. Here, we report and characterize the complete chloroplast (cp) genome of C. bodinieri to provide molecular basis for the further studies on the phylogeny analysis of this genus. The cp genome is 154,183 bp in length and is organized with a typical quadripartite structure, containing two inverted repeats of 25,701 bp separated by a large single-copy region of 84,956 bp and a small single-copy region of 17,825 bp. The cp genome of C. bodinieri contains 112 distinct genes, including 78 protein-coding, 30 tRNAs and 4 rRNAs genes. The phylogenetic analysis showed that C. bodinieri is fully resolved in a clade with C. nudiflora, sister to the clade of C. formosana and C. longifolia var. floccosa.
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Affiliation(s)
| | - Ji-Hong Luo
- Chongqing City Management College, Chongqing, China
| | - Hui-Liu He
- Chongqing City Management College, Chongqing, China
| | - Qian Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
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Mu J, Zhao Y, He Y, Sun J, Yuan Q. The complete chloroplast genome of Prunus japonica thunb.(Rosaceae), an ornamental and medicinal plant. Mitochondrial DNA B Resour 2021; 6:112-114. [PMID: 33521281 PMCID: PMC7819125 DOI: 10.1080/23802359.2020.1848477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Prunus japonica is an ornamental and medicinal plant that is widely cultivated. The complete chloroplast genome of P. japonica was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 158,080 bp in length, containing two short inverted repeat (IRa and IRb) regions of 26,385 bp, which was separated by a large single copy (LSC) region of 86,270 bp and a small single copy (SSC) region of 19,040 bp. The GC content of the whole chloroplast genome was 36.8%. The chloroplast DNA of P. japonica comprised 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. Phylogenetic analysis indicated that all species of Prunus formed a monophyletic group, P. japonica was closely related to P. hulimis.
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Affiliation(s)
- Jing Mu
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuyang Zhao
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yali He
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiahui Sun
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qingjun Yuan
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Wang M, Wan X, Liang J, Li T, Wang S. The complete chloroplast genome of Euphorbia ebracteolata Hayata (Euphorbiaceae). Mitochondrial DNA B Resour 2021; 6:151-153. [PMID: 33537425 PMCID: PMC7832473 DOI: 10.1080/23802359.2020.1852904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Euphorbia ebracteolata is a perennial medicinal plant and widely used in China for thousands of years. The complete chloroplast genome reported here is 163,090 bp in length, including two inverted repeats (IRs) of 26,699 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 91,943 and 17,749 bp, respectively. The whole chloroplast genome of E. ebracteolata contains 112 genes, including 78 protein-coding genes, 30 transfer RNA, and 4 ribosome RNA. Phylogenetic analysis result strongly indicated that E. ebracteolata is closely related to E. helioscopia.
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Affiliation(s)
- Mengli Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resources Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Xiufu Wan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resources Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Jiuwen Liang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resources Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Tan Li
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resources Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Sheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resources Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
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Yu J, Jin W, Wang Y, Yuan Q. The complete chloroplast genome of a medicinal plant, Abutilon theophrasti Medik. (Malvaceae). Mitochondrial DNA B Resour 2020; 5:3777-3778. [PMID: 33367099 PMCID: PMC7703700 DOI: 10.1080/23802359.2020.1835582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
Abutilon theophrasti Medik. is an annual weed, widely distributed in Asia and Europe. The complete chloroplast genome reported here is 160,446 bp in length, including two inverted repeats (IRs) of 25,064 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 89,089 and 21,229 bp, respectively. The whole chloroplast genome of A. theophrasti contains 113 distinct genes, including 79 protein-coding genes, 30 transfer RNA, and four ribosome RNA. Phylogenetic analysis indicated that A. theophrasti is located in the basal position in Malveae.
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Affiliation(s)
- Junlin Yu
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, PR China
| | - Weiyin Jin
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, PR China
| | - Yiheng Wang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Qingjun Yuan
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, PR 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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Du Y, Liu Y, Liu B, Wang T. Complete chloroplast genome of Callicarpa formosana Rolfe, a famous ornamental plant and traditional medicinal herb. Mitochondrial DNA B Resour 2020; 5:3383-3384. [PMID: 33458178 PMCID: PMC7781935 DOI: 10.1080/23802359.2020.1820399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Callicarpa formosana is a species of beauty-berry with large medicinal value belonging to the family Verbenaceae. In this study, the complete chloroplast genome of C. formosana was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 1,54,210 bp in length, containing two short inverted repeat (IRa and IRb) regions of 25,701 bp, which was separated by a large single copy (LSC) region of 84,938 bp and a small single copy (SSC) region of 17,870 bp. The GC content of the whole chloroplast genome was 38.1%. The chloroplast DNA of C. formosana comprised 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis indicated that the genus Callicarpa L. was located in the basal position within the family Verbenaceae. The chloroplast genome (cpDNA) of C. formosana was closely related to Callicarpa nudiflora.
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Affiliation(s)
- Yongxi Du
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, P. R. China
| | - Yanfeng Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Bo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Tielin Wang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, P. R. China
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Zhang Y, Guo X, Yan B. Characterization of the complete chloroplast genome of Arisaema erubescens (Wall.) Schott, a traditional Chinese medicinal herb. Mitochondrial DNA B Resour 2020; 5:3149-3150. [PMID: 33458090 PMCID: PMC7782955 DOI: 10.1080/23802359.2020.1797577] [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] [Indexed: 11/25/2022] Open
Abstract
Arisaema erubescens is a well-known medicinal plant in China. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. erubescens to investigate its phylogenetic relationship in the family Araceae. The cp genome was 167,607 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 26,193 bp) separated by a large single-copy region (LSC: 93,660 bp) and a small single-copy region (SSC: 21,561 bp). The GC content of whole cp genome is 35.3%. De novo assembly and annotation showed the presence of 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis indicated that A. erubescens was closely related to A. franchetianum, and the genus Arisaema was sister to the genus Pinellia.
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Affiliation(s)
- Yan Zhang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Xiuzhi Guo
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Binbin Yan
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
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Ma W, Lv C, Jiang D, Kang C, Zhao D. The complete chloroplast genome sequence of Euphorbia lathyris L. (Euphorbiaceae). Mitochondrial DNA B Resour 2020; 5:3678-3680. [PMID: 33367057 PMCID: PMC7646597 DOI: 10.1080/23802359.2020.1832601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Euphorbia lathyris L. is a well-known bioenergy plant cultivated in many parts of the world. In this study, we sequenced the complete chloroplast (cp) genome sequence of E. lathyris to investigate its phylogenetic relationship in the family Euphorbiaceae. The cp genome was 163,738 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 26,837 bp) separated by a large single-copy region (LSC: 91,783 bp) and a small single-copy region (SSC: 18,281 bp). The GC content of whole cp genome is 35.6%. Annotation showed the presence of 113 unique genes with 79 protein-coding genes, four tRNA genes, and 30 rRNA genes. Phylogenetic analysis indicated that E. lathyris was in the basal position of subgen. Esula, closely related to sect. Esula and sect. Helioscopiae.
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Affiliation(s)
- Wenqi Ma
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chaogeng Lv
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Daiquan Jiang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chuanzhi Kang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dan Zhao
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
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Wang Y, Luo J, Wang M, Ge Y, Guo L. The complete chloroplast genome of the Euphorbia maculata L. (Euphorbiaceae): characterization and phylogeny. Mitochondrial DNA B Resour 2020; 5:3713-3714. [PMID: 33367071 PMCID: PMC7655055 DOI: 10.1080/23802359.2020.1833778] [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: 11/30/2022] Open
Abstract
Euphorbia maculata is an important medicinal plants of the family Euphorbiaceae. The complete chloroplast genome reported here is 162,685 bp in length, including two inverted repeats (IRs) of 26,822 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 90,514 bp and 18,527 bp, respectively. The whole chloroplast genome of E. maculata contains 111 genes, including 77 protein-coding genes, 4 transfer RNA, and 30 ribosome RNA. Phylogenetic analysis indicated that E. maculata is closely related to E. milii and E. tirucalli.
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Affiliation(s)
- Yiheng Wang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Luo
- Natural Resources Bureau of Xishan District of Kunming City, Kunming City, People’s Republic of China
| | - Mengli Wang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yang Ge
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
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