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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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Xie J, Miao Y, Zhang X, Zhang G, Guo B, Luo G, Huang L. Comparative complete chloroplast genome of Geum japonicum: evolution and phylogenetic analysis. JOURNAL OF PLANT RESEARCH 2024; 137:37-48. [PMID: 37917204 DOI: 10.1007/s10265-023-01502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Geum japonicum (Rosaceae) has been widely used in China as a traditional herbal medicine due to its high economic and medicinal value. However, the appearance of Geum species is relatively similar, making identification difficult by conventional phenotypic methods, and the studies of genomics and species evolution are lacking. To better distinguish the medicinal varieties and fill this gap, we carried out relevant research on the chloroplast genome of G. japonicum. Results show a typical quadripartite structure of the chloroplast genome of G. japonicum with a length of 156,042 bp. There are totally 131 unique genes in the genome, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, and there were also 87 SSRs identified and mostly mononucleotide Adenine-Thymine. We next compared the plastid genomes among four Geum species and obtained 14 hypervariable regions, including ndhF, psbE, trnG-UCC, ccsA, trnQ-UUG, rps16, psbK, trnL-UAA, ycf1, ndhD, atpA, petN, rps14, and trnK-UUU. Phylogenetic analysis revealed that G. japonicum is most closely related to Geum aleppicum, and possibly has some evolutionary relatedness with an ancient relic plant Taihangia rupestris. This research enriched the genome resources and provided fundamental insights for evolutionary studies and the phylogeny of Geum.
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Affiliation(s)
- Junbo Xie
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330000, China
| | - Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Baolin Guo
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Guangming Luo
- School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330000, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
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Wang S, Liu Y, Li R, Wang S, Huang Y. The complete chloroplast genome of Ziziphus mairei Dode 1908 (Rhamnaceae), an endangered perennial plant in Yunnan, China. Mitochondrial DNA B Resour 2023; 8:1459-1463. [PMID: 38173918 PMCID: PMC10763858 DOI: 10.1080/23802359.2023.2290844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Ziziphus mairei Dode 1908 (Rhamnaceae) is a rare and endangered perennial plant in Yunnan, China. In this study, we sequenced, assembled, and annotated the complete chloroplast genome of Z. mairei. The complete chloroplast genome was a closed circular molecule of 161,546 bp with a typical tetrad structure, containing a large single-copy (LSC) region of 89,252 bp, a small single-copy (SSC) region of 19,364 bp, and a pair of inverted repeat (IR) regions of 26,465 bp. A total of 128 genes have been annotated, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content is 36.7%. Phylogenetic analysis revealed that Z. mairei is closely related to Z. hajarensis, Z. jujuba, and Z. jujuba var. spinosa. Our results provide useful genetic resources for further studies on the conservation and evolution of Z. mairei.
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Affiliation(s)
- Shidong Wang
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
| | - Yunqi Liu
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
| | - Rui Li
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
| | - Shubao Wang
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
| | - Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
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Zhang S, Li B, Han L, Yang M, Liu M. Sequencing the chloroplast genome of a jujube genotype ( Ziziphus jujuba Mill. 'Fengmiguan') uncovered a 101 bp insertion in the large-single copy region. Mitochondrial DNA B Resour 2023; 8:726-730. [PMID: 37426571 PMCID: PMC10327523 DOI: 10.1080/23802359.2023.2231246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 06/23/2023] [Indexed: 07/11/2023] Open
Abstract
Ziziphus jujuba Mill., commonly referred to as jujube, is a species of fruiting buckthorn (family Rhamnaceae) that is frequently found across the Shaanxi, Shanxi, and Hebei provinces of China. The 'Fengmiguan' variety of jujube, also known as 'Honey jar,' is distinguished by its high yield and sugar content, as well as its strong ability to adapt to different environments. In this study, we sequenced and assembled the chloroplast genome (i.e. the plastome) of 'Fengmiguan' jujube using a paired-end short-read sequencing technique. The plastome exhibits a quadripartite structure with a total length of 161,818 bp that consists of a large single-copy region (89,427 bp), a small single-copy region (19,361 bp), and two inverted repeats (26,515 bp). The GC content of the plastome is 36.75%. Annotation of the 'Fengmiguan' jujube plastome revealed 123 genes, including 79 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis revealed that the 'Fengmiguan' variety is closely related to the 'Bokjo' variety. Furthermore, we found four variations between these two varieties of jujube, one of which was a 101 bp insertion. Our findings enhance the current understanding of the phylogenetic relationship between different varieties of Z. jujuba Mill., which could possibly aid in the improvement of genetic breeding and population selection in jujubes.
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Affiliation(s)
- Shufeng Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Bin Li
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Lu Han
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Meng Yang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
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Shi W, Hu S, Song W, Huang Y, Shi C, Wang S. Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus ( Rhamnaceae). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:855-869. [PMID: 37520808 PMCID: PMC10382440 DOI: 10.1007/s12298-023-01331-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Rhamnus cathartica and Frangula alnus are economically valuable medicinal plants from the Rhamnaceae family. However, their chloroplast genome structure, phylogenetic position, relationships, and evolution remain poorly understood. Herein, the complete chloroplast genome resources of R. cathartica and F. alnus have been added. The first comparative analysis of the Rhamnus and Frangula species based on complete chloroplast genomes was provided. The chloroplast genomes of R. cathartica and F. alnus exhibited a quadripartite structure, with total lengths of 161,149 bp and 161,255 bp, respectively. The lack of the infA and psbL genes does not negatively impact the normal functioning of Rhamnus and Frangula species. The rpl20 and rpl33 genes are undergoing rapid evolution. Rhamnus and Frangula species prefer amino acids with A/U-terminal codons. There were between 100 and 126 simple sequence repeats and between 38 and 100 long repeats. Several highly divergent intergenic regions (trnK-UUU-trnQ-UUG, atpH-atpI, trnY-GUA-trnE-UUC, trnG-GCC-trnfM-CAU, trnT-UGU-trnF-GAA, rpl20-rps12, and rpl22-rps19) and highly divergent genes (ycf3, ndhA, rpl32, and ycf1) were identified, which could serve as potential phylogenetic markers due to their variability. We reconstructed the phylogenetic relationships among Rhamnus species and F. alnus using complete chloroplast genomes. There is no significant correlation between the medicinal value of the species analyzed and their phylogenetic relationships. These results provide valuable insights for understanding the phylogenetic relationship and evolution of Rhamnus and Frangula species. These findings could serve as a foundation for future studies on the Rhamnaceae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01331-7.
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Affiliation(s)
- Wenbo Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Siqi Hu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Yahui Huang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204 China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
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Ahmad W, Asaf S, Al-Rawahi A, Al-Harrasi A, Khan AL. Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). Sci Rep 2023; 13:7436. [PMID: 37156827 PMCID: PMC10167353 DOI: 10.1038/s41598-023-34477-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.
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Affiliation(s)
- Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, USA.
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Wee CC, Nor Muhammad NA, Subbiah VK, Arita M, Nakamura Y, Goh HH. Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:930. [PMID: 36840278 PMCID: PMC9966718 DOI: 10.3390/plants12040930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety that was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely, 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single-nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata, found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups, with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.
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Affiliation(s)
- Ching-Ching Wee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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Liu C, Deng J, Zhou R, Song B, Zhou S, He X. Plastid Phylogenomics Provide Evidence to Accept Two New Members of Ligusticopsis (Apiaceae, Angiosperms). Int J Mol Sci 2022; 24:ijms24010382. [PMID: 36613825 PMCID: PMC9820081 DOI: 10.3390/ijms24010382] [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: 11/09/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Peucedanum nanum and P. violaceum are recognized as members of the genus Peucedanum because of their dorsally compressed mericarps with slightly prominent dorsal ribs and narrowly winged lateral ribs. However, these species are not similar to other Peucedanum taxa but resemble Ligusticopsis in overall morphology. To check the taxonomic positions of P. nanum and P. violaceum, we sequenced their complete plastid genome (plastome) sequences and, together with eleven previously published Ligusticopsis plastomes, performed comprehensively comparative analyses. The thirteen plastomes were highly conserved and similar in structure, size, GC content, gene content and order, IR borders, and the patterns of codon bias, RNA editing, and simple sequence repeats (SSRs). Nevertheless, twelve mutation hotspots (matK, ndhC, rps15, rps8, ycf2, ccsA-ndhD, petN-psbM, psbA-trnK, rps2-rpoC2, rps4-trnT, trnH-psbA, and ycf2-trnL) were selected. Moreover, both the phylogenetic analyses based on plastomes and on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences robustly supported that P. nanum and P. violaceum nested in Ligusticopsis, and this was further confirmed by the morphological evidence. Hence, transferring P. nanum and P. violaceum into Ligusticopsis genus is reasonable and convincing, and two new combinations are presented.
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Affiliation(s)
| | | | | | | | - Songdong Zhou
- Correspondence: (S.Z.); (X.H.); Tel.: +028-85415006 (X.H.)
| | - Xingjin He
- Correspondence: (S.Z.); (X.H.); Tel.: +028-85415006 (X.H.)
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