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Till 2018: a survey of biomolecular sequences in genus Panax. J Ginseng Res 2020; 44:33-43. [PMID: 32095095 PMCID: PMC7033366 DOI: 10.1016/j.jgr.2019.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Ginseng is popularly known to be the king of ancient medicines and is used widely in most of the traditional medicinal compositions due to its various pharmaceutical properties. Numerous studies are being focused on this plant's curative effects to discover their potential health benefits in most human diseases, including cancer- the most life-threatening disease worldwide. Modern pharmacological research has focused mainly on ginsenosides, the major bioactive compounds of ginseng, because of their multiple therapeutic applications. Various issues on ginseng plant development, physiological processes, and agricultural issues have also been studied widely through state-of-the-art, high-throughput sequencing technologies. Since the beginning of the 21st century, the number of publications on ginseng has rapidly increased, with a recent count of more than 6,000 articles and reviews focusing notably on ginseng. Owing to the implementation of various technologies and continuous efforts, the ginseng plant genomes have been decoded effectively in recent years. Therefore, this review focuses mainly on the cellular biomolecular sequences in ginseng plants from the perspective of the central molecular dogma, with an emphasis on genomes, transcriptomes, and proteomes, together with a few other related studies.
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Methods and Tools for Plant Organelle Genome Sequencing, Assembly, and Downstream Analysis. Methods Mol Biol 2020; 2107:49-98. [PMID: 31893443 DOI: 10.1007/978-1-0716-0235-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Organelles play an important role in a eukaryotic cell. Among them, the two organelles, chloroplast and mitochondria, are responsible for the critical function of photosynthesis and aerobic respiration. Organellar genomes are also very important for plant systematic studies. Here we have described the methods for isolation of the mitochondrial and plastid DNA and its subsequent sequencing with the help of NGS technology. We have also discussed in detail the various tools available for assembly, annotation, and visualization of the organelle genome sequence.
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Antaky CC, Kitamura PK, Knapp IS, Toonen RJ, Price MR. The complete mitochondrial genome of the Band-rumped Storm Petrel ( Oceanodroma castro). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Carmen C. Antaky
- Department of Natural Resources and Environmental Management, University of Hawaiʻi at Mānoa, Honolulu, HI, USA
| | - Philip K. Kitamura
- Department of Natural Resources and Environmental Management, University of Hawaiʻi at Mānoa, Honolulu, HI, USA
| | - Ingrid S. Knapp
- Hawai’i Institute of Marine Biology, University of Hawaiʻi at Mānoa, Kāne‘ohe, HI, USA
| | - Robert J. Toonen
- Hawai’i Institute of Marine Biology, University of Hawaiʻi at Mānoa, Kāne‘ohe, HI, USA
| | - Melissa R. Price
- Department of Natural Resources and Environmental Management, University of Hawaiʻi at Mānoa, Honolulu, HI, USA
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Liu C, Yang Z, Yang L, Yang J, Ji Y. The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae). PLANT DIVERSITY 2018; 40:265-276. [PMID: 30740573 PMCID: PMC6317490 DOI: 10.1016/j.pld.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 06/03/2023]
Abstract
Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.
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Affiliation(s)
- Changkun Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhenyan Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lifang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- School of Life Science, Yunnan University, Kunming 650091, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yunheng Ji
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Jiang P, Shi FX, Li MR, Liu B, Wen J, Xiao HX, Li LF. Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax. FRONTIERS IN PLANT SCIENCE 2018; 9:359. [PMID: 29670636 PMCID: PMC5893753 DOI: 10.3389/fpls.2018.00359] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/05/2018] [Indexed: 05/30/2023]
Abstract
Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.
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Affiliation(s)
- Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Feng-Xue Shi
- Northeast Normal University Natural History Museum, Changchun, China
| | - Ming-Rui Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Hong-Xing Xiao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
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Zuo YJ, Wen J, Zhou SL. Intercontinental and intracontinental biogeography of the eastern Asian - Eastern North American disjunct Panax (the ginseng genus, Araliaceae), emphasizing its diversification processes in eastern Asia. Mol Phylogenet Evol 2017; 117:60-74. [PMID: 28743642 DOI: 10.1016/j.ympev.2017.06.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 06/08/2017] [Accepted: 06/20/2017] [Indexed: 12/01/2022]
Abstract
The intercontinental biogeography between eastern Asia and eastern North America has attracted much attention from evolutionary biologists. Further insights into understanding the evolution of the intercontinental disjunctions have been hampered by the lack of studies on the intracontinental biogeography in eastern Asia, a region with complex geology, geography, climates and habitats. Herein we studied the biogeographic history of the eastern Asian-eastern North American disjunct genus Panax with special emphasis on the investigation of its uneven diversification in Asia. This study reconstructs the diversification history of Panax and also emphasizes a large clade of Panax taxa, which has a wide distribution in eastern Asia, but was unresolved in previous studies. We examined the noncoding plastid DNA fragments of trnH-psbA, rps16, and psbM-trnD, the mitochondrial b/c intron of NAD1, and the nuclear ribosomal internal transcribed spacer (ITS) region of 356 samples from 47 populations. The results revealed the subtropical Northern Hemisphere origin (Asia or Asia and North America) of Panax in the Paleocene. Intercontinental disjunctions between eastern Asia and eastern North America formed twice in Panax, once estimated in early Eocene for the split of P. trifolius and another in mid-Miocene for the divergence of P. quinquefolius. Intercontinental diversifications in Panax showed temporal correlation with the increase of global temperature. The evolutionary radiation of the P. bipinnatifidus species complex occurred around the boundary of Oligocene and Miocene. Strong genetic structure among populations of the species complex was detected and the populations may be isolated by distance. The backbone network and the Bayesian clustering analysis revealed a major evolutionary radiation centered in the Hengduan Mountains of western China. Our results suggested that the evolutionary radiation of Panax was promoted by geographic barriers, including mountain ranges (Hengduan Mountains, Nanling Mountains and Wuyishan Mountains), oceans and altitudinal shifts, which further contribute to the knowledge of the uneven species diversification between eastern Asia and North America.
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Affiliation(s)
- Yun-Juan Zuo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences; Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | - Shi-Liang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Cheng Y, Zhou L, Dong Y. Complete mitochondrial genome of Tringa erythropus (Charadriiformes: Scolopacidae). Mitochondrial DNA B Resour 2016; 1:678-679. [PMID: 33473595 PMCID: PMC7799656 DOI: 10.1080/23802359.2016.1219637] [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: 11/24/2022] Open
Abstract
The spotted redshank Tringa erythropus is a shorebird in the large bird family Scolopacidae. In this study, we sequenced and characterized its complete mitochondrial genome. The mitogenome is a circular DNA molecule of 16,683 bp in length, containing 13 protein-coding genes, 22 tRNA, 2 rRNA genes, and an AT-rich region. Its gene arrangement pattern is identical with typical bird species. Based on our data combined with the mitgenome DNA sequences of 12 Scolopacidae birds from GenBank, phylogenetic analysis indicated that T. erythropus, Arenaria interpres, and Eurynorhynchus pygmeus formed a group.
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Affiliation(s)
- Yuanyuan Cheng
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Anhui Biodiversity Information Center, Hefei, China
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Anhui Biodiversity Information Center, Hefei, China
| | - Yuanqiu Dong
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Anhui Biodiversity Information Center, Hefei, China
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