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Yao R, Wang B, Heinrich M, Wang Q, Xiao P. Genetic diversity of food-medicinal Lycium spp. in China: Insights from chloroplast genome. CHINESE HERBAL MEDICINES 2024; 16:401-411. [PMID: 39072208 PMCID: PMC11283223 DOI: 10.1016/j.chmed.2024.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/09/2023] [Accepted: 02/08/2024] [Indexed: 07/30/2024] Open
Abstract
Objective Goji (fruits of Lycium spp.) is commonly consumed as food and medicine. The increasing market demand for goji has led to its wide cultivation and broad breeding, which might cause loss of genetic diversity. This study aims to uncover the genetic diversity of the cultivated and wild Lycium. Methods The chloroplast genome (CPG) of 34 accessions of Chinese food-medicinal Lycium spp., including the popular cultivars and their wild relatives, was re-sequenced and assembled, based on which the genetic diversity was evaluated. Results Sequence structural comparison shows that CPG is comparatively conserved within species. Phylogenetic analysis indicates that CPG is sufficient for the discrimination of Lycium species; combined with nuclear ribosomal internal transcribed spacer (Nr ITS) sequences, materials with mixed genetic backgrounds can be identified. Nucleotide diversity analysis reveals that the modern cultivars are probably with a common maternal parent, while the wild accessions are with higher level of genetic diversity. Conclusion For the first time this study reveals the intraspecies genetic diversity of Lycium spp. using CPG, highlighting the urgent conservation demand of wild genetic resources of Lycium. Our study also demonstrates that CPG provides crucial evidence for identification of Lycium species with mixed genetic backgrounds and highlights the importance of the wild relatives in genetic diversity conservation. This CPG-based technology will contribute to the sustainable development of medicinal plants broadly.
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Affiliation(s)
- Ruyu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Bin Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China
| | - Michael Heinrich
- Research Group ‘Pharmacognosy and Phytotherapy’, UCL School of Pharmacy, University of London, London WC1N1AX, United Kingdom
| | - Qiuling Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
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Hai Y, Qian Y, Yang M, Zhang Y, Xu H, Yang Y, Xia C. The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species. Sci Rep 2024; 14:13945. [PMID: 38886540 PMCID: PMC11183227 DOI: 10.1038/s41598-024-64896-7] [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: 12/25/2023] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129-134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.
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Affiliation(s)
- Yonglin Hai
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yan Qian
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Meihua Yang
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yue Zhang
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Huimei Xu
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yongcheng Yang
- College of Pharmacy, Dali University, Dali, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
| | - Conglong Xia
- College of Pharmacy, Dali University, Dali, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
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Ding Y, Wang Y, Chen Z, Dou J, Zhang Y, Zhang Y. Comparative chloroplast-specific SNP and nSCoT markers analysis and population structure study in kiwifruit plants. Hereditas 2024; 161:18. [PMID: 38760874 PMCID: PMC11102262 DOI: 10.1186/s41065-024-00321-3] [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: 01/22/2024] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Kiwifruit (Actinidiaceae family) is an economically important fruit tree in China and New Zealand. It is a typical dioecious plant that has undergone frequent natural hybridization, along with chromosomal ploidy diversity within the genus Actinidia, resulting in higher genetic differences and horticultural diversity between interspecific and intraspecific traits. This diversity provides a rich genetic base for breeding. China is not only the original center of speciation for the Actinidia genus but also its distribution center, housing the most domesticated species: A. chinensis var. chinensis, A. chinensis var. deliciosa, A. arguta, and A. polygama. However, there have been relatively few studies on the application of DNA markers and the genetic basis of kiwifruit plants. By combining information from chloroplast-specific SNPs and nuclear SCoT (nSCoT) markers, we can uncover complementary aspects of genetic variation, population structure, and evolutionary relationships. In this study, one chloroplast DNA (cpDNA) marker pair was selected out of nine cpDNA candidate pairs. Twenty nSCoT markers were selected and used to assess the population structure and chloroplast-specific DNA haplotype diversity in 55 kiwifruit plants (Actinidia), including 20 samples of A. chinensis var. chinensis, 22 samples of A. chinensis var. deliciosa, 11 samples of A. arguta, and two samples of A. polygama, based on morphological observations collected from China. RESULTS The average genetic distance among the 55 samples was 0.26 with chloroplast-specific SNP markers and 0.57 with nSCoT markers. The Mantel test revealed a very small correlation (r = 0.21). The 55 samples were categorized into different sub-populations using Bayesian analysis, the Unweighted Pair Group Method with the Arithmetic Mean (UPGMA), and the Principal Component Analysis (PCA) method, respectively. Based on the analysis of 205 variable sites, a total of 15 chloroplast-specific DNA haplotypes were observed, contributing to a higher level of polymorphism with an Hd of 0.78. Most of the chloroplast-specific DNA haplotype diversity was distributed among populations, but significant diversity was also observed within populations. H1 was shared by 24 samples, including 12 of A. chinensis var. chinensis and 12 of A. chinensis var. deliciosa, indicating that H1 is an ancient and dominant haplotype among the 55 chloroplast-specific sequences. H2 may not have evolved further.The remaining haplotypes were rare and unique, with some appearing to be exclusive to a particular variety and often detected in single individuals. For example, the H15 haplotype was found exclusively in A. polygama. CONCLUSION The population genetic variation explained by chloroplast-specific SNP markers has greater power than that explained by nSCoTs, with chloroplast-specific DNA haplotypes being the most efficient. Gene flow appears to be more evident between A. chinensis var. chinensis and A. chinensis var. deliciosa, as they share chloroplast-specific DNA haplotypes, In contrast, A.arguta and A. polygama possess their own characteristic haplotypes, derived from the haplotype of A. chinensis var. chinensis. Compared with A. chinensis, the A.arguta and A. polygama showed better grouping. It also seems crucial to screen out, for each type of molecular marker, especially haplotypes, the core markers of the Actinidia genus.
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Affiliation(s)
- Yinling Ding
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi Province, China
- Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, Shaanxi Province, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Hanzhong, Shaanxi Province, China
- Qinba State Key Laboratory of biological resources and ecological environment,, Hanzhong,, Shaanxi Province, China
| | - Yu Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi Province, China
- Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, Shaanxi Province, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Hanzhong, Shaanxi Province, China
- Qinba State Key Laboratory of biological resources and ecological environment,, Hanzhong,, Shaanxi Province, China
- Shaanxi Fruit Industry Group Limited Hanzhong Kiwifruit R&D Centre, Hanzhong, Shaanxi Province, China
| | - Zhe Chen
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi Province, China
- Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, Shaanxi Province, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Hanzhong, Shaanxi Province, China
- Qinba State Key Laboratory of biological resources and ecological environment,, Hanzhong,, Shaanxi Province, China
| | - Jiamin Dou
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi Province, China
- Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, Shaanxi Province, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Hanzhong, Shaanxi Province, China
- Qinba State Key Laboratory of biological resources and ecological environment,, Hanzhong,, Shaanxi Province, China
| | - Yihao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi Province, China
- Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, Shaanxi Province, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Hanzhong, Shaanxi Province, China
- Qinba State Key Laboratory of biological resources and ecological environment,, Hanzhong,, Shaanxi Province, China
| | - Yu Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi Province, China.
- Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, Shaanxi Province, China.
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Hanzhong, Shaanxi Province, China.
- Qinba State Key Laboratory of biological resources and ecological environment,, Hanzhong,, Shaanxi Province, China.
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Zhang L, Yi C, Xia X, Jiang Z, Du L, Yang S, Yang X. Solanum aculeatissimum and Solanum torvum chloroplast genome sequences: a comparative analysis with other Solanum chloroplast genomes. BMC Genomics 2024; 25:412. [PMID: 38671394 PMCID: PMC11046870 DOI: 10.1186/s12864-024-10190-9] [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: 09/30/2023] [Accepted: 03/05/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Solanum aculeatissimum and Solanum torvum belong to the Solanum species, and they are essential plants known for their high resistance to diseases and adverse conditions. They are frequently used as rootstocks for grafting and are often crossbred with other Solanum species to leverage their resistance traits. However, the phylogenetic relationship between S. aculeatissimum and S. torvum within the Solanum genus remains unclear. Therefore, this paper aims to sequence the complete chloroplast genomes of S. aculeatissimum and S. torvum and analyze them in comparison with 29 other previously published chloroplast genomes of Solanum species. RESULTS We observed that the chloroplast genomes of S. aculeatissimum and S. torvum possess typical tetrameric structures, consisting of one Large Single Copy (LSC) region, two reverse-symmetric Inverted Repeats (IRs), and one Small Single Copy (SSC) region. The total length of these chloroplast genomes ranged from 154,942 to 156,004 bp, with minimal variation. The highest GC content was found in the IR region, while the lowest was in the SSC region. Regarding gene content, the total number of chloroplast genes and CDS genes remained relatively consistent, ranging from 128 to 134 and 83 to 91, respectively. Nevertheless, there was notable variability in the number of tRNA genes and rRNAs. Relative synonymous codon usage (RSCU) analysis revealed that both S. aculeatissimum and S. torvum preferred codons that utilized A and U bases. Analysis of the IR boundary regions indicated that contraction and expansion primarily occurred at the junction between SSC and IR regions. Nucleotide polymorphism analysis and structural variation analysis demonstrated that chloroplast variation in Solanum species mainly occurred in the LSC and SSC regions. Repeat sequence analysis revealed that A/T was the most frequent base pair in simple repeat sequences (SSR), while Palindromic and Forward repeats were more common in long sequence repeats (LSR), with Reverse and Complement repeats being less frequent. Phylogenetic analysis indicated that S. aculeatissimum and S. torvum belonged to the same meristem and were more closely related to Cultivated Eggplant. CONCLUSION These findings enhance our comprehension of chloroplast genomes within the Solanum genus, offering valuable insights for plant classification, evolutionary studies, and potential molecular markers for species identification.
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Affiliation(s)
- Longhao Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Chengqi Yi
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Xin Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Lihui Du
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Shixin Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China.
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Yu W, Cai S, Zhao J, Hu S, Zang C, Xu J, Hu L. Beyond genome: Advanced omics progress of Panax ginseng. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112022. [PMID: 38311250 DOI: 10.1016/j.plantsci.2024.112022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Ginseng is a perennial herb of the genus Panax in the family Araliaceae as one of the most important traditional medicine. Genomic studies of ginseng assist in the systematic discovery of genes related to bioactive ginsenosides biosynthesis and resistance to stress, which are of great significance in the conservation of genetic resources and variety improvement. The transcriptome reflects the difference and consistency of gene expression, and transcriptomics studies of ginseng assist in screening ginseng differentially expressed genes to further explore the powerful gene source of ginseng. Protein is the ultimate bearer of ginseng life activities, and proteomic studies of ginseng assist in exploring the biosynthesis and regulation of secondary metabolites like ginsenosides and the molecular mechanism of ginseng adversity adaptation at the overall level. In this review, we summarize the current status of ginseng research in genomics, transcriptomics and proteomics, respectively. We also discuss and look forward to the development of ginseng genome allele mapping, ginseng spatiotemporal, single-cell transcriptome, as well as ginseng post-translational modification proteome. We hope that this review will contribute to the in-depth study of ginseng and provide a reference for future analysis of ginseng from a systems biology perspective.
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Affiliation(s)
- Wenjing Yu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Siyuan Cai
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiali Zhao
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Shuhan Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Chen Zang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China.
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Lubna, Asaf S, Jan R, Asif S, Bilal S, Khan AL, Al-Rawahi AN, Kim KM, Al-Harrasi A. The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary significance, structural features, and comparative analysis. Sci Rep 2024; 14:4006. [PMID: 38369569 PMCID: PMC10874969 DOI: 10.1038/s41598-024-54503-0] [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: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Parthenium hysterophorus, a globally widespread weed, poses a significant threat to agricultural ecosystems due to its invasive nature. We investigated the chloroplast genome of P. hysterophorus in this study. Our analysis revealed that the chloroplast genome of P. hysterophorus spans a length of 151,881 base pairs (bp). It exhibits typical quadripartite structure commonly found in chloroplast genomes, including inverted repeat regions (IR) of 25,085 bp, a small single copy (SSC) region of 18,052 bp, and a large single copy (LSC) region of 83,588 bp. A total of 129 unique genes were identified in P. hysterophorus chloroplast genomes, including 85 protein-coding genes, 36 tRNAs, and eight rRNAs genes. Comparative analysis of the P. hysterophorus plastome with those of related species from the tribe Heliantheae revealed both conserved structures and intriguing variations. While many structural elements were shared among the species, we identified a rearrangement in the large single-copy region of P. hysterophorus. Moreover, our study highlighted notable gene divergence in several specific genes, namely matK, ndhF, clpP, rps16, ndhA, rps3, and ndhD. Phylogenetic analysis based on the 72 shared genes placed P. hysterophorus in a distinct clade alongside another species, P. argentatum. Additionally, the estimated divergence time between the Parthenium genus and Helianthus (sunflowers) was approximately 15.1 million years ago (Mya). These findings provide valuable insights into the evolutionary history and genetic relationships of P. hysterophorus, shedding light on its divergence and adaptation over time.
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Affiliation(s)
- Lubna
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - 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 Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA
| | - Ahmed N Al-Rawahi
- Natural and Medical Sciences 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 Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
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Xiong C, Huang Y, Li Z, Wu L, Liu Z, Zhu W, Li J, Xu R, Hong X. Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China. BMC Genomics 2023; 24:648. [PMID: 37891463 PMCID: PMC10612195 DOI: 10.1186/s12864-023-09563-3] [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: 03/11/2023] [Accepted: 08/08/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND The Begonia species are common shade plants that are mostly found in southwest China. They have not been well studied despite their medicinal and decorative uses because gene penetration, decreased adaptability, and restricted availability are all caused by frequent interspecific hybridization. RESULT To understand the patterns of mutation in the chloroplast genomes of different species of Begonia, as well as their evolutionary relationships, we collected seven Begonia species in China and sequenced their chloroplast genomes. Begonia species exhibit a quadripartite structure of chloroplast genomes (157,634 - 169,694 bp), consisting of two pairs of inverted repeats (IR: 26,529 - 37,674 bp), a large single copy (LSC: 75,477 - 86,500 bp), and a small single copy (SSC: 17,861 - 18,367 bp). 128-143 genes (comprising 82-93 protein-coding genes, 8 ribosomal RNAs, and 36-43 transfer RNAs) are found in the chloroplast genomes. Based on comparative analyses, this taxon has a relatively similar genome structure. A total of six substantially divergent DNA regions (trnT-UGU-trnL-UAA, atpF-atpH, ycf4-cemA, psbC-trnS-UGA, rpl32-trnL-UAG, and ccsA-ndhD) are found in the seventeen chloroplast genomes. These regions are suitable for species identification and phylogeographic analysis. Phylogenetic analysis shows that Begonia species that were suited to comparable environments grouped in a small clade and that all Begonia species formed one big clade in the phylogenetic tree, supporting the genus' monophyly. In addition, positive selection sites were discovered in eight genes (rpoC1, rpoB, psbE, psbK, petA, rps12, rpl2, and rpl22), the majority of which are involved in protein production and photosynthesis. CONCLUSION Using these genome resources, we can resolve deep-level phylogenetic relationships between Begonia species and their families, leading to a better understanding of evolutionary processes. In addition to enhancing species identification and phylogenetic resolution, these results demonstrate the utility of complete chloroplast genomes in phylogenetically and taxonomically challenging plant groupings.
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Affiliation(s)
- Chao Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, People's Republic of China
| | - Yang Huang
- College of Tourism and Landscape Architecture, Guilin University of Technology, Guilin, Guangxi, 541006, People's Republic of China
| | - Zhenglong Li
- Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, 230601, People's Republic of China
| | - Lan Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Zhiguo Liu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, People's Republic of China
| | - Wenjun Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, People's Republic of China
| | - Jianhui Li
- College of Chemistry and Material Engineering, Quzhou University, Quzhou, Zhejiang, 324000, People's Republic of China
| | - Ran Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, People's Republic of China.
| | - Xin Hong
- Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, 230601, People's Republic of China.
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Wang X, Bai S, Zhang Z, Zheng F, Song L, Wen L, Guo M, Cheng G, Yao W, Gao Y, Li J. Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1179009. [PMID: 37229122 PMCID: PMC10203424 DOI: 10.3389/fpls.2023.1179009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average K A/K S ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.
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Affiliation(s)
- Xiaomin Wang
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Shengyi Bai
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Fushun Zheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lina Song
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lu Wen
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Meng Guo
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Guoxin Cheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Wenkong Yao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Yanming Gao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jianshe Li
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
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9
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Gao M, Huo X, Lu L, Liu M, Zhang G. Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome. CHINESE HERBAL MEDICINES 2023. [DOI: 10.1016/j.chmed.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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10
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Mohanan P, Yang TJ, Song YH. Genes and Regulatory Mechanisms for Ginsenoside Biosynthesis. JOURNAL OF PLANT BIOLOGY = SINGMUL HAKHOE CHI 2023; 66:87-97. [PMID: 36714200 PMCID: PMC9867542 DOI: 10.1007/s12374-023-09384-7] [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: 01/02/2023] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 05/13/2023]
Abstract
Panax ginseng is a medicinal plant belonging to the Araliaceae family. Ginseng is known as the king of oriental medicine, which has been practiced since ancient times in East Asian countries and globally in the modern era. Ginseng is used as an adaptogen, and research shows that it has several pharmacological benefits for various ailments such as cancer, inflammation, diabetes, and neurological symptoms. The pharmacological benefits of ginseng are attributed to the triterpenoid saponin ginsenosides found throughout the Panax ginseng species, which are abundant in its root and are found exclusively in P. ginseng and Panax quinquefolius. Recently, with the completion of the entire ginseng genome sequencing and the construction of the ginseng genome database, it has become possible to access information about many genes newly predicted to be involved in ginsenoside biosynthesis. This review briefly summarizes the current progress in ginseng genome analysis and genes involved in ginsenoside biosynthesis, proposing directions for functional studies of the predicted genes related to ginsenoside production and its regulation.
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Affiliation(s)
- Padmanaban Mohanan
- Plant Genomics and Breeding Research Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
| | - Tae-Jin Yang
- Plant Genomics and Breeding Research Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
| | - Young Hun Song
- Plant Genomics and Breeding Research Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Korea
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11
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Zhou Q, Chen Y, Wang J, Li M, Zeng W, Wang Y, Li Y, Zhao H. A comparative study of the chloroplast genomes of five Lepidium species with high medicinal value. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:29-45. [PMID: 36043226 DOI: 10.1071/fp22052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Plantgenomics is a rapidly developing field in medicinal plant research. This study analysed the relevant information of chloroplasts genome sequences of five medicinal plants from the genus Lepidium . We sequenced the complete chloroplast (cp) genomes of Lepidium apetalum Willd. and Lepidium perfoliatum Linnaeus., and assessed their genetic profiles against the reported profiles of Lepidium sativum Linnaeus., Lepidium meyenii Walp., and Lepidium virginicum Linn. We found that L. apetalum and L. perfoliatum possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. Our repeat analyses revealed that L. apetalum harboured 20 direct repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas, L. perfoliatum had 15 direct repeats, 20 palindrome repeats, four reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium medicinal plant cp genomes, and a high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium -specific gene fragments. Codon usage analysis showed that codon 14 was the most frequently used codon in the Lepidium coding sequences. Further, correlation investigations suggest that L. apetalum and L. perfoliatum originate from similar genetic backgrounds. Analysis of codon usage bias of Lepidium cp genome was strongly influenced by mutation and natural selection. We showed that L. apetalum and L. perfoliatum will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Yun Chen
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Jilian Wang
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Mingyuan Li
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Weijun Zeng
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Yuzhou Wang
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Yanhong Li
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Huixin Zhao
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
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12
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Duan N, Deng L, Zhang Y, Shi Y, Liu B. Comparative and phylogenetic analysis based on chloroplast genome of Heteroplexis (Compositae), a protected rare genus. BMC PLANT BIOLOGY 2022; 22:605. [PMID: 36550394 PMCID: PMC9773445 DOI: 10.1186/s12870-022-04000-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Heteroplexis Chang is an endangered genus endemic to China with important ecological and medicinal value. However, due to the lack of genetic data, our conservation strategies have repeatedly been delayed by controversial phylogenetic (molecular) relationships within the genera. In this study, we reported three new Heteroplexis chloroplast (cp.) genomes (H. vernonioides, H. impressinervia and H. microcephala) to clarify phylogenetic relationships between species allocated in this genus and other related Compositae. RESULTS All three new cp. genomes were highly conserved, showing the classic four regions. Size ranged from 152,984 - 153,221 bp and contained 130 genes (85 protein-coding genes, 37 tRNA, eight rRNA) and two pseudogenes. By comparative genomic and phylogenetic analyses, we found a large-scale inversion of the entire large single-copy (LSC) region in H. vernonioides, H. impressinervia and H. microcephala, being experimentally verified by PCR. The inverted repeat (IR) regions showed high similarity within the five Heteroplexis plastomes, showing small-size contractions. Phylogenetic analyses did not support the monophyly of Heteroplexis genus, whereas clustered the five species within two differentiated clades within Aster genus. These phylogenetic analyses suggested that the five Heteroplexis species might be subsumed into the Aster genus. CONCLUSION Our results enrich the data on the cp. genomes of the genus Heteroplexis, providing valuable genetic resources for future studies on the taxonomy, phylogeny, and evolution of Aster genus.
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Affiliation(s)
- Na Duan
- Department of Life Sciences, Changzhi University, 046011, Changzhi, Shanxi, China
- Institute of Loess Plateau, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Lili Deng
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, 541006, Guilin, Guangxi, China
| | - Ying Zhang
- Institute of Loess Plateau, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - YanCai Shi
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, 541006, Guilin, Guangxi, China.
| | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, 030006, Taiyuan, Shanxi, China.
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13
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Zhou D, Mehmood F, Lin P, Cheng T, Wang H, Shi S, Zhang J, Meng J, Zheng K, Poczai P. Characterization of the Evolutionary Pressure on Anisodus tanguticus Maxim. with Complete Chloroplast Genome Sequence. Genes (Basel) 2022; 13:2125. [PMID: 36421800 PMCID: PMC9690199 DOI: 10.3390/genes13112125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 10/15/2023] Open
Abstract
Anisodus tanguticus Maxim. (Solanaceae), a traditional endangered Tibetan herb, is endemic to the Qinghai-Tibet Plateau. Here, we report the de novo assembled chloroplast (cp) genome sequences of A. tanguticus (155,765 bp). The cp contains a pair of inverted repeated (IRa and IRb) regions of 25,881 bp that are separated by a large single copy (LSC) region (86,516 bp) and a small single copy SSC (17,487 bp) region. A total of 132 functional genes were annotated in the cp genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Moreover, 199 simple sequence repeats (SSR) and 65 repeat structures were detected. Comparative plastome analyses revealed a conserved gene order and high similarity of protein-coding sequences. The A. tanguticus cp genome exhibits contraction and expansion, which differs from Przewalskia tangutica and other related Solanaceae species. We identified 30 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which may be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Anisodus and family Solanaceae. Analysis of the Ka/Ks ratios of the Hyoscyameae tribe revealed significant positive selection exerted on the cemA, rpoC2, and clpP genes, which suggests that protein metabolism may be an important strategy for A. tanguticus and other species in Hyoscyameae in adapting to the adverse environment on the Qinghai-Tibetan Plateau. Phylogenetic analysis revealed that A. tanguticus clustered closer with Hyoscyamus niger than P. tangutica. Our results provide reliable genetic information for future exploration of the taxonomy and phylogenetic evolution of the Hyoscyameae tribe and related species.
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Affiliation(s)
- Dangwei Zhou
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Furrukh Mehmood
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Department of Biochemistry, Faculty of Sciences, University of Sialkot, Daska Road, Punjab 51040, Pakistan
| | - Pengcheng Lin
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Tingfeng Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Huan Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Shenbo Shi
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Jinkui Zhang
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Jing Meng
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Kun Zheng
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Péter Poczai
- Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland
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14
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Wang Y, Yu J, Chen YK, Wang ZC. Complete Chloroplast Genome Sequence of the Endemic and Endangered Plant Dendropanax oligodontus: Genome Structure, Comparative and Phylogenetic Analysis. Genes (Basel) 2022; 13:2028. [PMID: 36360265 PMCID: PMC9690231 DOI: 10.3390/genes13112028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2023] Open
Abstract
Dendropanax oligodontus, which belongs to the family Araliaceae, is an endemic and endangered species of Hainan Island, China. It has potential economic and medicinal value owing to the presence of phenylpropanoids, flavonoids, triterpenoids, etc. The analysis of the structure and characteristics of the D. oligodontus chloroplast genome (cpDNA) is crucial for understanding the genetic and phylogenetic evolution of this species. In this study, the cpDNA of D. oligodontus was sequenced for the first time using next-generation sequencing methods, assembled, and annotated. We observed a circular quadripartite structure comprising a large single-copy region (86,440 bp), a small single-copy region (18,075 bp), and a pair of inverted repeat regions (25,944 bp). The total length of the cpDNA was 156,403 bp, and the GC% was 37.99%. We found that the D. oligodontus chloroplast genome comprised 131 genes, with 86 protein-coding genes, 8 rRNA genes, and 37 tRNAs. Furthermore, we identified 26,514 codons, 13 repetitive sequences, and 43 simple sequence repeat sites in the D. oligodontus cpDNA. The most common amino acid encoded was leucine, with a strong A/T preference at the third position of the codon. The prediction of RNA editing sites in the protein-coding genes indicated that RNA editing was observed in 19 genes with a total of 54 editing sites, all of which involved C-to-T transitions. Finally, the cpDNA of 11 species of the family Araliaceae were selected for comparative analysis. The sequences of the untranslated regions and coding regions among 11 species were highly conserved, and minor differences were observed in the length of the inverted repeat regions; therefore, the cpDNAs were relatively stable and consistent among these 11 species. The variable hotspots in the genome included clpP, ycf1, rnK-rps16, rps16-trnQ, atpH-atpI, trnE-trnT, psbM-trnD, ycf3-trnS, and rpl32-trnL, providing valuable molecular markers for species authentication and regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. Evolutionary selection pressure analysis indicated that the atpF gene was strongly subjected to positive environmental selection. Phylogenetic analysis indicated that D. oligodontus and Dendropanax dentiger were the most closely related species within the genus, and D. oligodontus was closely related to the genera Kalopanax and Metapanax in the Araliaceae family. Overall, the cp genomes reported in this study will provide resources for studying the genetic diversity and conservation of the endangered plant D. oligodontus, as well as resolving phylogenetic relationships within the family.
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Affiliation(s)
- Yong Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Jing Yu
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University, Haikou 570228, China
| | - Yu-Kai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Zhu-Cheng Wang
- College of Life Sciences, Cangzhou Normal University, Cangzhou 061001, China
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15
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Li Y, Zhang L, Wang T, Zhang C, Wang R, Zhang D, Xie Y, Zhou N, Wang W, Zhang H, Hu B, Li W, Zhao Q, Wang L, Wu X. The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses. JOURNAL OF PLANT RESEARCH 2022; 135:723-737. [PMID: 36260182 DOI: 10.1007/s10265-022-01417-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
We sequenced and analyzed the complete chloroplast genomes of Lilium amoenum, Lilium souliei, and Nomocharis forrestii in detail, including the first sequence and structural comparison of Nomocharis forrestii. We found that the lengths and nucleotide composition of the three chloroplast genes showed little variation. The chloroplast genomes of the three Lilium species contain 87 protein coding genes (PCGs), 38 tRNAs, and 8 rRNA genes. The only difference is that Nomocharis forrestii had an additional infA pseudogene. In the sequence analysis of the Lilium chloroplast genomes, 216 SSRs, 143 pairs of long repeats, 571 SNPs, and 202 indels were detected. In addition, we identified seven hypervariable regions that can be used as potential molecular markers and DNA barcodes of Lilium through complete sequence alignment. The phylogenetic tree was constructed from the three chloroplast genome sequences of Lilium obtained here and 40 chloroplast genome sequences from the NCBI database (including 35 Lilium species, 4 Fritillaria species, and one species of Smilax). The analysis showed that the species clustering of the genus Lilium essentially conformed to the classical morphological classification system of Comber, but differences in the classification of individual species remained. In our report, we support the reclassification of Lilium henryi and Lilium rosthorniiy in the genus Lilium. In general, this study not only provides genome data for three Lilium species, but also provides a comparative analysis of the Lilium chloroplast genomes. These advances will help to identify Lilium species, clarify the phylogenetic analysis of the Lilium genus, and help to solve and improve the disputes and deficiencies in the traditional morphological classification.
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Affiliation(s)
- Yuan Li
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - LiNa Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - TianXi Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - ChaoChao Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - RuiJia Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - Da Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - YuQi Xie
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - NingNing Zhou
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - WeiZhen Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - HuiMin Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - Bin Hu
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - WenHan Li
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - QingQing Zhao
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - LiHua Wang
- Flower Research Institute, Yunnan Agriculture Academy of Science, Panlong District, Kunming, 650025, Yunnan, China.
| | - XueWei Wu
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China.
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16
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Lu QX, Chang X, Gao J, Wu X, Wu J, Qi ZC, Wang RH, Yan XL, Li P. Evolutionary Comparison of the Complete Chloroplast Genomes in Convallaria Species and Phylogenetic Study of Asparagaceae. Genes (Basel) 2022; 13:genes13101724. [PMID: 36292609 PMCID: PMC9601677 DOI: 10.3390/genes13101724] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Convallaria (Asparagaceae) comprises three herbaceous perennial species that are widely distributed in the understory of temperate deciduous forests in the Northern Hemisphere. Although Convallaria species have high medicinal and horticultural values, studies related to the phylogenetic analysis of this genus are few. In the present study, we assembled and reported five complete chloroplast (cp) sequences of three Convallaria species (two of C. keiskei Miq., two of C. majalis L., and one of C. montana Raf.) using Illumina paired-end sequencing data. The cp genomes were highly similar in overall size (161,365–162,972 bp), and all consisted of a pair of inverted repeats (IR) regions (29,140–29,486 bp) separated by a large single-copy (LSC) (85,183–85,521 bp) and a small single-copy (SSC) region (17,877–18,502 bp). Each cp genome contained the same 113 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene content, gene order, AT content and IR/SC boundary structure were nearly identical among all of the Convallaria cp genomes. However, their lengths varied due to contraction/expansion at the IR/LSC borders. Simple sequence repeat (SSR) analyses indicated that the richest SSRs are A/T mononucleotides. Three highly variable regions (petA-psbJ, psbI-trnS and ccsA-ndhD) were identified as valuable molecular markers. Phylogenetic analysis of the family Asparagaceae using 48 cp genome sequences supported the monophyly of Convallaria, which formed a sister clade to the genus Rohdea. Our study provides a robust phylogeny of the Asparagaceae family. The complete cp genome sequences will contribute to further studies in the molecular identification, genetic diversity, and phylogeny of Convallaria.
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Affiliation(s)
- Qi-Xiang Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiao Chang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xue Wu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Wu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312366, China
- Correspondence: (Z.-C.Q.); (R.-H.W.)
| | - Rui-Hong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Correspondence: (Z.-C.Q.); (R.-H.W.)
| | - Xiao-Ling Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Pan Li
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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17
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Wang R, Gao J, Feng J, Yang Z, Qi Z, Li P, Fu C. Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of Scrophularia incisa Complex (Scrophulariaceae). Genes (Basel) 2022; 13:1691. [PMID: 36292576 PMCID: PMC9601301 DOI: 10.3390/genes13101691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 10/14/2023] Open
Abstract
The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai-Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.
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Affiliation(s)
- Ruihong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jieying Feng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zhaoping Yang
- Key Laboratory of Biological Resources and Conservation and Application, College of Life 9 Sciences, Tarim University, Alaer 843300, China
| | - Zhechen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengxin Fu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Wen Y, Qin Y, Shao B, Li J, Ma C, Liu Y, Yang B, Jin X. The extremely reduced, diverged and reconfigured plastomes of the largest mycoheterotrophic orchid lineage. BMC PLANT BIOLOGY 2022; 22:448. [PMID: 36123622 PMCID: PMC9487142 DOI: 10.1186/s12870-022-03836-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/09/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Plastomes of heterotrophic plants have been greatly altered in structure and gene content, owing to the relaxation of selection on photosynthesis-related genes. The orchid tribe Gastrodieae is the largest and probably the oldest mycoheterotrophic clade of the extant family Orchidaceae. To characterize plastome evolution across members of this key important mycoheterotrophic lineage, we sequenced and analyzed the plastomes of eleven Gastrodieae members, including representative species of two genera, as well as members of the sister group Nervilieae. RESULTS The plastomes of Gastrodieae members contain 20 protein-coding, four rRNA and five tRNA genes. Evolutionary analysis indicated that all rrn genes were transferred laterally and together, forming an rrn block in the plastomes of Gastrodieae. The plastome GC content of Gastrodia species ranged from 23.10% (G. flexistyla) to 25.79% (G. javanica). The plastome of Didymoplexis pallens contains two copies each of ycf1 and ycf2. The synonymous and nonsynonymous substitution rates were very high in the plastomes of Gastrodieae among mycoheterotrophic species in Orchidaceae and varied between genes. CONCLUSIONS The plastomes of Gastrodieae are greatly reduced and characterized by low GC content, rrn block formation, lineage-specific reconfiguration and gene content, which might be positively selected. Overall, the plastomes of Gastrodieae not only serve as an excellent model for illustrating the evolution of plastomes but also provide new insights into plastome evolution in parasitic plants.
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Affiliation(s)
- Yingying Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Ying Qin
- Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, Guangxi, China
| | - Bingyi Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jianwu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan, 666303, China
| | - Chongbo Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yan Liu
- Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, Guangxi, China.
| | - Boyun Yang
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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Duan Q, Liu F, Gui D, Fan W, Cui G, Jia W, Zhu A, Wang J. Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:865606. [PMID: 35937320 PMCID: PMC9355515 DOI: 10.3389/fpls.2022.865606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/16/2022] [Indexed: 05/24/2023]
Abstract
Lilies are one of the most important ornamental flowers worldwide with approximately 100 wild species and numerous cultivars, but the phylogenetic relationships among wild species and their contributions to these cultivars are poorly resolved. We collected the major Lilium species and cultivars and assembled their plastome sequences. Our phylogenetic reconstruction using 114 plastid genomes, including 70 wild species representing all sections and 42 cultivars representing six hybrid divisions and two outgroups, uncovered well-supported genetic relationships within Lilium. The wild species were separated into two distinct groups (groups A and B) associated with geographical distribution, which further diversified into eight different clades that were phylogenetically well supported. Additional support was provided by the distributions of indels and single-nucleotide variants, which were consistent with the topology. The species of sections Archelirion, Sinomartagon III, and Leucolirion 6a and 6b were the maternal donors for Oriental hybrids, Asiatic hybrids, Trumpet hybrids, and Longiflorum hybrids, respectively. The maternal donors of the OT hybrids originated from the two sections Archelirion and Leucolirion 6a, and LA hybrids were derived from the two sections Leucolirion 6b and Sinomartagon. Our study provides an important basis for clarifying the infrageneric classification and the maternal origin of cultivars in Lilium.
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Affiliation(s)
- Qing Duan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guangfen Cui
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Wenjie Jia
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
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20
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Huang X, Coulibaly D, Tan W, Ni Z, Shi T, Li H, Hayat F, Gao Z. The analysis of genetic structure and characteristics of the chloroplast genome in different Japanese apricot germplasm populations. BMC PLANT BIOLOGY 2022; 22:354. [PMID: 35864441 PMCID: PMC9306182 DOI: 10.1186/s12870-022-03731-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chloroplast (cp) genomes are generally considered to be conservative and play an important role in population diversity analysis in plants, but the characteristics and diversity of the different germplasm populations in Japanese apricot are still not clear. RESULTS A total of 146 cp genomes from three groups of wild, domesticated, and bred accessions of Japanese apricot were sequenced in this study. The comparative genome analysis revealed that the 146 cp genomes were divided into 41 types, and ranged in size from 157,886 to 158,167 bp with a similar structure and composition to those of the genus Prunus. However, there were still minor differences in the cp genome that were mainly caused by the contraction and expansion of the IR region, and six types of SSR in which mono-nucleotide repeats were the most dominant type of repeats in the cp genome. The genes rpl33 and psbI, and intergenic regions of start-psbA, rps3-rpl22, and ccsA-ndhD, showed the highest nucleotide polymorphism in the whole cp genome. A total of 325 SNPs were detected in the 146 cp genomes, and more than 70% of the SNPs were in region of large single-copy (LSC). The SNPs and haplotypes in the cp genome indicated that the wild group had higher genetic diversity than the domesticated and bred groups. In addition, among wild populations, Southwest China, including Yunnan, Tibet, and Bijie of Guizhou, had the highest genetic diversity. The genetic relationship of Japanese apricot germplasm resources in different regions showed a degree of correlation with their geographical distribution. CONCLUSION Comparative analysis of chloroplast genomes of 146 Japanese apricot resources was performed to analyze the used to explore the genetic relationship and genetic diversity among Japanese apricot resources with different geographical distributions, providing some reference for the origin and evolution of Japanese apricot.
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Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Hantao Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Faisal Hayat
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
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21
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Yan L, Wang H, Huang X, Li Y, Yue Y, Wang Z, Tang S. Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution. Front Genet 2022; 13:925726. [PMID: 35873491 PMCID: PMC9305825 DOI: 10.3389/fgene.2022.925726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 11/26/2022] Open
Abstract
Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to the lack of sufficient distinguishable morphological and molecular characteristics, interspecific relationships in this genus are not clear. Chloroplast (cp) genomes are small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used in molecular systematics and phylogenetic analyses. Here, we sequenced and assembled cp genomes from T. endochrysea, T. tomentosa, T. miqueliana, T. americana and T. cordata, and compared them with those of seven previously reported Tilia species. Similar gene contents, gene orders and GC contents existed among the 12 cp genomes, which ranged from 162,564 to 162,855 bp and encoded 113 unique genes. Abundant simple sequence repeats (119–127) and dispersed repeats (97–135) were detected in Tilia cp genomes. In total, 11 hypervariable regions were identified that could be suitable for species identification and phylogenetic studies. A phylogenetic analysis of Malvaceae based on 5 hypervariable genes (matK + ndhF + rpoB + rpoC2+ycf1) revealed that all eight subfamilies were monophyletic groups. Additionally, the genus Tilia was divided into three groups on the basis of all 521 molecular variation loci. The current study provides valuable insights into the genomic evolution of the genus Tilia.
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Affiliation(s)
- Linjun Yan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Huanli Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Xi Huang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Yingchao Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuanhao Yue
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Zhongwei Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Shijie Tang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
- *Correspondence: Shijie Tang,
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Al-Kuraishy HM, Al-Hussaniy HA, Al-Gareeb AI, Negm WA, El-Kadem AH, Batiha GES, N. Welson N, Mostafa-Hedeab G, Qasem AH, Conte-Junior CA. Combination of Panax ginseng C. A. Mey and Febuxostat Boasted Cardioprotective Effects Against Doxorubicin-Induced Acute Cardiotoxicity in Rats. Front Pharmacol 2022; 13:905828. [PMID: 35814241 PMCID: PMC9257079 DOI: 10.3389/fphar.2022.905828] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022] Open
Abstract
Doxorubicin (DOX) is an anticancer agent for treating solid and soft tissue malignancies. However, the clinical use of DOX is restricted by cumulative, dose-dependent cardiotoxicity. Therefore, the present study aimed to assess the cardioprotective effects of P. ginseng C. A. Mey, febuxostat, and their combination against DOX-induced cardiotoxicity. Thirty-five Sprague Dawley male rats were used in this study. The animals were randomly divided into five groups, with seven rats per group. The control group received normal saline, the induced group received DOX only, and the treated group received P. ginseng, febuxostat, and their combination before DOX treatment. Biomarkers of acute cardiac toxicity were assessed in each group. Results showed that treatment with the combination of febuxostat and P. ginseng before DOX led to a significant improvement in the biomarkers of acute DOX-induced cardiotoxicity. In conclusion, the combination of P. ginseng and febuxostat produced more significant cardioprotective effects against DOX-induced cardiotoxicity when compared to either P. ginseng or febuxostat when used alone. The potential mechanism of this combination was mainly mediated by the anti-inflammatory and antioxidant effects of P. ginseng and febuxostat.
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Affiliation(s)
- Hayder M. Al-Kuraishy
- Department of Clinical Pharmacology and Therapeutic, College of Medicine, Al-Mustansiriyah University, Baghdad, Iraq
| | | | - Ali I. Al-Gareeb
- Department of Clinical Pharmacology and Therapeutic, College of Medicine, Al-Mustansiriyah University, Baghdad, Iraq
| | - Walaa A. Negm
- Pharmacognosy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Aya H. El-Kadem
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Nermeen N. Welson
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Gomaa Mostafa-Hedeab
- Pharmacology Department & Health Research Unit, Medical College, Jouf University, Sakakah, Saudi Arabia
- Pharmacology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Ahmed H Qasem
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Carlos Adam Conte-Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil
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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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Han Y, Gao Y, Li Y, Zhai X, Zhou H, Ding Q, Ma L. Chloroplast Genes Are Involved in The Male-Sterility of K-Type CMS in Wheat. Genes (Basel) 2022; 13:310. [PMID: 35205355 PMCID: PMC8871828 DOI: 10.3390/genes13020310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/30/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
The utilization of crop heterosis can greatly improve crop yield. The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.). The chloroplast genomes of two sterile lines and one maintainer were sequenced using second-generation high-throughput technology and assembled. The nonsynonymous mutated genes among the three varieties were identified, the expressed difference was further analyzed by qPCR, and finally, the function of the differentially expressed genes was analyzed by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method. A total of 16 genes containing 31 nonsynonymous mutations between K519A and 519B were identified. There were no base mutations in the protein-encoding genes between K519A and YS3038. The chloroplast genomes of 519B and K519A were closely related to the Triticum genus and Aegilops genus, respectively. The gene expression levels of the six selected genes with nonsynonymous mutation sites for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development. The seed setting rates of atpB-silenced or ndhH-silenced 519B plants by BSMV-VIGS method were significantly reduced. It can be concluded that atpB and the ndhH are likely to be involved in the reproductive transformation of 519B.
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Affiliation(s)
- Yucui Han
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; (Y.H.); (Y.L.)
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Yujie Gao
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Yun Li
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; (Y.H.); (Y.L.)
| | - Xiaoguang Zhai
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Hao Zhou
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Xianyang 712100, China
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
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Wang Y, Wen F, Hong X, Li Z, Mi Y, Zhao B. Comparative chloroplast genome analyses of Paraboea (Gesneriaceae): Insights into adaptive evolution and phylogenetic analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:1019831. [PMID: 36275537 PMCID: PMC9581172 DOI: 10.3389/fpls.2022.1019831] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/16/2022] [Indexed: 05/22/2023]
Abstract
Paraboea (Gesneriaceae) distributed in the karst areas of South and Southwest China and Southeast Asia, is an ideal genus to study the phylogeny and adaptive evolution of karst plants. In this study, the complete chloroplast genomes of twelve Paraboea species were sequenced and analyzed. Twelve chloroplast genomes ranged in size from 153166 to 154245 bp. Each chloroplast genome had a typical quartile structure, and relatively conserved type and number of gene components, including 131 genes which are composed of 87 protein coding genes, 36 transfer RNAs and 8 ribosomal RNAs. A total of 600 simple sequence repeats and 389 non-overlapped sequence repeats were obtained from the twelve Paraboea chloroplast genomes. We found ten divergent regions (trnH-GUG-psbA, trnM-CAU, trnC-GCA, atpF-atpH, ycf1, trnK-UUU-rps16, rps15, petL, trnS-GCU-trnR-UCU and psaJ-rpl33) among the 12 Paraboea species to be potential molecular markers. In the phylogenetic tree of 31 Gesneriaceae plants including twelve Paraboea species, all Paraboea species clustered in a clade and confirmed the monophyly of Paraboea. Nine genes with positive selection sites were detected, most of which were related to photosynthesis and protein synthesis, and might played crucial roles in the adaptability of Paraboea to diverse karst environments. These findings are valuable for further study of the phylogeny and karst adaptability of Gesneriaceae plants.
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Affiliation(s)
- Yifei Wang
- Department of Pharmacognosy, Guilin Medical University, Guilin, China
- Department of Pharmacy, Guilin Medical University, Guilin, China
| | - Fang Wen
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Xin Hong
- Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhenglong Li
- Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yaolei Mi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Bo Zhao, ; Yaolei Mi,
| | - Bo Zhao
- Department of Pharmacognosy, Guilin Medical University, Guilin, China
- Department of Pharmacy, Guilin Medical University, Guilin, China
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
- *Correspondence: Bo Zhao, ; Yaolei Mi,
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Li C, Cai C, Tao Y, Sun Z, Jiang M, Chen L, Li J. Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:754209. [PMID: 34721483 PMCID: PMC8551639 DOI: 10.3389/fpls.2021.754209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/21/2021] [Indexed: 06/02/2023]
Abstract
Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.
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Affiliation(s)
- Chenxin Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Yutian Tao
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
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Phylogenetic inference of Ericales based on plastid genomes and implication of cp-SSRs. BIOTECHNOLOGIA 2021; 102:277-283. [PMID: 36606144 PMCID: PMC9642927 DOI: 10.5114/bta.2021.108723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 01/09/2023] Open
Abstract
Ericales is an ancient eudicot order encompassing numerous species of economic and ornamental values. Despite several phylogenomic studies, the evolutionary relationship among certain families of this group remains uncertain. The present study assessed a multilocus species tree of Ericales based on 107 chloroplast genomes. The plastome derived microsatellite motifs were also simultaneously explored to check their dynamicity in corroboration of species phylogeny and systematics. In addition to resolving the usual hierarchy, the present phylogenetic analysis enabled to resolve the persisting lineage disparity with valid statistical support. Accordingly, divergence incongruences of Primulaceae, Ebenaceae, and Sapotaceae from earlier reports were reinstated in presently inferred phylogeny, which further supported the latest transcriptome-based relationship of the corresponding group. Various SSR motif characteristics emerged following the recognition of the evolutionary pathway. Numerical variation in tetranucleotide repeats showed even intraspecific or varietal differences in Camellia sinensis. Validation of plastome microsatellite-based polymorphism among the related taxa might pave the way for future phylogenetic and population studies of this economically important group.
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Singh NV, Patil PG, Sowjanya RP, Parashuram S, Natarajan P, Babu KD, Pal RK, Sharma J, Reddy UK. Chloroplast Genome Sequencing, Comparative Analysis, and Discovery of Unique Cytoplasmic Variants in Pomegranate ( Punica granatum L.). Front Genet 2021; 12:704075. [PMID: 34394192 PMCID: PMC8356083 DOI: 10.3389/fgene.2021.704075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022] Open
Abstract
Here we report on comprehensive chloroplast (cp) genome analysis of 16 pomegranate (Punica granatum L.) genotypes representing commercial cultivars, ornamental and wild types, through large-scale sequencing and assembling using next-generation sequencing (NGS) technology. Comparative genome analysis revealed that the size of cp genomes varied from 158,593 bp (in wild, “1201” and “1181”) to 158,662 bp (cultivar, “Gul-e-Shah Red”) among the genotypes, with characteristic quadripartite structures separated by a pair of inverted repeats (IRs). The higher conservation for the total number of coding and non-coding genes (rRNA and tRNA) and their sizes, and IRs (IR-A and IR-B) were observed across all the cp genomes. Interestingly, high variations were observed in sizes of large single copy (LSC, 88,976 to 89,044 bp) and small single copy (SSC, 18,682 to 18,684 bp) regions. Although, the structural organization of newly assembled cp genomes were comparable to that of previously reported cp genomes of pomegranate (“Helow,” “Tunisia,” and “Bhagawa”), the striking differences were observed with the Lagerstroemia lines, viz., Lagerstroemia intermedia (NC_0346620) and Lagerstroemia speciosa (NC_031414), which clearly confirmed previous findings. Furthermore, phylogenetic analysis also revealed that members outside the genus Punica were clubbed into a separate clade. The contraction and expansion analysis revealed that the structural variations in IRs, LSC, and SSC have significantly accounted for the evolution of cp genomes of Punica and L. intermedia over the periods. Microsatellite survey across cp genomes resulted in the identification of a total of 233 to 234 SSRs, with majority of them being mono- (A/T or C/G, 164–165 numbers), followed by di- (AT/AT or AG/CT, 54), tri- (6), tetra- (8), and pentanucleotides (1). Furthermore, the comparative structural variant analyses across cp genomes resulted in the identification of many varietal specific SNP/indel markers. In summary, our study has offered a successful development of large-scale cp genomics resources to leverage future genetic, taxonomical, and phylogenetic studies in pomegranate.
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Affiliation(s)
| | | | - Roopa P Sowjanya
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | | | - Purushothaman Natarajan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, West Virginia, WV, United States
| | | | - Ram Krishna Pal
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, West Virginia, WV, United States
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Xu J, Liu C, Song Y, Li M. Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships. Front Genet 2021; 12:687844. [PMID: 34386040 PMCID: PMC8354216 DOI: 10.3389/fgene.2021.687844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/21/2021] [Indexed: 01/22/2023] Open
Abstract
The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.
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Affiliation(s)
- Jin Xu
- Institute of Plant Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Chen Liu
- Institute of Plant Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Yun Song
- Institute of Plant Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Mingfu Li
- Institute of Plant Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
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Wu L, Wu M, Cui N, Xiang L, Li Y, Li X, Chen S. Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria. Chin Med 2021; 16:52. [PMID: 34225754 PMCID: PMC8256587 DOI: 10.1186/s13020-021-00460-z] [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: 02/14/2021] [Accepted: 06/26/2021] [Indexed: 12/21/2022] Open
Abstract
Background Although molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species. Methods We here compared 26 complete cp genomes of ten Fritillaria species including 18 new sequences sequenced in this study. Each species had repeats and the cp genomes were used as a whole DNA barcode to test whether they can distinguish Fritillaria species. Results The cp genomes of Fritillaria medicinal plants were conserved in genome structure, gene type, and gene content. Comparison analysis of the Fritillaria cp genomes revealed that the intergenic spacer regions were highly divergent compared with other regions. By constructing the phylogenetic tree by the maximum likelihood and maximum parsimony methods, we found that the entire cp genome showed a high discrimination power for Fritillaria species with individuals of each species in a monophyletic clade. These results indicate that cp genome can be used to effectively differentiate medicinal plants from the genus Fritillaria at the species level. Conclusions This study implies that cp genome can provide distinguishing differences to help identify closely related Fritillaria species, and has the potential to be served as a universal super-barcode for plant identification. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-021-00460-z.
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Affiliation(s)
- Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mingli Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ning Cui
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Wanga VO, Dong X, Oulo MA, Mkala EM, Yang JX, Onjalalaina GE, Gichua MK, Kirika PM, Gituru RW, Hu GW, Wang QF. Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement. FRONTIERS IN PLANT SCIENCE 2021; 12:691833. [PMID: 34194461 PMCID: PMC8238049 DOI: 10.3389/fpls.2021.691833] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/19/2021] [Indexed: 05/15/2023]
Abstract
Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas Xerophyta Juss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.
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Affiliation(s)
- Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Guy Eric Onjalalaina
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Moses Kirega Gichua
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | - Robert Wahiti Gituru
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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Huang X, Tan W, Li F, Liao R, Guo Z, Shi T, Gao Z. The chloroplast genome of Prunus zhengheensis: Genome comparative and phylogenetic relationships analysis. Gene 2021; 793:145751. [PMID: 34062257 DOI: 10.1016/j.gene.2021.145751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/06/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
Abstract
Prunus zhengheensis is a novel species originated in Fujian province, China. However, there is no further information available on its classification and molecular biology study. In this study, we first report the complete chloroplast (cp) genome sequence of P. zhengheensis. The cp genome of P. zhengheensis is 158,106 bp and GC content is 36.73%, is a circular structure composed of LSC (large single copy), SSC (small single copy), and IR (inverted repeat) regions, with the size of the three regions being 86,321 bp, 18,999 bp and 26,393 bp, respectively. The cp genome of P. zhengheensis contains 130 genes, and 242 SSRs are identified in the cp genome. The comparative analysis of cp genomes in eight Prunus plants demonstrates the subtle divergences occur in the protein-coding gene rps18, rps12, psbF, rpl33, matK, and rbcL, and that the KA/KS nucleotide substitution ratio of the ndhF of P. zhengheensis and P. armeniaca is 1.79636. The phylogenetic results indicate that the P. zhengheensis is closely related to P. mume, compared to other species of Prunus. Our research results provide the important genomic information for molecular phylogeny of P. zhengheensis.
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Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Li
- Jilin Academy of Agricultural Sciences, Jilin 136100, China.
| | - Ruyu Liao
- Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
| | - Zhongren Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Crosstalk of Multi-Omics Platforms with Plants of Therapeutic Importance. Cells 2021; 10:cells10061296. [PMID: 34071113 PMCID: PMC8224614 DOI: 10.3390/cells10061296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/25/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
From time immemorial, humans have exploited plants as a source of food and medicines. The World Health Organization (WHO) has recorded 21,000 plants with medicinal value out of 300,000 species available worldwide. The promising modern "multi-omics" platforms and tools have been proven as functional platforms able to endow us with comprehensive knowledge of the proteome, genome, transcriptome, and metabolome of medicinal plant systems so as to reveal the novel connected genetic (gene) pathways, proteins, regulator sequences and secondary metabolite (molecule) biosynthetic pathways of various drug and protein molecules from a variety of plants with therapeutic significance. This review paper endeavors to abridge the contemporary advancements in research areas of multi-omics and the information involved in decoding its prospective relevance to the utilization of plants with medicinal value in the present global scenario. The crosstalk of medicinal plants with genomics, transcriptomics, proteomics, and metabolomics approaches will be discussed.
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Xu G, Xu W. Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis. PROTOPLASMA 2021; 258:559-571. [PMID: 33230625 DOI: 10.1007/s00709-020-01585-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
As a basalmost family of Vitaceae, Chinese wild Vitis species offer key insights into the demographic history of grapes. In this study, we obtained 10 complete chloroplast (cp) genomes from Chinese wild-growing Vitis species based on our whole genome re-sequencing data. These chloroplast genomes ranged from 160,838 to 232,020 bp in size and exhibited typical quadripartite structures. Comparative analyses revealed that inverted repeat (IR) regions are especially abundant and contribute to cp genome arrangements. Phylogenetic analysis of the whole Vitis cp genomes supported three clearly partitioned main origins, in keeping with their geographic distributions, among which East Asian species from China were found to be sister species with Eurasian Vitis species but exhibited significant divergence from the North American group. Two well-supported subgroups were observed within the Chinese wild-growing Vitis species. Among these species, Vitis piasezkii and Vitis betulifolia were closely related species, exhibiting a support rate of 100%. The molecular clock-based divergence time suggested that the earliest split subspecies was Vitis pseudoreticulata, which further indicated that the origin and initial gene pool are located in southern China (the habitat of V. pseudoreticulata is located in the region). Coincidentally, the divergence time was during the Pleistocene period (2.6-0.1 Ma). Due to glacial/interglacial temperature fluctuations, cold-adapted subspecies, e.g., Vitis amurensis, could re-colonize new habitats. Our results may help to elucidate the adaptive radiation of Chinese wild Vitis species in different environments.
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Affiliation(s)
- Guangya Xu
- School of Agronomy, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China
| | - Weirong Xu
- School of Food & Wine, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China.
- Chinese Wine Industry Technology Institute, Yinchuan, 750021, China.
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Khan AL, Asaf S, Lubna, Al-Rawahi A, Al-Harrasi A. Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales. BMC Genomics 2021; 22:312. [PMID: 33926374 PMCID: PMC8086069 DOI: 10.1186/s12864-021-07626-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salvadora persica L. (Toothbrush tree - Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets available specifically on chloroplast (cp) genomics and taxonomic evolution. Herein, we have sequenced the complete chloroplast genome of S. persica for the first time and compared it with 11 related specie's cp genomes from the order Brassicales. RESULTS The S. persica cp genome was 153,379 bp in length containing a sizeable single-copy region (LSC) of 83,818 bp which separated from the small single-copy region (SSC) of 17,683 bp by two inverted repeats (IRs) each 25,939 bp. Among these genomes, the largest cp genome size (160,600 bp) was found in M. oleifera, while in S. persica it was the smallest (153,379 bp). The cp genome of S. persica encoded 131 genes, including 37 tRNA genes, eight rRNA genes and 86 protein-coding genes. Besides, S. persica contains 27 forward, 36 tandem and 19 palindromic repeats. The S. persica cp genome had 154 SSRs with the highest number in the LSC region. Complete cp genome comparisons showed an overall high degree of sequence resemblance between S. persica and related cp genomes. Some divergence was observed in the intergenic spaces of other species. Phylogenomic analyses of 60 shared genes indicated that S. persica formed a single clade with A. tetracantha with high bootstrap values. The family Salvadoraceae is closely related to Capparaceae and Petadiplandraceae rather than to Bataceae and Koberliniacaea. CONCLUSION The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, genome evolution and future genetic diversity-related studies of S. persica in complex angiosperm families.
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Affiliation(s)
- Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Lubna
- Department of Botany, Garden Campus, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
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Yuan C, Sha X, Xiong M, Zhong W, Wei Y, Li M, Tao S, Mou F, Peng F, Zhang C. Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications. Sci Rep 2021; 11:988. [PMID: 33441833 PMCID: PMC7806627 DOI: 10.1038/s41598-020-80225-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/16/2020] [Indexed: 12/02/2022] Open
Abstract
Ligusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.
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Affiliation(s)
- Can Yuan
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Xiufen Sha
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Miao Xiong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Wenjuan Zhong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Yu Wei
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingqian Li
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, Zhejiang, China
| | - Shan Tao
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Fangsheng Mou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China
| | - Fang Peng
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China. .,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China.
| | - Chao Zhang
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China. .,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China.
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Jiang M, Xu Y, Wang L, Liu J, Yu J, Chen H. High level of intraspecific divergence and low frequency of RNA editing in the chloroplast genome sequence of Tagetes erecta. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2948-2953. [PMID: 33458014 PMCID: PMC7782230 DOI: 10.1080/23802359.2020.1791001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tagetes erecta L. is an important commercial and medicinal plant. In this study, we reported the complete chloroplast genome sequence of T. erecta. The genome has a circular structure of 152,076 bp containing a large single-copy region (LSC) of 83,914 bp, a small copy region (SSC) of 18,064 bp, and two inverted repeats (IR) of 25,049 bp by each. It harbors 111 unique genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 28 transfer RNA genes. A total of 41 microsatellite, 20 tandem, and 37 interspersed repeats were detected in the genome. The phylogenomic analysis shows that T. erecta is a single phylogenetic cluster. The complete chloroplast genome of T. erecta lays the foundation for the phylogenetic, evolutionary, and conservation studies of the genus Tagetes. Furthermore, the intergenic region of atpB-rbcL was variable among the species T. erecta. This suggests that this region might be a mutation hotspot and will be useful for phylogenetic study and the development of molecular markers. At last, we systematically identified the RNA editing sites in the chloroplast genome of T. erecta based on the transcriptome downloaded from the SRA database. This study identified the characteristics of the T. erecta chloroplast genome, SNPs, and RNA editing sites, which will facilitate species identification and phylogenetic analysis within T. erecta.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Yicen Xu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
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Li C, Zheng Y, Huang P. Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling. Sci Rep 2020; 10:12188. [PMID: 32699274 PMCID: PMC7376030 DOI: 10.1038/s41598-020-68092-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.
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Affiliation(s)
- Changhong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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An W, Li J, Yang Z, Huang Y, Huang S, Zheng X. Characteristics analysis of the complete Wurfbainia villosa chloroplast genome. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:747-758. [PMID: 32255937 PMCID: PMC7113360 DOI: 10.1007/s12298-019-00748-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/25/2019] [Accepted: 12/13/2019] [Indexed: 05/05/2023]
Abstract
Wurfbainia villosa, which belongs to the huge family Zingiberaceae, is used in the clinic for the treatment of spleen and stomach diseases in southern China. The complete chloroplast genome of W. villosa was sequenced and analyzed using next-generation sequencing technology in the present work. The results showed that the W. villosa chloroplast genome is a circular molecule with 163,608 bp in length. It harbors a pair of inverted repeat regions (IRa and IRb) of 29,820 bp in length, which separate the large single copy (LSC, 88,680 bp) region and the small single copy (SSC, 15,288 bp) region. After annotation, 134 genes were identified in this plastome in total, comprising of 87 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes and one pseudogene (ycf1). Codon usage, RNA editing sites and single/long sequence repeats were investigated to understand the structural characteristics of the W. villosa chloroplast genome. Furthermore, IR contraction and expansion were analyzed by comparison of complete chloroplast genomes of W. villosa and four other Zingiberaceae species. Finally, a phylogeny study based on the chloroplast genome of W. villosa, along with that of 15 different species, was conducted to further investigate the relationship among these lineages. Overally, our results represented the first insight into the chloroplast genome of W. villosa, and could serve as a significant reference for species identification, genetic diversity analysis and phylogenetic research between W. villosa and other species within Zingiberaceae.
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Affiliation(s)
- Wenli An
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Jing Li
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510410 Guangdong China
- Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510410 China
| | - Zerui Yang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Yuying Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Song Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Xiasheng Zheng
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
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Yue J, Zuo Z, Huang H, Wang Y. Application of Identification and Evaluation Techniques for Ethnobotanical Medicinal Plant of Genus Panax: A Review. Crit Rev Anal Chem 2020; 51:373-398. [PMID: 32166968 DOI: 10.1080/10408347.2020.1736506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Genus Panax, as worldwide medicinal plants, has a medical history for thousands of years. Most of the entire genus are traditional ethnobotanical medicine in China, Myanmar, Thailand, Vietnam and Laos, which have given rise to international attention and use. This paper reviewed more than 210 articles and related books on the research of Panax medicinal plants and their Chinese patent medicines published in the last 30 years. The purpose was to review and summarize the species classification, geographical distribution, and ethnic minorities medicinal records of the genus Panax, and further to review the analytical tools and data analysis methods for the authentication and quality assessment of Panax medicinal materials and Chinese patent medicines. Five main technologies applied in the identification and evaluation of Panax have been introduced and summarized. Chromatography was the most widely used one. Further research and development of molecular identification technology had the potential to become a mainstream identification technology. In addition, some novel, controversial, and worthy methods including electronic noses, electronic eyes, and DNA barcoding were also introduced. At the same time, more than 80% of the researches were carried out by a combination of chemometric pattern-recognition technologies and multi-analysis technologies. All the technologies and methods applied can provide strong support and guarantee for the identification and evaluation of genus Panax, and also conduce to excellent reference value for the development and in-depth research of new technologies in Panax.
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Affiliation(s)
- Jiaqi Yue
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Zhitian Zuo
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hengyu Huang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Yuanzhong Wang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Asaf S, Khan AL, Lubna, Khan A, Khan A, Khan G, Lee IJ, Al-Harrasi A. Expanded inverted repeat region with large scale inversion in the first complete plastid genome sequence of Plantago ovata. Sci Rep 2020; 10:3881. [PMID: 32127603 PMCID: PMC7054531 DOI: 10.1038/s41598-020-60803-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
Plantago ovata (Plantaginaceae) is an economically and medicinally important species, however, least is known about its genomics and evolution. Here, we report the first complete plastome genome of P. ovata and comparison with previously published genomes of related species from Plantaginaceae. The results revealed that P. ovata plastome size was 162,116 bp and that it had typical quadripartite structure containing a large single copy region of 82,084 bp and small single copy region of 5,272 bp. The genome has a markedly higher inverted repeat (IR) size of 37.4 kb, suggesting large-scale inversion of 13.8 kb within the expanded IR regions. In addition, the P. ovata plastome contains 149 different genes, including 43 tRNA, 8 rRNA, and 98 protein-coding genes. The analysis revealed 139 microsatellites, of which 71 were in the non-coding regions. Approximately 32 forward, 34 tandem, and 17 palindromic repeats were detected. The complete genome sequences, 72 shared genes, matK gene, and rbcL gene from related species generated the same phylogenetic signals, and phylogenetic analysis revealed that P. ovata formed a single clade with P. maritima and P. media. The divergence time estimation as employed in BEAST revealed that P. ovata diverged from P. maritima and P. media about 11.0 million years ago (Mya; 95% highest posterior density, 10.06-12.25 Mya). In conclusion, P. ovata had significant variation in the IR region, suggesting a more stable P. ovata plastome genome than that of other Plantaginaceae species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.
| | - Lubna
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Adil Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Oldenburg, Germany
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.
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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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Zhang Z, Zhang Y, Song M, Guan Y, Ma X. Species Identification of Dracaena Using the Complete Chloroplast Genome as a Super-Barcode. Front Pharmacol 2019; 10:1441. [PMID: 31849682 PMCID: PMC6901964 DOI: 10.3389/fphar.2019.01441] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/12/2019] [Indexed: 01/04/2023] Open
Abstract
The taxonomy and nomenclature of Dracaena plants are much disputed, particularly for several Dracaena species in Asia. However, neither morphological features nor common DNA regions are ideal for identification of Dracaena spp. Meanwhile, although multiple Dracaena spp. are sources of the rare traditional medicine dragon's blood, the Pharmacopoeia of the People's Republic of China has defined Dracaena cochinchinensis as the only source plant. The inaccurate identification of Dracaena spp. will inevitably affect the clinical efficacy of dragon's blood. It is therefore important to find a better method to distinguish these species. Here, we report the complete chloroplast (CP) genomes of six Dracaena spp., D. cochinchinensis, D. cambodiana, D. angustifolia, D. terniflora, D. hokouensis, and D. elliptica, obtained through high-throughput Illumina sequencing. These CP genomes exhibited typical circular tetramerous structure, and their sizes ranged from 155,055 (D. elliptica) to 155,449 bp (D. cochinchinensis). The GC content of each CP genome was 37.5%. Furthermore, each CP genome contained 130 genes, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. There were no potential coding or non-coding regions to distinguish these six species, but the maximum likelihood tree of the six Dracaena spp. and other related species revealed that the whole CP genome can be used as a super-barcode to identify these Dracaena spp. This study provides not only invaluable data for species identification and safe medical application of Dracaena but also an important reference and foundation for species identification and phylogeny of Liliaceae plants.
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Affiliation(s)
- Zhonglian Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, China
| | - Yue Zhang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, China
| | - Meifang Song
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, China
| | - Yanhong Guan
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, China
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Zhang T, Xing Y, Xu L, Bao G, Zhan Z, Yang Y, Wang J, Li S, Zhang D, Kang T. Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae. Chin Med 2019; 14:53. [PMID: 31798674 PMCID: PMC6883693 DOI: 10.1186/s13020-019-0274-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/04/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Baitouweng is a traditional Chinese medicine with a long history of different applications. Although referred to as a single medicine, Baitouweng is actually comprised of many closely related species. It is therefore critically important to identify the different species that are utilized in these medicinal applications. Knowledge about their phylogenetic relationships can be derived from their chloroplast genomes and may provide additional insights into development of molecular markers. METHODS Genomic DNA was extracted from six species of Pulsatilla and then sequenced on an Illumina HiSeq 4000. Sequences were assembled into contigs by SOAPdenovo 2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the cp genomes of the six species were analyzed and compared with closely related species. Additionally, phylogenetic trees were constructed, based on single nucleotide polymorphisms (SNPs) and 51 shared protein-coding gene sequences in the cp genome among all 31 species via maximum likelihood. RESULTS The size of cp genomes of P. chinensis (Bge.) Regel, P. chinensis (Bge.) Regel var. kissii (Mandl) S. H. Li et Y. H. Huang, P. cernua (Thunb.) Bercht. et Opiz f. plumbea J. X. Ji et Y. T. zhao, P. dahurica (Fisch.) Spreng, P. turczaninovii Kryl. et Serg, and P. cernua (Thunb.) Bercht. et Opiz. were 163,851 bp, 163,756 bp, 162,481 bp, 162,450 bp, 162,795 bp, and 162,924 bp, respectively. Each species included two inverted repeat regions, a small single-copy region, and a large single-copy region. A total of 134 genes were annotated, including 90 protein-coding genes, 36 tRNAs, and eight rRNAs across all species. In simple sequence repeat analysis, only P. dahurica was found to contain hexanucleotide repeats. A total of 26, 39, 32, 37, 32 and 43 large repeat sequences were identified in the genic regions of the six Pulsatilla species. Nucleotide diversity analysis revealed that the rpl36 gene and ccsA-ndhD region have the highest Pi value. In addition, two phylogenetic trees of the cp genomes were constructed, which laced all Pulsatilla species into one branch within Ranunculaceae. CONCLUSIONS We identified and analyzed the cp genome features of six species of P. Miller, with implications for species identification and phylogenetic analysis.
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Affiliation(s)
- Tingting Zhang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
- Liaoning Quality Monitoring and Technology Service Center for Chinese Materia Medica Raw Materials, Dalian, China
| | - Guihua Bao
- School of Mongol Medicine, Inner Mongolia University for Nationalities, Tongliao, China
| | - Zhilai Zhan
- Traditional Chinese Medicine Resource Center, Chinese Academy of Traditional Chinese Medicine, Beijing, China
| | - Yanyun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Jiahao Wang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Shengnan Li
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Dachuan Zhang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Tingguo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
- Liaoning Quality Monitoring and Technology Service Center for Chinese Materia Medica Raw Materials, Dalian, China
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Yang Y, Zhang Y, Chen Y, Gul J, Zhang J, Liu Q, Chen Q. Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species. PeerJ 2019; 7:e7713. [PMID: 31579601 PMCID: PMC6756139 DOI: 10.7717/peerj.7713] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022] Open
Abstract
As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees.
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Affiliation(s)
- Yong Yang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Ying Zhang
- Life Sciences and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Yukai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Juma Gul
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jingwen Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Qiang Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Qing Chen
- Bawangling National Nature Reserve, Changjiang, Hainan Province, China
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Liu J, Wen J. The complete chloroplast genome of Aralia atropurpurea (Araliaceae, the ginseng family) from the Sino-Himalayan region, China. Mitochondrial DNA B Resour 2019; 4:2773-2774. [PMID: 33365722 PMCID: PMC7710312 DOI: 10.1080/23802359.2019.1643805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Aralia atropurpurea (Araliaceae) is a perennial medicinal herb endemic to southwest China. In this study, the complete chloroplast (cp) genome of A. atropurpurea was reported and phylogenetic analysis was conducted. The cp genome of A. atropurpurea is 156,272 bp in length, consisting two inverted repeats (IRs, 25,963 bp), a small single copy (SSC, 18,080 bp), and a large single copy (LSC, 86,266 bp) region. It encodes 133 genes including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum-likelihood tree shows A. atropurpurea grouping with the other two Aralia sect. Aralia species, and a close relationship between Aralia and Panax.
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Affiliation(s)
- Jing Liu
- College of Life Science, Sichuan Agricultural University, Ya'an, China.,Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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Zheng X, Ren C, Huang S, Li J, Zhao Y. Structure and features of the complete chloroplast genome of Melastoma dodecandrum. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1043-1054. [PMID: 31404219 PMCID: PMC6656900 DOI: 10.1007/s12298-019-00651-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/27/2018] [Accepted: 02/19/2019] [Indexed: 05/29/2023]
Abstract
Melastoma dodecandrum, the only creeping species in the Melastoma genus, serves as a medicinal herb in southeast China. It belongs to the huge family Melastomataceae, which contains over 5000 species worldwide. In this study, we used next-generation sequencing to determine the complete chloroplast genome sequences of M. dodecandrum, which is a circular molecule of 156,611 bp in length. After annotation, we identified 131 putative genes in total, comprised of 85 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Genome structure, GC content, repeat sequences and codon usage were investigated to gain a comprehensive understanding of this genome. Furthermore, we conducted comparative genome analyses between the M. dodecandrum genome and that of four other Melastomataceae species. Additionally, a phylogenetic analysis was performed based on available chloroplast genomes of Melastomataceae species and several Myrtaceae species, revealing the taxonomic relationships between M. dodecandrum and related species. In conclusion, our study represents the first look into the complete chloroplast genome of M. dodecandrum, providing abundant information for further studies such as species identification, taxonomy and phylogenetic resolution of Melastomataceae species.
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Affiliation(s)
- Xiasheng Zheng
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Changwei Ren
- Department of Cardiovascular Surgery Center, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029 China
| | - Song Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Jing Li
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Ying Zhao
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
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Yang Z, Huang Y, An W, Zheng X, Huang S, Liang L. Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill. PLANTS (BASEL, SWITZERLAND) 2019; 8:E87. [PMID: 30987216 PMCID: PMC6524360 DOI: 10.3390/plants8040087] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 01/01/2023]
Abstract
Lycium chinense Mill, an important Chinese herbal medicine, is widely used as a dietary supplement and food. Here the chloroplast (CP) genome of L. chinense was sequenced and analyzed, revealing a size of 155,756 bp and with a 37.8% GC content. The L. chinense CP genome comprises a large single copy region (LSC) of 86,595 bp and a small single copy region (SSC) of 18,209 bp, and two inverted repeat regions (IRa and IRb) of 25,476 bp separated by the single copy regions. The genome encodes 114 genes, 16 of which are duplicated. Most of the 85 protein-coding genes (CDS) had standard ATG start codons, while 3 genes including rps12, psbL and ndhD had abnormal start codons (ACT and ACG). In addition, a strong A/T bias was found in the majority of simple sequence repeats (SSRs) detected in the CP genome. Analysis of the phylogenetic relationships among 16 species revealed that L. chinense is a sister taxon to Lycium barbarum. Overall, the complete sequence and annotation of the L. chinense CP genome provides valuable genetic information to facilitate precise understanding of the taxonomy, species and phylogenetic evolution of the Solanaceae family.
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Affiliation(s)
- Zerui Yang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Yuying Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Wenli An
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Xiasheng Zheng
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Song Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Lingling Liang
- Pharmaceutical School, YouJiang Medical University for Nationalities, Baise 533000, China.
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Thode VA, Lohmann LG. Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:796. [PMID: 31275342 PMCID: PMC6594259 DOI: 10.3389/fpls.2019.00796] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/03/2019] [Indexed: 05/13/2023]
Abstract
Chloroplast (cp) genome organization, gene order, and content have long been considered conserved among land plants. Despite that, the generation of thousands of complete plastomes through next-generation sequencing (NGS) has challenged their conserved nature. In this study, we analyze 11 new complete plastomes of Amphilophium (Bignonieae, Bignoniaceae), a diverse genus of Neotropical lianas, and that of Anemopaegma prostratum. We explored the structure and content of the assembled plastomes and performed comparative analyses within Amphilophium and among other plastomes available for Bignoniaceae. The overall gene content and orientation of plastomes is similar in all species studied. Plastomes are not conserved among Amphilophium, showing significant differences in length (155,262-164,786 bp), number of genes duplicated in the IRs (eight, 18, or 19), and location of the SC/IR boundaries (i.e., LSC/IRa junction between rps19 and rpl2 genes, within petD, or within petB). Length differences reflect expansions of the IRs and contractions of the LSC regions. The plastome of A. prostratum is 168,172 bp, includes 19 duplicated genes, and has the LSC/IRa boundary located within the petB gene. Amphilophium plastomes show high nucleotide diversity, with many hypervariable regions, and 16 genes with signatures of positive selection. Multiple SSRs and repeat regions were identified for Amphilophium and Anemopaegma prostratum. The differences in structure detected within Amphilophium plastomes in terms of LSC/IR and IR/SSC boundaries, number of duplicated genes, and genome sizes are mostly shared between taxa that belong to the same clade. Our results bring new insights into the evolution of plastomes at low taxonomic levels.
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Nock CJ, Hardner CM, Montenegro JD, Ahmad Termizi AA, Hayashi S, Playford J, Edwards D, Batley J. Wild Origins of Macadamia Domestication Identified Through Intraspecific Chloroplast Genome Sequencing. FRONTIERS IN PLANT SCIENCE 2019; 10:334. [PMID: 30949191 PMCID: PMC6438079 DOI: 10.3389/fpls.2019.00334] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/04/2019] [Indexed: 05/13/2023]
Abstract
Identifying the geographic origins of crops is important for the conservation and utilization of novel genetic variation. Even so, the origins of many food crops remain elusive. The tree nut crop macadamia has a remarkable domestication history, from subtropical rain forests in Australia through Hawaii to global cultivation all within the last century. The industry is based primarily on Macadamia integrifolia and M. integrifolia-M. tetraphylla hybrid cultivars with Hawaiian cultivars the main contributors to world production. Sequence data from the chloroplast genome assembled using a genome skimming strategy was used to determine population structure among remnant populations of the main progenitor species, M. integrifolia. Phylogenetic analysis of a 506 bp chloroplast SNP alignment from 64 wild and cultivated accessions identified phylogeographic structure and deep divergences between clades providing evidence for historical barriers to seed dispersal. High levels of variation were detected among wild accessions. Most Hawaiian cultivars, however, shared a single chlorotype that was also present at two wild sites at Mooloo and Mt Bauple from the northernmost distribution of the species in south-east Queensland. Our results provide evidence for a maternal genetic bottleneck during early macadamia domestication, and pinpoint the likely source of seed used to develop the Hawaiian cultivars. The extensive variability and structuring of M. integrifolia chloroplast genomic variation detected in this study suggests much unexploited genetic diversity is available for improvement of this recently domesticated crop.
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Affiliation(s)
- Catherine J. Nock
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
- *Correspondence: Catherine J. Nock,
| | - Craig M. Hardner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | | | - Ainnatul A. Ahmad Termizi
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Satomi Hayashi
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Julia Playford
- Queensland Department of Environment and Science, Brisbane, QLD, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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