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Yang J, Zhang X, Hua Z, Jia H, Li K, Ling C. High-Quality Assembly and Analysis of the Complete Mitogenomes of German Chamomile ( Matricaria recutita) and Roman Chamomile ( Chamaemelum nobile). Genes (Basel) 2024; 15:301. [PMID: 38540360 PMCID: PMC10970603 DOI: 10.3390/genes15030301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 06/14/2024] Open
Abstract
German chamomile (Matricaria chamomilla L.) and Roman chamomile (Chamaemelum nobile) are the two well-known chamomile species from the Asteraceae family. Owing to their essential oils and higher medicinal value, these have been cultivated widely across Europe, Northwest Asia, North America, and Africa. Regarding medicinal applications, German chamomile is the most commonly utilized variety and is frequently recognized as the "star among medicinal species". The insufficient availability of genomic resources may negatively impact the progression of chamomile industrialization. Chamomile's mitochondrial genome is lacking in extensive empirical research. In this study, we achieved the successful sequencing and assembly of the complete mitochondrial genome of M. chamomilla and C. nobile for the first time. An analysis was conducted on codon usage, sequence repeats within the mitochondrial genome of M. chamomilla and C. nobile. The phylogenetic analysis revealed a consistent positioning of M. chamomilla and C. nobile branches within both mitochondrial and plastid-sequence-based phylogenetic trees. Furthermore, the phylogenetic analysis also showed a close relationship between M. chamomilla and C. nobile within the clade comprising species from the Asteraceae family. The results of our analyses provide valuable resources for evolutionary research and molecular barcoding in chamomile.
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Affiliation(s)
- Jun Yang
- College of Food and Bioengineering, Bengbu University, Bengbu 233030, China; (X.Z.); (Z.H.); (H.J.); (K.L.); (C.L.)
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Seliem MK, Taha NA, El-Feky NI, Abdelaal K, El-Ramady H, El-Mahrouk ME, Bayoumi YA. Evaluation of Five Chrysanthemum morifolium Cultivars against Leaf Blight Disease Caused by Alternaria alternata at Rooting and Seedling Growth Stages. PLANTS (BASEL, SWITZERLAND) 2024; 13:252. [PMID: 38256805 PMCID: PMC10820434 DOI: 10.3390/plants13020252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024]
Abstract
During the winter of 2018, leaf blight on florist's daisy (Chrysanthemum morifolium L.) was noticed in Egypt. The disease, which was identified as caused by Alternaria alternata, was widely spread and led to serious damage for the exportation sector of this crop. Therefore, a study was conducted to better understand what can be conducted to minimize the problem in the future. Isolates were gathered and evaluated on five chrysanthemum cultivars (i.e., 'Feeling Green Dark', 'Talitha', 'Chrystal Regan', 'Arctic queen', and 'Podolsk Purple') grown in a greenhouse. The objectives were to isolate and identify the phytopathogen and detect the resistant degree of these cultivars with emphasis on the early growth stages of the crop. The results showed that 'Podolsk Purple' was the most resistant cultivar against the different isolates during the rooting and seedling growth stages. 'Chrystal Regan' was very susceptible to the different isolates. In addition, the isolate from 'Feeling Green Dark' was the strongest, which negatively affected the chlorophyll content and its fluorescence parameters besides other measured vegetative and anatomical features. The findings indicated that the best anatomical characters of the stem and leaf, like the thickness of cuticle and cortex, stem diameter, xylem vessel diameter, and thickness of epidermis as well as lamina thickness were recorded in the 'Podolsk Purple' cultivar. This study highlighted that by using the right cultivars, chrysanthemum can be cultivated during the winter season under Egyptian conditions. These results can be a part of solution to overcome the leaf blight caused by A. alternata on chrysanthemum during the early growing stages.
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Affiliation(s)
- Mayada K. Seliem
- Ornamental and Floriculture Department, Horticulture Research Institute, El-Sabahia, Alexandria 21599, Egypt;
| | - Naglaa A. Taha
- Plant Pathology Research Institute, Agriculture Research Center, Giza 12619, Egypt; (N.A.T.); (N.I.E.-F.)
| | - Nahla I. El-Feky
- Plant Pathology Research Institute, Agriculture Research Center, Giza 12619, Egypt; (N.A.T.); (N.I.E.-F.)
| | - Khaled Abdelaal
- EPCRS Excellence Center, Plant Pathology and Biotechnology Lab., Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt;
| | - Hassan El-Ramady
- Soil and Water Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Mohammed E. El-Mahrouk
- Horticulture Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt;
| | - Yousry A. Bayoumi
- Horticulture Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt;
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Sun J, Wang Y, Qiao P, Zhang L, Li E, Dong W, Zhao Y, Huang L. Pueraria montana Population Structure and Genetic Diversity Based on Chloroplast Genome Data. PLANTS (BASEL, SWITZERLAND) 2023; 12:2231. [PMID: 37375857 DOI: 10.3390/plants12122231] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Despite having a generally conserved structure, chloroplast genome data have been helpful for plant population genetics and evolution research. To mine Pueraria montana chloroplast genome variation architecture and phylogeny, we investigated the chloroplast variation architecture of 104 P. montana accessions from across China. P. montana's chloroplast genome showed high diversity levels, with 1674 variations, including 1118 single nucleotide polymorphisms and 556 indels. The intergenic spacers, psbZ-trnS and ccsA-ndhD, are the two mutation hotspot regions in the P. montana chloroplast genome. Phylogenetic analysis based on the chloroplast genome dataset supported four P. montana clades. P. montana variations were conserved among and within clades, which showed high gene flow levels. Most P. montana clades were estimated to have diverged at 3.82-5.17 million years ago. Moreover, the East Asian summer monsoon and South Asian summer monsoon may have accelerated population divergence. Our results show that chloroplast genome sequences were highly variable and can be used as molecular markers to assess genetic variation and relationships in P. montana.
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Affiliation(s)
- Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing 100700, China
| | - Yiheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing 100700, China
| | - Ping Qiao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lei Zhang
- China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yuping Zhao
- China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars. Int J Mol Sci 2023; 24:ijms24043606. [PMID: 36835020 PMCID: PMC9964644 DOI: 10.3390/ijms24043606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/30/2022] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Lagerstroemia indica L. is a well-known ornamental plant with large pyramidal racemes, long flower duration, and diverse colors and cultivars. It has been cultivated for nearly 1600 years and is essential for investigating the germplasm and assessing genetic variation to support international cultivar identification and breeding programs. In this study, 20 common Lagerstroemia indica cultivars from different varietal groups and flower morphologies, as well as multiple wild relative species, were analyzed to investigate the maternal donor of Lagerstroemia indica cultivars and to discover the genetic variation and relationships among cultivars based on plastome and nuclear ribosomal DNA (nrDNA) sequences. A total of 47 single nucleotide polymorphisms (SNPs) and 24 insertion/deletions (indels) were identified in the 20 L. indica cultivars' plastome and 25 SNPs were identified in the nrDNA. Phylogenetic analysis based on the plastome sequences showed that all the cultivars formed a clade with the species of L. indica, indicating that L. indica was the maternal donor of the cultivars. Population structure and PCA analyses supported two clades of cultivars, which exhibited significant genetic differences according to the plastome dataset. The results of the nrDNA supported that all 20 cultivars were divided into three clades and most of the cultivars had at least two genetic backgrounds and higher gene flow. Our results suggest that the plastome and nrDNA sequences can be used as molecular markers for assessing the genetic variation and relationships of L. indica cultivars.
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Xu Y, Liu Y, Yu Z, Jia X. Complete Chloroplast Genome Sequence of the Long Blooming Cultivar Camellia 'Xiari Qixin': Genome Features, Comparative and Phylogenetic Analysis. Genes (Basel) 2023; 14:460. [PMID: 36833387 PMCID: PMC9956581 DOI: 10.3390/genes14020460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The camellia flower is a famous woody plant with a long-cultivated history and high ornamental value. It is extensively planted and utilized around the world and owns a massive germplasm resource. Camellia 'Xiari Qixin' belongs to one of the typical cultivars in the four seasons camellia hybrids series. Due to its long flowering period, this kind of cultivar is identified as a precious resource of camellia flowers. In this study, the complete chloroplast genome sequence of C. 'Xiari Qixin' was first reported. Its whole chloroplast genome is 157,039 bp in length with an overall GC content of 37.30%, composed of a large single copy region (LSC, 86,674 bp), a small single copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,042 bp each). A total of 134 genes were predicted in this genome, including 8 ribosomal RNA genes, 37 transfer RNA genes, and 89 protein-coding genes. In addition, 50 simple sequence repeats (SSRs) and 36 long repeat sequences were detected. By comparing C. 'Xiari Qixin' and seven Camellia species on the chloroplast genome, seven mutation hotspot regions were identified, including psbK, trnS (GCU)-trnG(GCC), trnG(GCC), petN-psbM, trnF(GAA)-ndhJ, trnP(UGG)-psaJ, and ycf1. Phylogenetic analysis of 30 chloroplast genomes showed that the genetic relationship between C. 'Xiari Qixin' and Camellia azalea is quite close in evolution. These results could not only provide a valuable database for determining the maternal origin of Camellia cultivars, but also contribute to the exploration of the phylogenetic relationship and utilization of germplasm resources for Camellia.
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Affiliation(s)
| | | | | | - Xiaocheng Jia
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
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Li J, Ye Z, Wei M, Deng C, Chi L, Xu L, Han Z, Wei W. Evaluation of Chrysanthemi Indici Flos germplasms based on nine bioactive constituents and color parameters. PLoS One 2023; 18:e0283498. [PMID: 37083577 PMCID: PMC10121038 DOI: 10.1371/journal.pone.0283498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 03/11/2023] [Indexed: 04/22/2023] Open
Abstract
Chrysanthemi Indici Flos (CIF) is the inflorescence of Chrysanthemum indicum L., which exists in various shades of yellow and has pharmacologically active constituents. It is widely used for medicinal purposes in China, Japan, and South Korea to treat inflammatory diseases. Its external color is usually used to judge its internal quality in trade; however, the correlation between its color and chemical constituents is unknown. Here, we simultaneously determined five phenylpropanoids (neochlorogenic acid, chlorogenic acid, and isochlorogenic acids A, B, and C) and four flavonoids (linarin, luteolin, apigenin, and acacetin) of 70 CIF germplasms using a newly established UPLC method; furthermore, we measured their color parameters (L*, a*, and b*) using a spectrophotometer. Our results showed considerable variations in the bioactive constituent contents and color parameters of CIF. The content of the five phenylpropanoids and the relative correlation degree γi of the nine constituents were positively correlated with color parameters, which could be rapidly predicted based on L* and/or b*. Moreover, we screened out a high-quality germplasm with a high linarin content and bright colors using the hierarchical clustering method. Our results provide comprehensive insight into CIF's quality evaluation process, particularly the methods for procuring high-quality medicinal materials and breeding by color.
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Affiliation(s)
- Jianling Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Tree Genetics and Breeding Laboratory, Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, China
- Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen Traditional Chinese Medicine Manufacturing Innovation Center Co., Ltd., China Resources Sanjiu Modern Chinese Medicine Pharmaceutical Co., Ltd., Shenzhen, 518110, China
| | - Zi Ye
- Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen Traditional Chinese Medicine Manufacturing Innovation Center Co., Ltd., China Resources Sanjiu Modern Chinese Medicine Pharmaceutical Co., Ltd., Shenzhen, 518110, China
| | - Min Wei
- Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen Traditional Chinese Medicine Manufacturing Innovation Center Co., Ltd., China Resources Sanjiu Modern Chinese Medicine Pharmaceutical Co., Ltd., Shenzhen, 518110, China
| | - Changrong Deng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Tree Genetics and Breeding Laboratory, Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Lianfeng Chi
- Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen Traditional Chinese Medicine Manufacturing Innovation Center Co., Ltd., China Resources Sanjiu Modern Chinese Medicine Pharmaceutical Co., Ltd., Shenzhen, 518110, China
| | - Lei Xu
- Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen Traditional Chinese Medicine Manufacturing Innovation Center Co., Ltd., China Resources Sanjiu Modern Chinese Medicine Pharmaceutical Co., Ltd., Shenzhen, 518110, China
| | - Zhengzhou Han
- Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen Traditional Chinese Medicine Manufacturing Innovation Center Co., Ltd., China Resources Sanjiu Modern Chinese Medicine Pharmaceutical Co., Ltd., Shenzhen, 518110, China
| | - Weifeng Wei
- Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen Traditional Chinese Medicine Manufacturing Innovation Center Co., Ltd., China Resources Sanjiu Modern Chinese Medicine Pharmaceutical Co., Ltd., Shenzhen, 518110, China
- China Resources Sanjiu (Lu'an) Chinese Traditional Medicine Industry Development Co., Ltd., Lu'an, 237321, China
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Zhao Y, Qu D, Ma Y. Characterization of the Chloroplast Genome of Argyranthemum frutescens and a Comparison with Other Species in Anthemideae. Genes (Basel) 2022; 13:genes13101720. [PMID: 36292605 PMCID: PMC9602088 DOI: 10.3390/genes13101720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Argyranthemum frutescens, which belongs to the Anthemideae (Asteraceae), is widely cultivated as an ornamental plant. In this study, the complete chloroplast genome of A. frutescens was obtained based on the sequences generated by Illumina HiSeq. The chloroplast genome of A. frutescens was 149,626 base pairs (bp) in length, containing a pair of inverted repeats (IR, 24,510 bp) regions separated by a small single-copy (SSC, 18,352 bp) sequence and a large single-copy (LSC, 82,254 bp) sequence. The genome contained 132 genes, consisting of 85 coding DNA sequences, 37 tRNA genes, and 8 rRNA genes, with nineteen genes duplicated in the IR region. A comparison chloroplast genome analysis among ten species from the tribe of Anthemideae revealed that the chloroplast genome size varied, but the genome structure, gene content, and oligonucleotide repeats were highly conserved. Highly divergent regions, e.g., ycf1, trnK-psbK, petN-psbM intronic, were detected. Phylogenetic analysis supported Argyranthemum as a separate genus. The findings of this study will be helpful in the exploration of the phylogenetic relationships of the tribe of Anthemideae and contribute to the breeding improvement of A. frutescens.
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