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Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, Chen G, Ng WL, Islam MN, Punnarak P, Zheng H, Zhu X. A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea. FRONTIERS IN PLANT SCIENCE 2023; 13:1075353. [PMID: 36684775 PMCID: PMC9845719 DOI: 10.3389/fpls.2022.1075353] [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: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
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Affiliation(s)
- Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuchen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qianying Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Luzhen Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Md Nazrul Islam
- Forestry and Wood Technology Discipline, Khulna University, Khulna, Bangladesh
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Wang R, Liao N, Liu X, Qin Y, Xiao Y, Wang Y, Huang R. Characterization of the complete chloroplast genome of Carallia diplopetala (Rhizophoraceae). Mitochondrial DNA B Resour 2022; 7:1870-1872. [PMID: 36325279 PMCID: PMC9621227 DOI: 10.1080/23802359.2022.2135398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Carallia diplopetala (Rhizophoraceae) is an important economic tree species narrowly distributed endemic to East Asia. In this study, We generate the complete chloroplast genome of C. diplopetala using next-generation sequencing technology, which is 162,052 bp in size and consists of a large single copy (LSC) of 89,556 bp and a small single copy (SSC) of 18,814 bp, separated a pair of inverted repeats (IRb and IRa) of 26,841 bp. The overall GC content is 36.4%. A total of 130 genes are annotated, including 83 protein-coding genes, 37 tRNAs, eight rRNAs and two pseudogenes (ψycf1 and ψrps19). The phylogenetic analysis indicated that C. diplopetala and C. brachiate formed a monophyletic clade with strong support and then sister to Pellacalyx yunnanensis. The plastome of C. diplopetala will provide informative genomic resources for further conservation applications.
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Affiliation(s)
- Renjie Wang
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - Nanyan Liao
- Guangxi Fangcheng Golden, Camellias National Nature Reserve, Fangchenggang, China
| | - Xiongsheng Liu
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - Yi Qin
- Guangxi Fangcheng Golden, Camellias National Nature Reserve, Fangchenggang, China
| | - Yufei Xiao
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - Yong Wang
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - Ronglin Huang
- Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, China,CONTACT Ronglin Huang Guangxi Forestry Research Institute, Nanning, China
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Zhang JY, Chen DQ, Xiang S, Wu X, Wang YF, Le YX, Sun WH, Zou SQ, Zhou YW, Zou XX. The complete chloroplast genome sequence of Tapiscia sinensis (Staphyleaceae). Mitochondrial DNA B Resour 2020; 5:2658-2660. [PMID: 33457896 PMCID: PMC7781918 DOI: 10.1080/23802359.2020.1781565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 11/04/2022] Open
Abstract
Tapiscia sinensis, belong to Tapisciaceae, is endangered tree endemic to China. Here, we provide the complete plastid genomic data of T. sinensis with the aim of providing data for future conservation efforts research and revealing its phylogenetic position. The complete chloroplast sequence is 161,093 bp, including a large single-copy (LSC) region of 87,782 bp, a small single-copy (SSC) region of 18,517 bp, a pair of invert repeats (IR) regions of 27,387 bp. Plastid genome contains 131 genes, 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis base on 19 plastid genomes indicates that T. sinensis located Malvids branch, and is more closely related to the species of the order Sapindales than those of the order Malvales.
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Affiliation(s)
- Jing-Yao Zhang
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - De-Qiang Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuang Xiang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi-Fan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi-Xun Le
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Hong Sun
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuang-Quan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yun-Wei Zhou
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Xiao-Xing Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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Wang N, Qiu MY, Yang Y, Li JW, Zou XX. Complete chloroplast genome sequence of Bougainvillea Spectabilis (Nyctaginaceae). Mitochondrial DNA B Resour 2019; 4:4010-4011. [PMID: 33366293 PMCID: PMC7707718 DOI: 10.1080/23802359.2019.1688716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 11/26/2022] Open
Abstract
Bougainvillea spectabilis is an important ornamental plant in tropical and subtropical regions, whose complex and diverse germplasm has brought great difficulties to variety selection and identification. Here, to provide data support for the identification of the relationship between cultivars of B. spectabilis, we sequenced the chloroplast genome of B. spectabilis. The chloroplast genome is 154,520 bp in length, including a large single-copy (LSC) region of 88,101 bp and small single-copy (SSC) region of 17,729 bp, and a pair of invert repeats (IR) regions of 24,171 bp. The chloroplast genome contains 129 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis based on 14 chloroplast genome demonstrated a close relationship between B. spectabilis and other plant species in Caryophyllales. The chloroplast genome will help for further of taxonomy research and provide data support for the identification of genetic relationship among different cultivars of B. spectabilis.
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Affiliation(s)
- Ning Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources
- Fujian Provincial Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center
| | - Meng-Yuan Qiu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources
- Fujian Provincial Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center
| | - Yi Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources
- Fujian Provincial Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center
| | - Jun-Wei Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources
- Fujian Provincial Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center
| | - Xiao-Xing Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources
- Fujian Provincial Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center
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