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Jang JE, Jeong HJ, Kim AL, Choi YR, Lazkov GA, Jang CG, Choi HJ, Gil HY. The complete chloroplast genome of Eremurus zoae Vved. (Asphodelaceae), an endemic species of Kyrgyz Republic. Mitochondrial DNA B Resour 2024; 9:437-441. [PMID: 38586509 PMCID: PMC10993749 DOI: 10.1080/23802359.2024.2336003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/23/2024] [Indexed: 04/09/2024] Open
Abstract
Eremurus zoae Vved. 1971 is a perennial herbaceous plant in the family Asphodelaceae and an endemic species of the Kyrgyz Republic; however, its complete chloroplast genome sequence has not been reported. Here, we investigated the complete chloroplast (cp) genome of E. zoae using next-generation sequencing. The cp genome was 153,744 bp long, with a large single copy (84,020 bp), a small single copy (16,766 bp), and a pair of inverted repeats (26,479 bp). The genome encodes 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that the genus Eremurus forms a monophyletic group and E. zoae is closely related to E. chinensis. This study provides a molecular foundation for future phylogenetic studies of Eremurus.
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Affiliation(s)
- Ju Eun Jang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Hyeon Jin Jeong
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Aleksey L. Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Ye-Rim Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Georgii A. Lazkov
- Institute for Biology, National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Chang-Gee Jang
- Department of Biology Education, Kongju University, Gongju, South Korea
| | - Hyeok Jae Choi
- Department of Biology & Chemistry, Changwon National University, Changwon, South Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
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Liu H, Wagutu GK, Chen Y, Li X, Fan X. The complete chloroplast genome sequence of Myricaria wardii Marquand 1929 (Tamaricaceae): a shrub species endemic to the Tibet Plateau. Mitochondrial DNA B Resour 2024; 9:367-370. [PMID: 38529113 PMCID: PMC10962288 DOI: 10.1080/23802359.2024.2329666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Myricaria wardii Marquand 1929, endemic to the Tibet Plateau, is a perennial shrub with important medicinal and ecological values. In this study, the complete chloroplast (cp) genome of M. wardii was assembled, and the phylogenetic tree was reconstructed to evaluate the phylogenetic location of the species. The results showed that the cp genome size of the M. wardii was 155,299 bp, which contained a pair of inverted repeat (IR) regions (26,150 bp), a large single copy (LSC) region (84,715 bp), and a small single copy (SSC) region (18,284 bp). The total GC content of the cp genome was 36.30%. A total of 128 genes were annotated, consisting of 83 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic analysis showed that M. wardii was closely related to M. prostrata. This study provides useful information for the conservation of this species and the phylogenetic analysis of Tamaricaceae.
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Affiliation(s)
- Haoran Liu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Godfrey Kinyori Wagutu
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China
- Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing, Beijing, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yuanyuan Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiuling Li
- College of Life Science, Linyi University, Linyi, Shandong, China
- National Forest Eco-system Research Station of Linyi City, Linyi, Shandong, China
| | - Xiangrong Fan
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
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Huang Y, Cao J, Zhao M, Guo J, Li J, Wang R. The complete chloroplast genome sequence of an invasive plant, Tragopogon dubius Scopoli (asteraceae). Mitochondrial DNA B Resour 2024; 9:352-356. [PMID: 38487811 PMCID: PMC10939102 DOI: 10.1080/23802359.2024.2329668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
Tragopogon dubius Scopoli is native to Europe and western Asia and is considered an invasive plant in China. In this study, the complete chloroplast genome of T. dubius was obtained using high-throughput next-generation sequencing technology. The whole chloroplast genome was 153,017 bp long with a GC content of 38% and comprised 130 genes (86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes). Phylogenetic analysis based on the concatenated chloroplast protein-coding sequences showed that T. dubius is most closely related to Tragopogon pratensis. This study provides valuable genetic data for further phylogenetic analysis and molecular identification of species in the genus Tragopogon.
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Affiliation(s)
- Yue Huang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingjing Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengxin Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianying Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiamei Li
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Rui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Nah G, Jeong JR, Lee JH, Soh SY, Nam SY. The complete chloroplast genome of Philodendron hederaceum (Jacq.) Schott 1829 (Alismatales: Araceae). Mitochondrial DNA B Resour 2024; 9:262-266. [PMID: 38348093 PMCID: PMC10860476 DOI: 10.1080/23802359.2024.2311748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Philodendron hederaceum (Jacq.) Schott 1829, a species of the Araceae family, is a foliage plant of ornamental value. The complete chloroplast genome sequence of Philodendron hederaceum was obtained by the de novo assembly of NovaSeq 6000 (Illumina Co., San Diego, CA) paired-end short reads and Oxford Nanopore long reads. The complete chloroplast genome of P. hederaceum was 168,609 bp in length, with a large single-copy (LSC) region of 94,393 bp, a small single-copy (SSC) region of 25,774 bp, and a pair of identical inverted repeat regions (IRs) of 24,221 bp. The genome contained a total of 129 genes, including 85 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis of P. hederaceum with 19 related species and two outgroup species revealed the closest taxonomical relationship with Philodendron lanceolatum in the Araceae family.
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Affiliation(s)
- Gyoungju Nah
- Genome Analysis Center at National Instrumentation Center for Environmental Management, Seoul National University, Seoul, South Korea
| | - Ji Ran Jeong
- Genome Analysis Center at National Instrumentation Center for Environmental Management, Seoul National University, Seoul, South Korea
| | - Jae Hwan Lee
- Department of Environmental Horticulture, Sahmyook University, Seoul, South Korea
- Natural Science Research Institute, Sahmyook University, Seoul, South Korea
| | - Soon Yil Soh
- Natural Science Research Institute, Sahmyook University, Seoul, South Korea
| | - Sang Yong Nam
- Department of Environmental Horticulture, Sahmyook University, Seoul, South Korea
- Natural Science Research Institute, Sahmyook University, Seoul, South Korea
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Li Z, Liu Y, Ma Y. Characterization and phylogenetic analysis of the complete chloroplast genome of Asterothamnus centraliasiaticus Novopokr. (Asteraceae: Asterothamnus). Mitochondrial DNA B Resour 2024; 9:168-172. [PMID: 38274851 PMCID: PMC10810623 DOI: 10.1080/23802359.2024.2306207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Asterothamnus centraliasiaticus Novopokr., a species of perennial deciduous semi-shrub within the family Asteraceae, has excellent medical, economic, ecological and genetic value. In this study, the chloroplast genome of A. centraliasiaticus was first assembled using Illumina HiSeq2500 sequences. The results indicate that the complete cp genome of A. centraliasiaticus is 152,205 bp in length, and comprises a pair of inverted repeat (IR) regions of 25,031 bp each, a large single-copy (LSC) region of 83,956 bp and a small single-copy (SSC) region of 18,187 bp. The GC content of A. centraliasiaticus is 37.3%. A total of 130 genes were successfully annotated containing 85 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The maximum likelihood (ML) phylogenetic analysis based on the complete chloroplast genome data highly supported that A. centraliasiaticus was close to Aster lavandulifolius. These results will provide significant genetic information for the germplasm protection and reasonable development.
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Affiliation(s)
- Zhengsheng Li
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, Qinghai, China
| | - Ying Liu
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, Qinghai, China
| | - Yushou Ma
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, Qinghai, China
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Pan L, Chen K, Liao X. The complete chloroplast genome and phylogenetic analysis of Cyperus malaccensis Lam (Cyperaceae). Mitochondrial DNA B Resour 2024; 9:114-118. [PMID: 38274852 PMCID: PMC10810665 DOI: 10.1080/23802359.2024.2305413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Cyperus malaccensis Lam is a perennial herbaceous plant that is distributed over a large area along the southern coast of China. Some plants of the Cyperaceae family are highly similar morphologically, which makes them difficult to classify and identify. In this study, the complete chloroplast genome of C. malaccensis was sequenced and assembled. The chloroplast genome is 186,098 bp long with a 33.18% content of GC. The structure of chloroplast genome includes a quadripartite structure that is composed of a pair of inverted repeats (IRs) of 37,434 bp, a small single copy (SSC) region of 10,296 bp, and a large single copy (LSC) region of 100,934 bp. The genome contains 141 genes, including 94 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. A phylogenetic analysis showed that C. malaccensis is the most closely related to the congeneric species C. rotundus. These results enrich the genetic resources of the Cyperaceae and provide a molecular basis for further study on the phylogeny of this family.
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Affiliation(s)
- Lianghao Pan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Marine Sciences, Beihai, China
- Institute of Biodiversity Science, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Kun Chen
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Marine Sciences, Beihai, China
| | - Xin Liao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Marine Sciences, Beihai, China
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Park MS, Na NR, Jang CG, Gulomov R, Tojibaev K. The complete chloroplast genome sequence of Phlomoides kirghisorum Adylov, Kamelin & Makhmedov 1987 (Lamiaceae), an endemic species of Fergana Valley. Mitochondrial DNA B Resour 2024; 9:104-108. [PMID: 38239371 PMCID: PMC10795634 DOI: 10.1080/23802359.2023.2292159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/02/2023] [Indexed: 01/22/2024] Open
Abstract
Phlomoides kirghisorum Adylov, Kamelin & Makhmedov 1987 is one of the poorly studied narrow endemics of Fergana Valley, one of Central Asia's most densely human-populated regions. In this study, we sequenced, assembled, and characterized the complete plastome of P. kirghisorum by using high-throughput Illumina reads. The complete chloroplast genome consisted of 151,324 bp, including a large single-copy (LSC) region (82,775 bp), a small single-copy (SSC) region (17,357 bp), and two inverted repeat regions (25,596 bp each). In the chloroplast genome of P. kirghisorum, 133 genes were detected, comprising 88 protein-encoding genes, eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. The phylogenetic analysis indicated that the genetic relationship between P. kirghisorum and P. alpina was very close. This study provides basic information to explore the molecular evolution of the Phlomoides genus and the Lamiaceae family.
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Affiliation(s)
- Min-Su Park
- International Biological Material Research Center, Korea Research Instituto of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Nu-Ree Na
- Department of Biology Education, Kongju National University, Kongju, Republic of Korea
| | - Chang-Gee Jang
- Department of Biology Education, Kongju National University, Kongju, Republic of Korea
| | - Rustam Gulomov
- Department of Biology, Namangan State University, Namangan, Republic of Uzbekistan
| | - Komiljon Tojibaev
- Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Republic of Uzbekistan
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Li N, Chen H, Zhou Y, Chong X, Zhou T, Zhang F. Characterization of chloroplast genome and phylogenetic analysis of the Elaeagnus hybrid variety E. 'viridis' (Elaeagnaceae). Mitochondrial DNA B Resour 2023; 8:1416-1420. [PMID: 38130732 PMCID: PMC10732183 DOI: 10.1080/23802359.2023.2292156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
Elaeagnus 'viridis', an artificial hybrid of E. macrophylla (♂) Thunb. (1784) × E. pungens (♀) Thunb. (1784), is known for its economic and ecological value. In this study, we sequenced and assembled the whole chloroplast (cp) genome of E. 'viridis'. The results showed that its cp genome was 152,284 bp long, showing a typical quadripartite structure and containing a large single-copy region (LSC, 82,299 bp), a small single-copy region (SSC, 18,239 bp), and a pair of inverted repeats (IRs, 51,746 bp). The cp genome contains 132 genes, including 86 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 66 common PCGs revealed that E. 'viridis' is most closely related to its maternal parent E. pungens. The chloroplast genomic information reported in this study will shed some useful light for further genetic studies in the genus Elaeagnus.
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Affiliation(s)
- Naiwei Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Hong Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Yanwei Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xinran Chong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Ting Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Fan Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
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Cheng Y, Xu X, Tong L, Tian L, Xia C, Yu X. Complete chloroplast genome and phylogenetic analysis of Meliosma oldhamii Miq. ex Maxim. (Sabiaceae). Mitochondrial DNA B Resour 2023; 8:1306-1310. [PMID: 38188441 PMCID: PMC10769540 DOI: 10.1080/23802359.2023.2281034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/02/2023] [Indexed: 01/09/2024] Open
Abstract
Meliosma oldhamii Miq. is a deciduous arbor and a member of Sabiaceae. It is one of the rare and protected plants with outstanding ornamental and economic value in Jiangsu, China. In addition to the resource values indicated above, there are numerous other elements that require additional research, including the chloroplast (cp) genomic information. In this work, the complete cp genome sequence of M. oldhamii was assembled and characterized for the first time. The complete cp genome of M. oldhamii was 159,950 base pair (bp) in length, including a large single-copy (LSC) region of 87,147 bp, a small single-copy (SSC) region of 18,015 bp, and the inverted repeats (IRs) region of 27,394 bp. It contains 131 genes, including 37 tRNA genes, eight rRNA genes, 85 protein-coding genes, and one pseudogene. The overall GC content of M. oldhamii cp genome was 37.95%. The placement of M. oldhamii in the phylogenetic tree constructed using the complete cp genome is largely congruent with previous studies. The clustering of Meliosma is non-monophyletic, aligns more closely with existing morphological taxonomic studies, thereby enhancing the scholarly and scientific nature of this research.
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Affiliation(s)
- Yao Cheng
- College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
| | - Xiaogang Xu
- College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
| | - Lili Tong
- College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Lu Tian
- College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
| | - Chongli Xia
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Xunlin Yu
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
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Li Y, Qiu Y, Yang M, Yin Y, Li M, Zhang Y. Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus chingii Hu 1925 from the family Rosaceae. Mitochondrial DNA B Resour 2023; 8:1280-1284. [PMID: 38566881 PMCID: PMC10986437 DOI: 10.1080/23802359.2023.2268220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/03/2023] [Indexed: 04/04/2024] Open
Abstract
Rubus chingii Hu 1925 is an important medicinal vine shrub in the Rosaceae family, widely distributed in China and Japan. In this study, the complete chloroplast genome of R. chingii was sequenced and identified. The chloroplast genome was 155,563 bp in size with a total GC content of 37.06%. Two 25,749-bp inverted repeat (IRA and IRB) regions divided the genome as four sections, with the remainder forming a large single-copy (LSC, 85,322 bp) and a small single-copy (SSC, 18,743 bp) regions. This genome contained a total of 131 genes, of which 86 were protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that R. chingii, along with several other R. longisepalus, R. tsangii, R. hirsutus, R. taiwanicola, R. rubroangustifolius, and R. glandulosopunctatus, formed the monophylic group. Interestingly, the chloroplast genome structure we reported was different from the previously reported structure and provided richer phylogenetic analysis information in the Rubus genus compared to previous studies. The genome information reported in this paper will provide some useful information for further investigation on the evolution of the family Rosaceae.
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Affiliation(s)
- Yuxian Li
- Traditional Chinese Medicine Department, Jilin Agricultural Science and Technology University, Jilin, PR China
| | - Ying Qiu
- Traditional Chinese Medicine Department, Jilin Agricultural Science and Technology University, Jilin, PR China
| | - Min Yang
- Traditional Chinese Medicine Department, Jilin Agricultural Science and Technology University, Jilin, PR China
| | - Yongfei Yin
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, PR China
| | - Min Li
- Traditional Chinese Medicine Department, Jilin Agricultural Science and Technology University, Jilin, PR China
| | - Ying Zhang
- Traditional Chinese Medicine Department, Jilin Agricultural Science and Technology University, Jilin, PR China
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Liu XF, Luo JJ, Li TY, Chen H, Liu JY, Li B, Dou L, Fu ZX. Characterization and phylogenetic analysis of the complete chloroplast genome of Saussurea sagittifolia (Asteraceae, Cardueae). Mitochondrial DNA B Resour 2023; 8:1268-1272. [PMID: 38188437 PMCID: PMC10769533 DOI: 10.1080/23802359.2023.2281704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/03/2023] [Indexed: 01/09/2024] Open
Abstract
The species of Saussurea sagittifolia Y. S. Chen & S. R. Yi belongs to the family Asteraceae (Cardueae). The complete chloroplast genome of S. sagittifolia was assembled and annotated for the first time in this study. The complete chloroplast genome of S. sagittifolia was 152,535 bp, including a large single-copy (LSC) region of 83,511 bp, a small single-copy (SSC) region of 18,632 bp, and a pair of inverted repeats (IRs) of 25,196 bp. The overall GC content of the chloroplast genome was 37.7%. The chloroplast genome encoded 131 genes, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete chloroplast sequences revealed that it related closely to Saussurea medusa.
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Affiliation(s)
- Xiao-Feng Liu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Jun-Jia Luo
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Ting-Yu Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Hui Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | | | - Bo Li
- Sichuan Environmental Monitoring Center, Chengdu, China
| | - Liang Dou
- Museum of Natural History/School of Life Sciences, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Key Laboratory of Conservation Biology on Endangered Wildlife of Sichuan Province, Sichuan University, Chengdu, China
| | - Zhi-Xi Fu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
- Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, China
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Phan QC, Nagasaki R, Inoue Y, Tsubota H. The complete chloroplast genome of Callicarpa dichotoma (Lour.) K.Koch (Lamiaceae). Mitochondrial DNA B Resour 2023; 8:1174-1178. [PMID: 38188443 PMCID: PMC10769526 DOI: 10.1080/23802359.2023.2275332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/19/2023] [Indexed: 01/09/2024] Open
Abstract
Callicarpa dichotoma (Lour.) K.Koch is a shrub species with distribution from East Asia to Southeast Asia. We assembled and annotated for the first time the complete chloroplast (cp) genome of C. dichotoma. The cp genome of C. dichotoma is 154,110 bp long with the GC content of 38.09% and consists of four subregions: a large single-copy (LSC) region of 84,915 bp, a small single-copy (SSC) region of 17,783 bp and a pair of inverted repeats (IRs) of 25,706 bp each. The cp genome of C. dichotoma encodes a total of 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic trees based on the coding sequences strongly support the position of C. dichotoma within the genus Callicarpa, confirming the previously reported monophyly of the genus.
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Affiliation(s)
- Quynh Chi Phan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Ryohei Nagasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuya Inoue
- Department of Botany, National Museum of Nature and Science, Ibaraki, Japan
- Hattori Botanical Laboratory, Miyazaki, Japan
| | - Hiromi Tsubota
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Miyajima Natural Botanical Garden, Green Innovation Division, Seto Inland Sea Carbon Neutral Research Center, Hiroshima University, Hiroshima, Japan
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Zhu W, Cui H, Xiang X. The complete chloroplast genome of Torenia violacea (Azaola) Pennell 1943 (Linderniaceae). Mitochondrial DNA B Resour 2023; 8:1145-1148. [PMID: 38188442 PMCID: PMC10769558 DOI: 10.1080/23802359.2023.2274619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/18/2023] [Indexed: 01/09/2024] Open
Abstract
Torenia violacea (Azaola) Pennell 1943 as a traditional Chinese medicine plant, has been used to treat multiple diseases. In this study, we sequenced, assembled, and characterized the complete plastome of T. violacea. The plastome (OQ167784) exhibited a typical quadripartite structure, with a total length of 154,007 bp, comprising a pair of inverted repeats (IRs; 24,809 bp) separated by a large single-copy (LSC) region (85,559 bp) and a small single-copy (SSC) region (18,830 bp). Through genome annotation, we identified 133 genes, including 87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Phylogenetic analysis revealed a close relationship between T. violacea and T. fournieri. The research results provide basic genetic resources for the development of species identification and investigation of phylogenetic relationships in the Torenia genus.
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Affiliation(s)
- Wanhui Zhu
- Key Laboratory of Biodiversity and Ecology Conservation in Southwest Anhui, Anqing Normal University, Anqing, China
- College of Life Sciences, Anqing Normal University, Anqing, China
| | - Hanqing Cui
- College of Life Sciences, Anqing Normal University, Anqing, China
| | - Xiaoyan Xiang
- Key Laboratory of Biodiversity and Ecology Conservation in Southwest Anhui, Anqing Normal University, Anqing, China
- College of Life Sciences, Anqing Normal University, Anqing, China
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14
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Zhang XY, Zhang ZL, Zhang LQ, Zhang LF, Zhu JY, Xue CS. Complete chloroplast genome of Adonis pseudoamurensis W.T.Wang (Ranunculaceae). Mitochondrial DNA B Resour 2023; 8:981-984. [PMID: 37727834 PMCID: PMC10506428 DOI: 10.1080/23802359.2023.2256493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/02/2023] [Indexed: 09/21/2023] Open
Abstract
Adonis pseudoamurensis W.T. Wang 1980 is an important traditional medicinal plant used for the treatment of cardiac diseases. The complete chloroplast (cp) genome of Adonis pseudoamurensis is reported for the first time in this study. The circular cp genome is 156,917 bp in length, consisting of a large single-copy region (86,262 bp), a small single-copy region (18,067 bp), and two inverted repeat regions (26,294 bp). The genome encodes 129 genes, comprising 84 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that A. pseudoamurensis is closely related to A. amurensis.
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Affiliation(s)
- Xiao-Yan Zhang
- School of Food Science and Engineering, Tonghua Normal University, Tonghua, P.R. China
| | - Zhao-Lei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Li-Qiu Zhang
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, P.R. China
| | - Li-Fan Zhang
- School of Life Science, Tonghua Normal University, Tonghua, P.R. China
| | - Jun-Yi Zhu
- School of Life Science, Tonghua Normal University, Tonghua, P.R. China
| | - Chang-Song Xue
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, P.R. China
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15
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Wang XY, Liu Y. The complete chloroplast genome of Aster altaicus Willd. (Asteraceae: Aster) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:819-822. [PMID: 37545551 PMCID: PMC10399466 DOI: 10.1080/23802359.2023.2238358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/13/2023] [Indexed: 08/08/2023] Open
Abstract
Aster altaicus Willd. is an important medicinal plant and can also be used as a forage grass. To better understand the diversity and phylogeny between A. altaicus and other Aster species, we sequenced and annotated the complete chloroplast genome of A. altaicus by using the Illumina Hiseq 2500 platform. This complete chloroplast genome is 152,473 bp long and the GC content is 37.3% presented a negative AT-skew (-0.002) and a positive GC-skew (0.003). The genome contains a large single-copy region (LSC) of 84,235 bp, a small single-copy region (SSC) of 18,212 bp, which separated by a pair of inverted repeat regions (IRA and IRB) of 25,013 bp. Moreover, 129 genes were found in the chloroplast of A. altaicus, including 85 protein-coding genes (PCGs), 36 transfer RNA genes (tRNAs), 8 ribosomal RNA unit genes (rRNAs). Phylogenetic analysis showed that A. altaicus was more closely related to A. altaicus and A. altaicus var. uchiyamae. This study lays the foundation for further studies on the evolution and phylogeny of Aster.
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Affiliation(s)
- Xin-You Wang
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai University, Xining, China
| | - Ying Liu
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai University, Xining, China
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16
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Zhang Y, Jiao W, Jiao W, Qiao T, Su Z, Feng S. [Analysis of the chloroplast genome of Incarvillea younghusbandii Sprague]. Sheng Wu Gong Cheng Xue Bao 2023; 39:2954-2964. [PMID: 37584142 DOI: 10.13345/j.cjb.220933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Incarvillea younghusbandii Sprague is a traditional tonic herb. The roots are used as herbal medicine for nourishing and strengthening, as well as treating postpartum milk deficiency and weakness. In this study, the chloroplast genome of I. younghusbandii was sequenced and assembled by the high-throughput sequencing technology. The sequence characteristics, sequence repeats, codon usage bias, phylogenetic relationships and estimated divergence time of I. younghusbandii were analyzed. The 159 323 bp sequence contained a large single copy (80 197 bp), a small single copy (9 030 bp) and two inverted repeat sequences (35 048 bp). It contained 120 genes, including 77 protein coding genes, 8 ribosomal RNA genes and 35 transfer RNA genes. AAA was the most frequent codon in the chloroplast coding sequence of I. younghusbandii. A total of 42 simple sequence repeats were identified in the chloroplast genome. Phylogenetic analysis revealed I. younghusbandii was mostly like its taxonomically close relative Incarvillea compacta. The divergence between I. younghusbandii and I. compacta was dated to 4.66 million years ago. This study was significant for the scientific conservation and development of resources related to I. compacta. It also provides a basic genetic resource for the subsequent species identification of the genus Incarvillea, and the population genetic diversity study of Bignoniaceae.
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Affiliation(s)
- Yaying Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Wanyao Jiao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Wenrui Jiao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Tianle Qiao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Zhiyang Su
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
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Xu Q, Li Z, Wu N, Yang J, Yuan L, Zhao T, Sima Y, Xu T. Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants. Genes (Basel) 2023; 14:1262. [PMID: 37372442 DOI: 10.3390/genes14061262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The genus Houpoea belongs to the family Magnoliaceae, and the species in this genus have important medicinal values. However, the investigation of the correlation between the evolution of the genus and its phylogeny has been severely hampered by the unknown range of species within the genus and the paucity of research on its chloroplast genome. Thus, we selected three species of Houpoea: Houpoea officinalis var officinalis (OO), Houpoea officinalis var. biloba (OB), and Houpoea rostrata (R). With lengths of 160,153 bp (OO), 160,011 bp (OB), and 160,070 bp (R), respectively, the whole chloroplast genomes (CPGs) of these three Houpoea plants were acquired via Illumina sequencing technology, and the findings were annotated and evaluated. These three chloroplast genomes were revealed by the annotation findings to be typical tetrads. A total of 131, 132, and 120 different genes were annotated. The CPGs of the three species had 52, 47, and 56 repeat sequences, which were primarily found in the ycf2 gene. A useful tool for identifying species is the approximately 170 simple sequence repeats (SSRs) that have been found. The border area of the reverse repetition region (IR) was studied, and it was shown that across the three Houpoea plants, it is highly conservative, with only changes between H. rostrata and the other two plants observed. Numerous highly variable areas (rps3-rps19, rpl32-trnL, ycf1, ccsA, etc.) have the potential to serve as the barcode label for Houpoea, according to an examination of mVISTA and nucleotide diversity (Pi). Phylogenetic relation indicates that Houpoea is a monophyletic taxon, and its genus range and systematic position are consistent with the Magnoliaceae system of Sima Yongkang-Lu Shugang, including five species and varieties of H. officinalis var. officinalis, H. rostrata, H. officinalis var. biloba, Houpoea obovate, and Houpoea tripetala, which evolved and differentiated from the ancestors of Houpoea to the present Houpoea in the above order. This study provides valuable information on the genus Houpoea, enriches the CPG information on Houpoea genus, and provides genetic resources for the further classification of and phylogenetic research on Houpoea.
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Affiliation(s)
- Qinbin Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Zhuoran Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Nannan Wu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Jing Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Lang Yuan
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Tongxing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yongkang Sima
- Kunming Arboretum, Yunnan Academy of Forestry & Grassland Science, Kunming 650201, China
| | - Tao Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
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Zhang LJ, Liu Y, Shi JJ. The complete chloroplast genome of Corethrodendron multijugum (Fabaceae: Corethrodendron) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:624-628. [PMID: 37275398 PMCID: PMC10236963 DOI: 10.1080/23802359.2023.2209387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/26/2023] [Indexed: 06/07/2023] Open
Abstract
Corethrodendron multijugum (Maxim.) (Fabaceae: Corethrodendron), also known as Hedysarum multijugum, is an important medicinal plant and is widely used in traditional Chinese medicine. To better understand the diversity and phylogeny of C. multijugum and other Fabaceae species, we sequenced and annotated the complete chloroplast genome of C. multijugum using the Illumina HiSeq 2500 platform. This complete genome was 122,994 bp long, and encodes a total of 110 genes, including 76 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA unit genes (rRNAs). The C. multijugum plastid with a G + C content of 34.5% presents a negative AT -skew (-0.002) and a positive GC -skew (0.032). Phylogenetic analysis revealed that C. multijugum is more closely related to Hedysarum petrovii. This study provides genetic resource information for the further study of Corethrodendron.
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Affiliation(s)
- Li-Jun Zhang
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, China
| | - Ying Liu
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, China
| | - Jian-Jun Shi
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, China
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19
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Lee SR, Ha YH, Son DC, Kim SC. First record of the complete chloroplast genome of Polygonatum infundiflorum (Asparagaceae), a Korean endemic species. Mitochondrial DNA B Resour 2023; 8:603-606. [PMID: 37250207 PMCID: PMC10215011 DOI: 10.1080/23802359.2023.2215349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/07/2023] [Indexed: 05/31/2023] Open
Abstract
Polygonatum infundiflorum Y.S. Kim, B.U. Oh & C.G. Jang et al. 1998 is a Korean endemic species. This is first report on the complete chloroplast genome sequence of P. infundiflorum. The complete chloroplast genome length was 154,578 bp with a GC content of 37.7%. The large single-copy (LSC) region was 83,527 bp long, and the small single-copy (SSC) region was 18,457 bp long. The paired inverted repeats (IRs) were 26,297 bp and separated the LCS and SSC regions. There were 113 genes, comprising 78 protein-coding genes, four rRNA genes, 30 tRNA genes, and one pseudogene (infA). In total, 16 genes contained one intron, and two genes contained two introns. Phylogenetic analysis suggested that Polygonatum was divided into three sections, each forming a monophyletic group. P. infundiflorum was sister to P. macropodum and formed a monophyletic group with P. inflatum. This study provides basic information for future research and contributes to taxonomic and genetic studies on Polygonatum.
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Affiliation(s)
- Se Ryeong Lee
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Dong Chan Son
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
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20
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Zhao H, Zhang Z, Li X, Tian Y, Zhao J, Liu J, Shi L. The complete chloroplast genome of Pseudostellaria davidii (franch.) Pax, 1934. Mitochondrial DNA B Resour 2023; 8:471-474. [PMID: 37025399 PMCID: PMC10071897 DOI: 10.1080/23802359.2023.2195514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Pseudostellaria davidii (Franch.) Pax belongs to subseries distancs of Pseudostellaria (Caryophyllaceae), and is mainly distributed in north-eastern Asia. The complete chloroplast (cp) genome of P. davidii was assembled and annotated for the first time in this study. The cp genome of P. davidii is 149,732 bp in length with the GC content of 36.57%, and it consists of four subregions: a large single-copy (LSC) region of 81,156 bp, a small single-copy (SSC) region of 16,894 bp and two inverted repeats (IR) regions of 25,841 bp each. The cp genome of P. davidii encodes a total of 111 unique genes, which are 77 protein-coding genes, four rRNA genes, and 30 tRNA genes. The results of phylogenetic analysis strongly suggested that Pseudostellaria was a monophyletic group and P. davidii forms an independent sister clade to other species of Pseudostellaria.
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Affiliation(s)
- Hongye Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Xinyi Li
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Yu Tian
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Jingyi Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
| | - Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- CONTACT Jinxin Liu
| | - Linchun Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Linchun Shi Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, P.R. China
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Xiang R, Wang S, Wan H. The complete chloroplast genome of Holarrhena pubescens and its phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:266-269. [PMID: 36816055 PMCID: PMC9937002 DOI: 10.1080/23802359.2022.2162349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Holarrhena pubescens Wall. ex G. Don, 1837 is an important medicinal plant belonging to the Holarrhena genus in the Apocynaceae family. In this study, the complete chloroplast (cp) genome sequence of H. pubescens was sequenced using the Illumina NovaSeq platform. The cp genome of H. pubescens was 160,108 bp in length with 37.21% overall GC content. The cp genome of H. pubescens containing a large single-copy region (LSC, 88,685 bp), a small single-copy region (SSC, 18,671 bp), and a pair of inverted repeat regions (SSC, 26,376 bp). The cp genome encoded 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete protein coding genes sequences revealed that H. pubescens was closest to Beaumontia murtonii.
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Affiliation(s)
- Rushuang 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, China,College of Pharmaceutical, Dali University, Dali, China
| | - Sijia Wang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China,School of Landscape Architecture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China,CONTACT Huihua Wan Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100070, China
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Carvalho Leonardo I, Alberti A, Denoeud F, Barreto Crespo MT, Capelo J, Bustos Gaspar F. The complete plastome of Glandora prostrata subsp. lusitanica (Samp.) D.C.Thomas (Boraginaceae), the first chloroplast genome belonging to the Glandora genus. Mitochondrial DNA B Resour 2023; 8:270-273. [PMID: 36816053 PMCID: PMC9937008 DOI: 10.1080/23802359.2023.2175976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Glandora prostrata (Loisel.) D.C.Thomas (Thomas et al., 2008), besides being a common plant of western and south-western Europe and north-western Africa, is a species with a wealth of reported uses in traditional and folk medicine. The chloroplast genome of Glandora prostrata subsp. lusitanica (Samp.) D.C.Thomas (Thomas et al., 2008) isolate BPTPS049 described in this study is the first publicly available complete plastome belonging to the Glandora genus. The chloroplast genome (GenBank accession number: ON641304) is 150,041 bp in length with 37.5% GC content, displaying a quadripartite structure that contains a pair of inverted repeat regions (25,833 bp each), separated by a large (81,222 bp) and small (17,153 bp) single-copy regions. It has 131 annotated genes including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis performed confirms that G. prostrata subsp. lusitanica is placed under the Boraginaceae family, which belongs to the Boraginales order. This study will contribute to conservation, phylogenetic, and evolutionary studies that comprise this traditional species relevant to the landscape of aromatic, medicinal, and condiment plants from Portugal.
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Affiliation(s)
- Inês Carvalho Leonardo
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal,ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Évry, Université Paris-Saclay, Évry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Évry, Université Paris-Saclay, Évry, France
| | - Maria Teresa Barreto Crespo
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal,ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jorge Capelo
- ECOCHANGE, CIBIO-InBIO – Research Centre in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal,INIAV, Instituto Nacional de Investigação Agrária e Veterinária I.P., Quinta do Marquês, Oeiras, Portugal
| | - Frédéric Bustos Gaspar
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal,ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal,CONTACT Frédéric Bustos Gaspar Food Safety and Microbiology Laboratory, Food & Health Division, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901Oeiras, Portugal
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Jin GZ, Wen ZB, Song F, Feng Y. The complete chloroplast genome of an endangered plant Artemisia borotalensis (Asteraceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:145-148. [PMID: 36685653 PMCID: PMC9848251 DOI: 10.1080/23802359.2022.2163599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Artemisia borotalensis Poljakov is an endemic and endangered herb in China. In this study, we sequenced and analyzed the complete chloroplast genome of this species. Sequencing revealed the genome to be 151,179 bp in length, containing a large single copy region (82,862 bp), a small single copy region (18,377 bp), and a pair of inverted repeat regions (24,970 bp each). Our analyses demonstrated that it contained 133 genes, including 87 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes, and one pseudogene (ycf1). Furthermore, we found the genome to have an overall GC content of 37.4%. A phylogenetic analysis indicated that A. borotalensis and A. maritima clustered together as sister group to A. annua and A. fukudo clade.
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Affiliation(s)
- Guang-Zhao Jin
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China,The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China,University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-bin Wen
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China,The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Feng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China,The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China,CONTACT Ying Feng State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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Carvalho Leonardo I, Alberti A, Denoeud F, Barreto Crespo MT, Capelo J, Bustos Gaspar F. The complete plastome of Centaurium erythraea subsp. majus (Hoffmanns. & Link) M.Laínz (Gentianaceae), the first chloroplast genome belonging to the Centaurium genus. Mitochondrial DNA B Resour 2023; 8:86-90. [PMID: 36685651 PMCID: PMC9848357 DOI: 10.1080/23802359.2022.2160670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Despite having many historically reported ethnomedicinal uses, Centaurium erythraea Rafn (Rafn and Buchs, 1800; common centaury) also produces cytotoxic secondary metabolites, and its presence should be carefully monitored. In this study, the complete chloroplast of Centaurium erythraea subsp. majus (Hoffmanns. & Link) M.Laínz (Laínz, 1971) isolate BPTPS121 is described, being the first available plastome belonging to the Centaurium genus. The chloroplast genome (GenBank accession number: ON641347) is 153,107 bp in length with 37.9% GC content, displaying a quadripartite structure that contains a pair of inverted repeat regions (25,166 bp each), separated by a large single-copy (84,388 bp) and small single-copy (18,387 bp) regions. A total of 129 genes were predicted, including 37 tRNA genes, eight rRNA genes, and 84 protein-coding genes. The phylogenetic analysis showed that isolate BPTPS121 is placed under the Gentianaceae family, belonging to the Gentianales order. The maximum-likelihood tree supports the already described lineage divergence in the Gentianaceae family, with C. erythraea subsp. majus belonging to the Chironieae tribe positioned below the Exaceae tribe and above the Potalieae and the entire Gentianeae tribes. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food, feed, and supplements safety purposes.
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Affiliation(s)
- Inês Carvalho Leonardo
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal,ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Évry, Université Paris-Saclay, Évry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Évry, Université Paris-Saclay, Évry, France
| | - Maria Teresa Barreto Crespo
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal,ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jorge Capelo
- ECOCHANGE, CIBIO-InBIO – Research Centre in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal,INIAV, Instituto Nacional de Investigação Agrária e Veterinária I.P., Quinta do Marquês, Oeiras, Portugal
| | - Frédéric Bustos Gaspar
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal,ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal,CONTACT Frédéric Bustos Gaspar Food & Health Division, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901Oeiras, Portugal
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25
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Park JM, Koo J. The complete chloroplast genome sequence of Berchemia racemosa Siebold & Zucc. (Rhamnaceae), a rare plant species in Korea. Mitochondrial DNA B Resour 2023; 8:69-72. [PMID: 36620322 PMCID: PMC9817123 DOI: 10.1080/23802359.2022.2161329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Berchemia racemosa Siebold & Zucc., 1845 is a rare species distributed in restricted areas in the western Korean peninsula. In this study, the complete chloroplast genome (plastome) of B. racemosa was sequenced and assembled by Illumina paired-end sequencing. The plastome of B. racemosa was 161,187 bp in length and was quadripartite in structure, including a large single-copy (LSC) region of 89,503 bp, a small single-copy (SSC) region of 18,214 bp, and two inverted repeats of 26,735 bp. The GC content was 37.2%. The plastome of B. racemosa contains 130 genes, including eight ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and 85 protein-coding genes. Phylogenetic analysis using complete genome sequences showed that B. racemosa is most closely related to Berchemia flavescens.
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Affiliation(s)
- Joon Moh Park
- Forest Resource Research Division, Jeollabuk-do Forest Environment Research Institute, Jinan, South Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, South Korea,CONTACT Jachoon Koo Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, South Korea
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Shao YZ, Wang Z, Liu WJ, Zhao PF, Wu S. Complete chloroplast genome features and phylogenetic analysis of Abies ernestii var. salouenensis (Bordères and Gaussen) W. C. Cheng and L. K. Fu from southwest China. Mitochondrial DNA B Resour 2023; 8:550-556. [PMID: 37197650 PMCID: PMC10184594 DOI: 10.1080/23802359.2023.2209384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/26/2023] [Indexed: 05/19/2023] Open
Abstract
Abies ernestii var. salouenensis (Bordères & Gaussen) W. C. Cheng & L. K. Fu is endemic to southwest China, including the southeastern Tibetan Plateau and the northwestern Yunnan Province. The taxonomic relationships between A. ernestii var. salouenensis and two other closely related fir species (A. chensiensis Tiegh. and A. ernestii Rehd.) still need to be determined. Here, we report for the first time the whole chloroplast genome of A. ernestii var. salouenensis. Its genome is 121,759 bp long and is characterized by a circular structure with 68 peptide-encoding genes, 16 tRNAs, six ORFs, and four rRNAs. We also identified 70 microsatellite repeat sequences and 14 tandem repeat sequences in the chloroplast genome of A. ernestii var. salouenensis. Comparative genome analysis indicated considerable variation in ycf1 and ycf2. Phylogenetic analysis supported the monophyly of A. ernestii var. salouenensis, A. chensiensis Tiegh., and A. ernestii Rehd. The relationships among them should be surveyed using more samples at the species level. This study will facilitate taxonomic studies and the development of suitable chloroplast markers for fir species.
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Affiliation(s)
- Yi-Zhen Shao
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Zhao Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Wen-Jun Liu
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Peng-Fei Zhao
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
- CONTACT Peng-Fei Zhao College of Life Science, Henan Agriculture University, Zhengzhou, China
| | - Si Wu
- School of Life Sciences, Zhengzhou Normal University, Zhengzhou, China
- Si Wu School of Life Sciences, Zhengzhou Normal University, Zhengzhou, China
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27
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Yan S, Wang T, Wang Z, Ren W, Liu C, Ma W, Dong S. The chloroplast genome of Lappula myosotis V. Wolf, a medicinal species. Mitochondrial DNA B Resour 2023; 8:30-33. [PMID: 36620320 PMCID: PMC9815226 DOI: 10.1080/23802359.2022.2158692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Lappula myosotis V. Wolf 1776 is an annual or biennial plant with important medicinal value. In the present study, we report the complete chloroplast genome data of L. myosotis, which has a length of 146,668 bp, including a small single-copy (SSC) region of 17,059 bp, a large single-copy (LSC) region of 79,691 bp, and a pair of inverted repeats (IRs) of 24,959 bp. A total of 127 genes encoding tRNA and rRNA were annotated. The total CG content of the chloroplast genome was 37.7%. The maximum-likelihood (ML) phylogenetic tree strongly supported that L. myosotis is closely related to Trigonotis peduncularis. The complete chloroplast genome of L. myosotis provides useful information on the evolution and phylogenetic relationship among Boraginaceae plants.
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Affiliation(s)
- Song Yan
- Pharmacy College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Tianhao Wang
- College of Mechanical and Electrical Engineering, Northeast Forestry University, Harbin, China
| | - Zhen Wang
- Pharmacy College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Weichao Ren
- Pharmacy College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Chi Liu
- Faculty of Electrical Engineering and Information Technology, Technical University of Chemnitz, Chemnitz, Germany
| | - Wei Ma
- Pharmacy College, Heilongjiang University of Chinese Medicine, Harbin, China,CONTACT Wei Ma Pharmacy College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shang Dong
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China,Shang Dong Yichun Branch of Heilongjiang Academy of Forestry, Heilongjiang, China
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28
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Wu YM, Mu XY, Qin YH. The first complete chloroplast genome in Engelhardia sensu stricto, Engelhardia hainanensis Chen: genome characterization and its phylogenetic relationships within the family Juglandaceae. Mitochondrial DNA B Resour 2023; 8:479-483. [PMID: 37063241 PMCID: PMC10101671 DOI: 10.1080/23802359.2023.2196359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Trees of Engelhardia are important components of subtropical and tropical forests in South-eastern Asia with great ecological and economic values. However, phylogenetic relationships within Engelhardioideae (Juglandaceae) remains obscure. In this study, we report the first complete chloroplast genome sequences of Engelhardia sensu stricto, Engelhardia hainanensis Chen, a rare species endemic in southern China. Its complete chloroplast genome is 161,574 bp in length, with a typical quadripartite structure that includes a large single-copy region of 91,158 bp, a small single-copy region of 18,790 bp, and its GC content is 35.8%. A total of 128 genes were identified, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Furthermore, a phylogenetic tree of Juglandaceae was constructed based the complete chloroplast genome sequence, which strongly support the three-subfamily classification system in Juglandaceae, and E. hainanensis was resolved sister to two Alfaropsis species. This study provides valuable genomic information for the species identification and phylogenetic study of Juglandaceae.
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Affiliation(s)
- Yuan-Mi Wu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, P. R. China
| | - Xian-Yun Mu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, P. R. China
- CONTACT Xian-Yun Mu College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, P. R. China
| | - Yong-Hua Qin
- Guangxi Forestry Inventory and Planning Institute, Nanning, P. R. China
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29
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Li M, Gong Q, Zhou M, Liu Q, Cheng R. Characterization of the complete chloroplast genome of the medicinal herb Eleutherococcus nodiflorus and its phylogenetic implications. Mitochondrial DNA B Resour 2022; 7:1890-1892. [PMID: 36340921 PMCID: PMC9629086 DOI: 10.1080/23802359.2022.2116954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Eleutherococcus nodiflorus (Dunn) S. Y. Hu is a momentous medicinal plant belonging to the Araliaceae family. In the current investigation, we determined the complete chloroplast genome of E. nodiflorus and analyzed the phylogenetic relationship among Eleutherococcus plants. The chloroplast genome of E. nodiflorus exhibited a typical quadripartite structure with a full length of 156,770 bp, including 133 genes, containing 88 protein-coding genes, 8 rRNA genes, 37 tRNA genes, and 1 presumed pseudogene (ycf1). The overall GC content observed was 37.95%, with the highest GC content of 43.02% found in the IR region. Comparative genome analysis revealed five highly variable regions among Eleutherococcus species, providing potential markers for further investigations on species identification and population genetics. A total of 44 small simple repeats were identified throughout the chloroplast genome of E. nodiflorus. The phylogenetic analysis indicated a sister relationship between E. nodiflorus and E. eleutheristylus, suggesting a close genetic relationship between the two Eleutherococcus plants. These results enhance the understanding of the plant evolution within Eleutherococcus plants and provide basic genetic resources for the development of species identification and investigation of population genetic diversity of the Eleutherococcus genus and Araliaceae.
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Affiliation(s)
- Minjun Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiuyi Gong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Manjia Zhou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiang Liu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China,CONTACT Rubin Cheng School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou310053, China
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30
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Zhang K, Yin Y, Yi S, Li H. Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus quinquefoliolatus T.T.Yu & L.T.Lu (family Rosaceae). Mitochondrial DNA B Resour 2022; 7:1364-1366. [PMID: 35903303 PMCID: PMC9318300 DOI: 10.1080/23802359.2022.2098859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rubus quinquefoliolatus T.T.Yu & L.T.Lu is a climbing shrub belonging to the Rosaceae family. It is widely distributed in the provinces of Yunnan and Guizhou in China. In this study, we sequenced the first complete chloroplast genome (cpDNA) sequence of R. quinquefoliolatus. The results showed a genome length of 156,489 bp, which is composed of a large single-copy (LSC) of 86,103 bp, small single-copy (SSC) of 18,844 bp, and two inverted repeats of 25,771 bp each. The whole chloroplast genome encodes 131 genes, including 86 coding sequences, 37 tRNAs, and eight rRNAs. Phylogenetic analysis revealed that R. quinquefoliolatus is closely related to R. lineatus and R. pentagonus.
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Affiliation(s)
- Ke Zhang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, PR China
| | - Yongfei Yin
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, PR China
| | - Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, PR China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, PR China
| | - Haitao Li
- Yunnan Branch Institute of Medicinal Plant, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong, PR China
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31
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Wang W, Xu T, Song X, Chen C, Liu D, Han B, Yi S. The complete chloroplast genome of the medicinal plant Paederia foetida L. Mitochondrial DNA B Resour 2022; 7:1218-1220. [PMID: 35837498 PMCID: PMC9275490 DOI: 10.1080/23802359.2022.2087563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Paederia foetida L. belonging to Rubiaceae family is a perennial medicinal herb widely distributed in India and China. The first complete chloroplast genome sequence of P. foetida was assembled and characterized in this study. The total chloroplast genome was 153,591 bp in length with 37.74% GC content, composed of a large single-copy (LSC) region of 83,677 bp, a small single-copy (SSC) region of 16,888 bp and a pair of inverted repeat (IR) regions of 26,513 bp. The whole chloroplast genome encoded 133 genes, including 88 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis of 30 chloroplast genomes strongly suggested that P. foetida was closely related to P. scandens.
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Affiliation(s)
- Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, P. R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, Anhui, P. R. China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, P. R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, Anhui, P. R. China
| | - Xiangwen Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, P. R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, Anhui, P. R. China
| | - Cunwu Chen
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, P. R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, Anhui, P. R. China
| | - Dong Liu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, P. R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, Anhui, P. R. China
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, P. R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, Anhui, P. R. China
| | - Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, P. R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, Anhui, P. R. China
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Wang W, Xu T, Song X, Chen C, Liu D, Han B, Yi S. Sequencing of the complete chloroplast genome of Rubia yunnanensis Diels and its phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:1087-1089. [PMID: 35756430 PMCID: PMC9225772 DOI: 10.1080/23802359.2022.2086496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Rubia yunnanensis Diels, an important medicinal herb, is mainly distributed in Yunnan province, Southwest China. In this study, the complete chloroplast genome of R. yunnanensis was successfully sequenced. The assembled chloroplast genome was 155,108 bp in length with an overall GC content of 36.98%, including a pair of inverted repeat (IR) regions (26,573 bp, each), respectively, a large single-copy (LSC) region (84,848 bp) and a small single-copy (SSC) region (17,114 bp). The genome contained 131 genes, comprising 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. The phylogenetic analysis indicated that R. yunnanensis was closely related to R. cordifolia.
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Affiliation(s)
- Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Xiangwen Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Cunwu Chen
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Dong Liu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
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Luo J, Gong Q, Zhou M, Liu Q, Cheng R, Ge Y. Complete chloroplast genome of the medicinal herb Veronicastrum axillare (Sieb. et Zucc.) Yamazaki and the phylogenetic relationship analysis within the tribe Veroniceae. Mitochondrial DNA B Resour 2022; 7:783-785. [PMID: 35558172 PMCID: PMC9090389 DOI: 10.1080/23802359.2022.2071651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Veronicastrum axillare (Sieb. et Zucc.) Yamazaki is a traditional medical plant with versatile biological activities. Here, we reported the complete chloroplast genome sequence of V. axillare with a total length of 152,691 bp, containing two IR regions of 25,765 bp each, an LSC region of 83,559 bp, and an SSC region of 17,602 bp. The genome encodes 131 genes, including 85 protein-coding genes, 37 tRNAs, eight rRNAs, and one pseudogene (ycf1). The overall GC content is 38.3%, with the highest content of 43.31% in IR region. Comparative analysis revealed 4 potential hotspots among V. axillare and other Veroniceae plants, providing potential markers for population investigations in the tribe Veroniceae. A total of 56 simple sequence repeats were identified in V. axillare. Phylogenetic analysis indicated a sister relationship between V. axillare and V. sibiricum, suggesting a close genetic relationship between the two Veronicastrum species. Our results provide basic genetic resources for investigating the evolutionary status of V. axillare within the tribe Veroniceae.
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Affiliation(s)
- Jiawen Luo
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiuyi Gong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Manjia Zhou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiang Liu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University
| | - Yuqing Ge
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
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34
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Guo S, Liao X, Chen S, Liao B, Guo Y, Cheng R, Xiao S, Hu H, Chen J, Pei J, Chen Y, Xu J, Chen S. A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants. Front Genet 2022; 13:764534. [PMID: 35547259 PMCID: PMC9084321 DOI: 10.3389/fgene.2022.764534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Polygonum is a generalized genus of the Polygonaceae family that includes various herbaceous plants. In order to provide aid in understanding the evolutionary and phylogenetic relationship in Polygonum at the chloroplast (cp) genome-scale level, we sequenced and annotated the complete chloroplast genomes of four Polygonum species using next-generation sequencing technology and CpGAVAS. Then, repeat sequences, IR contractions, and expansion and transformation sites of chloroplast genomes of four Polygonum species were studied, and a phylogenetic tree was built using the chloroplast genomes of Polygonum. The results indicated that the chloroplast genome construction of Polygonum also displayed characteristic four types of results, comparable to the published chloroplast genome of recorded angiosperms. The chloroplast genomes of the four Polygonum plants are highly consistent in genome size (159,015 bp-163,461 bp), number of genes (112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes), gene types, gene order, codon usage, and repeat sequence distribution, which identifies the high preservation among the Polygonum chloroplast genomes. The Polygonum phylogenetic tree was recreated by a full sequence of the chloroplast genome, which illustrates that the P. bistorta, P. orientale, and P. perfoliatum are divided into the same branch, and P. aviculare belongs to Fallopia. The precise system site of lots base parts requires further verification, but the study would provide a basis for developing the available genetic resources and evolutionary relationships of Polygonum.
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Affiliation(s)
- Shuai Guo
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuejiao Liao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shiyu Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiming Guo
- Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ruiyang Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haoyu Hu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Chen
- Beijing Engineering Research Center of Pediatric Surgery, Engineering and Transformation Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yangjin Chen
- Department of City and Regional Planning, Nanjing University, Nanjing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Guzmán-Díaz S, Núñez FAA, Veltjen E, Asselman P, Larridon I, Samain MS. Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion. Plants (Basel) 2022; 11:plants11030448. [PMID: 35161429 PMCID: PMC8838774 DOI: 10.3390/plants11030448] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 05/13/2023]
Abstract
Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.
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Affiliation(s)
- Salvador Guzmán-Díaz
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
- Correspondence:
| | - Fabián Augusto Aldaba Núñez
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
| | - Emily Veltjen
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
- Ghent University Botanical Garden, Ghent University, 9000 Gent, Belgium
| | - Pieter Asselman
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
| | - Isabel Larridon
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Marie-Stéphanie Samain
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
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Abstract
Camellia gigantocarpa Hu et T. C. Huang, belonging to the Theaceae family, is an excellent landscape tree species with high ornamental value. It is also an important woody oil-bearing plant with high economic value. This study reports the first complete chloroplast genome sequence of C. gigantocarpa (GenBank accession number: MZ054232). Its whole chloroplast genome is 156,953 bp long with an overall GC content of 37.31%, which is composed of a large single copy region (86,631 bp), a small single copy region (18,402 bp), and a pair of inverted repeat regions (25,960 bp each). A total of 135 genes were predicted in this genome, namely eight ribosomal RNA genes, 37 transfer RNA genes, and 90 protein-coding genes. Based on maximum likelihood analysis results, we found that the Camellia species are clustered into a distinct branch, and the phylogenetic relationships among C. gigantocarpa, C. crapnelliana, and C. kissii were the closest.
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Affiliation(s)
- Yufen Xu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yanju Liu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Xiaocheng Jia
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Ulaszewski B, Jankowska-Wróblewska S, Świło K, Burczyk J. Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp. Plants (Basel) 2021; 10:plants10112534. [PMID: 34834899 PMCID: PMC8618278 DOI: 10.3390/plants10112534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Several genera formerly contained within the genus Sorbus L. sensu lato have been proposed as separate taxa, including Aria, Chamaemespilus and Torminalis. However, molecular evidence for such distinctions are rather scarce. We assembled the complete chloroplast genome of Sorbus aucuparia, another representative of Sorbus s.s., and performed detailed comparisons with the available genomes of Aria edulis, Chamaemespilus alpina and Torminalis glaberrima. Additionally, using 110 complete chloroplast genomes of the Maleae representatives, we constructed the phylogenetic tree of the tribe using Maximum Likelihood methods. The chloroplast genome of S. aucuparia was found to be similar to other species within Maleae. The phylogenetic tree of the Maleae tribe indicated that A. edulis, C. alpina and T. glaberrima formed a concise group belonging to a different clade (related to Malus) than the one including Sorbus s.s. (related to Pyrus). However, Aria and Chamaemespilus appeared to be more closely related to each other than to Torminalis. Our results provide additional support for considering Aria, Chamaemespilus and Torminalis as separate genera different from Sorbus s.s.
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Han M, Xu M, Wang S, Wu L, Shi Y, Su T. The complete chloroplast genome sequence of Myricaria elegans: an endemic species to the Himalayas. Mitochondrial DNA B Resour 2021; 6:3343-3345. [PMID: 34746409 PMCID: PMC8567946 DOI: 10.1080/23802359.2021.1997111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
Myricaria elegans, an endemic species to the Himalayas, is a distinctive deciduous shrubbery plant-primarily distributed in the Qinghai-Tibet Plateau and adjacent regions in China. It is a kind of fuelwood, medicinal, and ecology-protecting woody plant species. In this study, the whole chloroplast (cp) genome sequence of M. elegans was assembled and characterized by high-throughput sequencing data. The complete cp genome of M. elegans was 155,245 bp in length with a GC content of 37.4%. It contained a large single-copy region (LSC) of 84,846 bp, and a small single-copy region (SSC) of 18,290 bp, which were separated by a pair of 26,053 bp inverted repeat regions (IRs). The cp genome of M. elegans was composed of 130 genes, including 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis revealed that M. elegans formed a clade with Myricaria, and it showed a close relationship with Myricaria prostrata.
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Affiliation(s)
- Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mingyue Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shizhen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Liangdan Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yuan Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China
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39
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Tian L, Xu X, Tong L, Xia C, Cheng Y. The complete chloroplast genome sequence of Styrax serrulatus Roxburgh (Styracaceae). Mitochondrial DNA B Resour 2021; 6:3156-3158. [PMID: 34746391 PMCID: PMC8567904 DOI: 10.1080/23802359.2021.1987170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Styrax serrulatus Roxburgh (William Roxburgh 1832), which plays an important role in ecology and economy, is a deciduous species of Styracaceae. In this paper, we sequenced, assembled, and annotated the chloroplast (cp) genome of S. serrulatus by using the sequencing data from Illumina Novaseq platform (Illumina, San Diego, CA). The complete cp genome of S. serrulatus is 157,929 base pairs (bp) in length, containing a pair of inverted repeat regions (IRs) of 26,048 bp each, a large single-copy (LSC) region of 87,552 bp, and a small single-copy (SSC) region of 18,281 bp. It contains 133 genes, including 8 rRNA genes, 37 tRNA genes, 87 protein-coding genes, and 1 pseudo gene. The GC content of S. serrulatus cp genome is 36.96%. The phylogenetic analysis suggests that S. serrulatus is a sister species to Styrax agrestis in Styracaceae.
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Affiliation(s)
- Lu Tian
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing, China
| | - Xiaogang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing, China
| | - Lili Tong
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Chongli Xia
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Yao Cheng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing, China
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40
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Abstract
Gentiana is an important but complicated group in Gentianaceae. The genus covers numerous medicinal plants which are difficult to be identified. In the present study, several medicinal species in Gentiana from Yunnan province, including G. rigescens, G.rhodantha, and G. delavayi, were sequenced using the Illumina HiSeq 2500 system. Three complete chloroplast genome sequences were obtained after assembly and annotation. According to several published genome sequences of G. crassicaulis, the DNA super-barcoding of species in Gentiana was preliminarily carried out. The results revealed that chloroplast genomes of the three species were conservative with short lengths(146 944, 148 992, and 148 796 bp, respectively). The genomes encoded 114 genes, including 78 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Furthermore, these medicinal species in Yunnan province were identified using DNA super-barcoding based on chloroplast genomes. The results showed that the Gentiana species could be gathered into monophyletic branches with a high support value(100%). It indicated that DNA super-barcoding possessed obvious advantages in discriminating species in complicated genera. This study is expected to provide a scientific basis for the identification, utilization, and conservation of Gentiana species.
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Affiliation(s)
- Hai-Su Hu
- College of Pharmacy, Dali University Dali 671000, China
| | - De-Quan Zhang
- College of Pharmacy, Dali University Dali 671000, China Institute of Materia Medica, Dali University Dali 671000, China
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41
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Yi S, Xu T, Song X, Wang W, Yu W, Han B. Sequencing and phylogenetic analysis of the complete chloroplast genome of Arisaema heterophyllum Blume. Mitochondrial DNA B Resour 2021; 6:3297-3299. [PMID: 34712816 PMCID: PMC8547874 DOI: 10.1080/23802359.2021.1993460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Arisaema heterophyllum Blume is a perennial medicinal herb widely distributed in China, Korea and Japan. In this study, the complete chloroplast genome sequence of A. heterophyllum was assembled and characterized based on high-throughput sequencing data. The whole chloroplast genome is 170,610 bp in length and contains 95,485 bp large single-copy (LSC) and 22,605 bp small single-copy (SSC) regions separated by a pair of 26,260 bp inverted repeat (IR) regions. It contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, with an overall GC content of 34.5%. A phylogenetic tree reconstructed by 30 chloroplast genomes reveals that A. heterophyllum is mostly related to the same genus A. ringens, A. franchetianum and A. erubescens. The complete chloroplast genome of A. heterophyllum was the firstly reported and deposited at GenBank under accession number MZ424448.
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Affiliation(s)
- Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Xiangwen Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Wangyang Yu
- Anhui Qiansouyan Biotechnology Co., Ltd, Lu'an, P.R. China
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
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42
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Sun ZY, Liu J, Wambulwa MC, Li ZH, Wu ZY. The complete chloroplast genome sequences of an endemic species of Urticaceae ( Debregeasia hekouensis). Mitochondrial DNA B Resour 2021; 6:3300-3302. [PMID: 34712817 PMCID: PMC8547858 DOI: 10.1080/23802359.2021.1993761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Debregeasia hekouensis, which belongs to the nettle family (Urticaceae), is a local endemic species in Hekou County, Yunnan Province, China. To provide a basis for the development of effective molecular markers for its conservation, we sequenced the chloroplast (cp) genome of D. hekouensis in the present study. The total length of the chloroplast(cp) genome was 155,941 bp, and exhibited a typical quadripartite structure, with a pair of IRs (inverted repeats; 25,664 bp in length) being separated by a small single copy (SSC) region of 19,085 bp and a large single copy (LSC) region of 85,528 bp. The cp genome contained a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The GC content of the entire cp genome, LSC region, SSC region, and IR region was 36.3%, 34.0%, 29.4%, and 42.7%, respectively. Phylogenetic analysis indicated that D. hekouensis is evolutionarily closer to Debregeasia orientalis and Debregeasia squamata.
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Affiliation(s)
- Zhao-Yang Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Jie Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Moses C Wambulwa
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,Department of Life Sciences, South Eastern Kenya University, Kitui, Kenya
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Yi S, Xu T, Song X, Wang W, Wang G, Yu W, Han B. The complete chloroplast genome of Arisaema bockii Engler and its phylogenetic analysis in the family Araceae. Mitochondrial DNA B Resour 2021; 6:3283-3285. [PMID: 34712813 PMCID: PMC8547865 DOI: 10.1080/23802359.2021.1993107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Arisaema bockii Engler is a perennial herbaceous medicinal plant, which is widely distributed in many provinces in China such as Anhui, Jiangsu, and Zhejiang. In this study, the complete chloroplast genome sequence of A. bockii was assembled and characterized based on high-throughput sequencing data. The total length of chloroplast genome was 175,537 bp, including large single-copy (LSC) and small single-copy (SSC) regions of 98,870 bp and 23,345 bp, respectively, which were separated by a pair of 27,161 bp inverted repeat (IR) regions. The genome contained 129 genes, including 84 protein-coding genes, 36 tRNA genes, 8 rRNA genes, and one pseudogene. The overall GC content of the genome was 33.6%. A phylogenetic tree reconstructed by 30 chloroplast genomes revealed that A. bockii was mostly related to the same genus species A. ringens, A. franchetianum and A. erubescens. The work reported the first complete chloroplast genome of A. bockii, which may provide some useful information to the evolution of the family Araceae.
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Affiliation(s)
- Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Xiangwen Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Guanglin Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Analytical and Testing Center, West Anhui University, Lu'an, P.R. China
| | - Wangyang Yu
- Anhui Qiansouyan Biotechnology Co., Ltd, Lu'an, P.R. China
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
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44
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Du Y, Wang YY, Xiang CL, Yang MQ. Characterization of the complete chloroplast genome of Salvia trijuga Diels (Lamiaceae). Mitochondrial DNA B Resour 2021; 6:3248-3249. [PMID: 34693012 PMCID: PMC8530471 DOI: 10.1080/23802359.2021.1991243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The complete cp genome of Salvia trijuga Diels was 151,345 bp in length, including a large single-copy region (LSC) of 82,577 bp, a small single-copy region (SSC) of 17,584 bp and a pair of inverted repeats (IRs) of 25,592 bp. The genome contained 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of this genome was 37.9%, with the corresponding values of LSC, SSC and IR regions being 36.0%, 31.7% and 43.1%, respectively. Further, the phylogenomic analysis strongly supported the sister relationship of Salvia trijuga and Salvia plebeia R. Br.
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Affiliation(s)
- Yan Du
- Baotou Medical College, Baotou, Inner Mongolia, China
| | | | - Chun-Lei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming Yunnan, China
| | - Mei-Qing Yang
- Baotou Medical College, Baotou, Inner Mongolia, China
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Xie J, Yong Y, Li T, Lv Y, Zou L, Li T, Li Z, Fu Z. Characterization of the complete chloroplast genome sequence of Chinese endemic species of Aster batangensis (Asteraceae: Astereae) and its phylogenetic implications. Mitochondrial DNA B Resour 2021; 6:3224-3225. [PMID: 34676295 PMCID: PMC8526030 DOI: 10.1080/23802359.2021.1990148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
This study was the first report complete chloroplast genome of Aster batangensis (Astereae: Asteraceae), the perennial herb endemic to China. The plastid genome of Aster batangensis include 132 unique genes, with 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among these genes, 21 duplicate genes, including10 protein-coding genes, 7 tRNA genes, and 4 rRNA genes were detected. The complete genome size of Aster batangensis has a typical quadripartite circular structure with 152,605 bp in total length, consisting a large single copy (LSC) of 84,351 bp and a small single copy (SSC) of 18,212 bp, separated by a pair of invested repeats (IR) of 25,021 bp. The average GC content of whole plastome sequence is 37.3%, and the LSC, SSC and IR regions is 35.3%, 31.3%, and 43.0%, respectively. The phylogenetic analysis by the maximum likelihood method showed that A. batangensis was closely related to the other members of Astereae (e.g. Aztecaster matudae, Conyza bonariensis, Lagenophora cuchumatanica, Baccharis tricuneata, Baccharis genistelloides)
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Affiliation(s)
- Jiani Xie
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yuan Yong
- College of Chemistry and Environment Protection Engineering, Southwest Minzu University, Chengdu, China
| | - Tian Li
- College of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yaqi Lv
- College of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Luyao Zou
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Tingyu Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Zhuojin Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, China.,College of Chemistry and Environment Protection Engineering, Southwest Minzu University, Chengdu, China.,College of Life Sciences, Zhengzhou University, Zhengzhou, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China.,Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, China.,Institute of Application and development of plant resources, Sichuan Normal University, Chengdu, China
| | - Zhixi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu, China.,Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, China.,Institute of Application and development of plant resources, Sichuan Normal University, Chengdu, China
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46
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Abstract
Rubus rufus Focke is a deciduous shrub species native to subtropical China and is valuable resources for the Raspberry cultivation by virtue of prolific fruits and stout resistances to hash stress. In this study, we assembled and characterized the complete chloroplast genome of R. rufus as resources for the future study. The chloroplast genome was 156,232 bp in length, composing of one large single copy (LSC; 85,840 bp) and one small single copy (SSC; 18,850 bp), separated by two inverted repeats (IRs; 25,771 bp). A total of 130 genes were predicted, including eight rRNAs, 36 tRNAs, and 86 protein-coding genes. The phylogenetic analysis showed a close relationship between R. rufus and Rubus cochinchinensis in the tribe Rubeae.
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Affiliation(s)
- Weicheng Huang
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Fei Qiao
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Wu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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47
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Tong L, Tian L, Xu X, Xia C, Cheng Y, Jiang X, Wang H, Tian Y. The complete chloroplast genome sequence of Xylosma racemosa (Siebold & Zucc.) Miq. (Salicaceae). Mitochondrial DNA B Resour 2021; 6:2975-2976. [PMID: 34553064 PMCID: PMC8451645 DOI: 10.1080/23802359.2021.1975509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Xylosma racemosa (Siebold & Zucc.) Miq. which plays an important role in ecology, medicine and economy, is a deciduous species of Salicaceae. In this paper, we sequenced, assembled, and annotated the chloroplast (cp) genome of X. racemosa (Siebold & Zucc.) Miq. by using the sequencing data from Illumina Novaseq platform. The complete cp genome of X. racemosa is 157,262 bp in length, containing a large single-copy (LSC) region of 84,289 bp, and a small single-copy (SSC) region of 17,817 bp. It contains 131 genes, including 8 rRNA genes, 37 tRNAs genes and 86 protein-coding genes. The GC content of X. racemosa cp genome is 36.74%. The phylogenetic analysis suggests that X. racemosa is a sister species to Xylosma congesta in Salicaceae.
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Affiliation(s)
- Lili Tong
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Lu Tian
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
| | - Xiaogang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
| | - Chongli Xia
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Yao Cheng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
| | - Xiaoyu Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
| | - Hongchao Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
| | - Yukun Tian
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China
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48
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Fan YY, Ye XX, Wei M, Li B, Zhu YL, Xing-Wen Z. The complete chloroplast genome sequence of rare and endangered Camellia pubipetala Y. Wan & S. Z. Huang (Theaceae) of South China. Mitochondrial DNA B Resour 2021; 6:2893-2895. [PMID: 34532581 PMCID: PMC8439226 DOI: 10.1080/23802359.2021.1915207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The complete chloroplast genome sequence of rare and endangered Camellia pubipetala Y. Wan & S. Z. Huang (Theaceae) was mentioned in this research. By studying comparatively, we found that the C. pubipetala Y. Wan & S. Z. Huang chloroplast genome was 156,993 bp in length and composed of 86,590 bp LSC, 18,211 bp SSC, and two reverse repeating regions with 26,090 bp. The whole GC content was 37.33%. The genome encoded 116 functional genes, including 80 protein-coding genes, 32 tRNA genes, and 4 rRNA genes. In order to find the phylogenetic relationship of C. pubipetala Y. Wan & S. Z. Huang within Camellia genus, we reconstructed phylogenetic tree. The results indicate that C. pubipetala Y. Wan & S. Z. Huang was closely related to Camellia huana voucher and Camellia ptilosperma.
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Affiliation(s)
- Yuan-Yuan Fan
- College of Pharmacy, Guilin Medical University, Guilin, PR China
| | - Xiao-Xia Ye
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin, PR China
| | - Min Wei
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin, PR China
| | - Bo Li
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin, PR China
| | - Yu-Lin Zhu
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin, PR China
| | - Zhou Xing-Wen
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin, PR China
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49
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Yang L, Wu Q, Yang M, Zhang D, Dong S, Cheng J. The complete chloroplast genome sequence of the endemic and rare orchid Nothodoritis zhejiangensis (Orchidaceae) in China. Mitochondrial DNA B Resour 2021; 6:2931-2932. [PMID: 34532589 PMCID: PMC8439232 DOI: 10.1080/23802359.2021.1972867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Nothodoritis zhejiangensis (Orchidaceae) is a rare orchid unique to China of great horticultural value. The complete chloroplast (cp) genome of this species is 143,522 bp in length and the total GC content is 36.8%. It includes a large single copy (LSC) region of 83,830 bp in length, a small single copy (SSC) region of 10,764 bp, and a pair of inverted repeat regions (IRs) with 24,464 bp. The cp genome contains 120 functional genes, including 74 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic tree constructed by the maximum-likelihood method showed that the taxonomic status of N. zhejiangensis was clustered with the species in Phalaenopsis.
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Affiliation(s)
- Lei Yang
- College of Biological Sciences and Technology, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Qi Wu
- College of Biological Sciences and Technology, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Mingqi Yang
- Beijing Forestry University Forest Science Company Ltd., Beijing, China
| | - Dong Zhang
- Beijing Forestry University Forest Science Company Ltd., Beijing, China
| | - Shubin Dong
- College of Biological Sciences and Technology, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
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50
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Chong X, Zhang F, Li Y, Wang C, Zhou Y, Zhou T, Wang Y, Lu X, Chen H. Complete chloroplast genome sequence and phylogenetic analysis of Ilex × attenuata 'Fosteri' (Aquifoliaceae). Mitochondrial DNA B Resour 2021; 6:2799-2800. [PMID: 34514131 PMCID: PMC8425775 DOI: 10.1080/23802359.2021.1970637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ilex × attenuata ‘Fosteri’ is an important ornamental plant widely distributed in mid-southern China and south-eastern United States. In this study, we assembled the complete chloroplast (cp) genome of I. attenuata by high-throughput sequencing and bioinformatics. The full length of cp genome was 157,833 bp with 37.63% overall GC content, which contained two inverted repeats (IR) of 26,093 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 87,188 bp and 18,459 bp, respectively. The cp genome contained 135 genes, including 88 protein-coding genes, 8 rRNA genes and 39 tRNA genes. Phylogenetic tree showed that the close relationship of three species of Ilex (I. attenuata, I. viridis and I. szechwanensis) in the Aquifoliaceae family.
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Affiliation(s)
- Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fan Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yunlong Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chuanyong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yanwei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ting Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yinjie Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiaoqing Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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