501
|
Zhang G, Liu Y, Hai P. The complete chloroplast genome of Tibetan medicinal plant Rubus phoenicolasius Maxim. Mitochondrial DNA B Resour 2021; 6:886-887. [PMID: 33796668 PMCID: PMC7971196 DOI: 10.1080/23802359.2021.1886013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Rubus phoenicolasius Maxim. is a traditional Tibetan medicine and widely used in the clinical pharmacology. In current study, the complete chloroplast genome of R. phoenicolasius was reported. The total length of the genome was 155,144 bp with the GC content of 37.9%. We predicted 130 genes in the genome including 84 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 1 pseudogene. 17 genes were duplicated in the IR regions including 7 tRNA, 4 rRNA and 6 protein-coding genes. Phylogenomic analysis revealed that R. phoenicolasius forms a strong supported branch with R. amabilis and R. coreanus under the Rosaceae clade.
Collapse
Affiliation(s)
- Guoying Zhang
- Qinghai Provincial Key Laboratory of Modernization of Traditional Chinese and Tibetan Medicine, Qinghai Provincial Drug Inspection and Testing Institute, Xining, China
| | - Yarong Liu
- Qinghai Provincial Key Laboratory of Modernization of Traditional Chinese and Tibetan Medicine, Qinghai Provincial Drug Inspection and Testing Institute, Xining, China
| | - Ping Hai
- Qinghai Provincial Key Laboratory of Modernization of Traditional Chinese and Tibetan Medicine, Qinghai Provincial Drug Inspection and Testing Institute, Xining, China
| |
Collapse
|
502
|
Tian X, Wariss HM. The complete chloroplast genome sequence of Metabriggsia ovalifolia W. T. Wang (Gesneriaceae), a national key protected plant endemic to Karst areas in China. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:833-834. [PMID: 33763595 PMCID: PMC7954431 DOI: 10.1080/23802359.2021.1884021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Metabriggsia ovalifolia W. T. Wang is one of the first-class national protected plants endemic to Karst areas in China. In this study, the complete chloroplast genome was sequenced using Illumina pair-end sequencing data. The chloroplast genome was 153,333 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 25,448 bp), separated by a large single copy region (LSC: 84,381 bp) and a small single copy region (SSC: 18,056 bp). The chloroplast genome encodes 131 genes, including 87 protein-coding genes, 36 transfer RNA, and eight ribosomal RNA genes. The overall GC content of the chloroplast genome was 37.55%. M. ovalifolia phylogenetic analysis indicated close relationship with Oreocharis mileensis of Gesneriaceae family. These genomic resources will be helpful for conservation of this endemic plant species.
Collapse
Affiliation(s)
- Xiaoling Tian
- The College of Humanities and Sciences of Guizhou Minzu University, Guiyang, China
| | - Hafiz Muhammad Wariss
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
503
|
Yi D, Jiang W, Ma L, Pang Y. The complete chloroplast genome of Desmodium uncinatum (Fabaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:715-717. [PMID: 33763558 PMCID: PMC7954487 DOI: 10.1080/23802359.2020.1852896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Desmodium uncinatum is one of the most important legume forage which distributes in tropical and subtropical regions of the world. In our study, we obtained the complete chloroplast genome of D. uncinatum with a length of 148,853 bp, including a large single copy region of 84,019 bp, small single copy region of 18,223 bp, and a pair of inverted repeat regions of 20,672 bp. The GC content in the whole chloroplast genome of D. uncinatum is 35.16%. Among the 133 unique genes in the circular genome, 37 tRNA, 12 rRNA and 84 protein-coding genes were successfully annotated. We constructed the Maximum likelihood (ML) tree with 11 species, and came to the conclusion that D. uncinatum was phylogenetically closely related to the genus of Glycine and Trifolium.
Collapse
Affiliation(s)
- Dengxia Yi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbo Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhen Pang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
504
|
Jiang M, Wang J, Chen M, Zhang H. Complete chloroplast genome of a rare and endangered plant species Osteomeles subrotunda: genomic features and phylogenetic relationships with other Rosaceae plants. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:762-768. [PMID: 33763572 PMCID: PMC7954488 DOI: 10.1080/23802359.2021.1881835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Osteomeles subrotunda is a rare and endangered plant species with extremely small populations. In our study, we sequenced the complete chloroplast (CP) genome of O. subrotunda and described its structural organization, and performed comparative genomic analyses with other Rosaceae CP genomes. The plastome of O. subrotunda was 159,902 bp in length with 36.6% GC content and contained a pair of inverted repeats of 26,367 bp which separated a large single-copy region of 87,933 bp and a small single-copy region of 19,235 bp. The CP genome included 130 genes, of which 85 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Two genes, rps19 and ycf1, which are located at the borders of IRB/SSC and IRB/LSC, were presumed to be pseudogenes. A total of 61 SSRs were detected, of which, 59 loci were mono-nucleotide repeats, and two were di-nucleotide repeats. The phylogenic analysis indicated that the 14 Rosaceae species were divided into three groups, among which O. subrotunda grouped with P. rupicola, E. japonica, P. pashia, C. japonica, S. torminalis, and M. florentina, and it was found to be a sister clade to C. japonica. Our newly sequenced CP genome of O. subrotunda will provide essential data for further studies on population genetics and biodiversity.
Collapse
Affiliation(s)
- Ming Jiang
- College of Life Sciences, Taizhou University, Taizhou, P. R. China
| | - Junfeng Wang
- Scientific Research Management Center, East China Medicinal Botanical Garden, Lishui, P. R. China
| | - Minghui Chen
- College of Life Sciences, Taizhou University, Taizhou, P. R. China
| | - Huijuan Zhang
- College of Life Sciences, Taizhou University, Taizhou, P. R. China
| |
Collapse
|
505
|
Sun J, Sun R, Liu H, Chang L, Li S, Zhao M, Shennan C, Lei J, Dong J, Zhong C, Xue L, Gao Y, Wang G, Zhang Y. Complete chloroplast genome sequencing of ten wild Fragaria species in China provides evidence for phylogenetic evolution of Fragaria. Genomics 2021; 113:1170-1179. [PMID: 33705887 DOI: 10.1016/j.ygeno.2021.01.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/02/2021] [Accepted: 01/23/2021] [Indexed: 02/04/2023]
Abstract
Complete chloroplast genomes of ten wild Fragaria species native to China were sequenced. Phylogenetic analysis clustered Fragaria species into two clades: The south clade (F. iinumae, F. chinensis, F. pentaphylla, F. nilgerrensis, F. daltoniana, F. corymbosa, F. moupinensis, F. tibetica, F. nipponica, F. gracilis, and F. nubicola and north clade (F. viridis, F. orientalis, F. moschata, F. mandshurica, F. vesca, F. chiloensis, F. virginiana, and F. × ananassa), while F. iinumae is the oldest extant species. Molecular clock analysis suggested present Fragaria species share a common ancestor 3.57 million years ago (Ma), F. moschata and octoploid species evolve 0.89 and 0.97 Ma, respectively, but F. moschata be not directly involved in current octoploid species formation. Drastic global temperature change since the Palaeocene-Eocene, approx. 55 Ma, especially during uplifting of the Qinghai-Tibet plateau and quaternary glaciation may have driven the formation of Fragaria, separation of two groups and polyploidization.
Collapse
Affiliation(s)
- Jian Sun
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Rui Sun
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Huabo Liu
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Linlin Chang
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Shuangtao Li
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Mizhen Zhao
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, 210014 Nanjing, China
| | - Carol Shennan
- Environmental Studies, University of California Santa Cruz, 95064 Santa Cruz, CA, USA.
| | - Jiajun Lei
- Department of Horticulture, Shenyang Agricultural University, 110866 Shenyang, China
| | - Jing Dong
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Chuanfei Zhong
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Li Xue
- Department of Horticulture, Shenyang Agricultural University, 110866 Shenyang, China
| | - Yongshun Gao
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Guixia Wang
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China.
| | - Yuntao Zhang
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China.
| |
Collapse
|
506
|
Lim SY, Jang JH, Lee HJ, Park SS, Kim SR, Lee KM, Kim JK, Park H, Jung HK. Characteristics and phylogenetic analysis of the complete chloroplast genome of Paeonia japonica (Paeoniaceae). Mitochondrial DNA B Resour 2021; 6:734-735. [PMID: 33763563 PMCID: PMC7954510 DOI: 10.1080/23802359.2020.1860718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Paeonia japonica, distributed throughout Asia, is a traditional medicinal herb in Korea, with many potential beneficial effects including pain-relieving, anti-inflammatory, and anti-cancer activities. Despite its high pharmacological value, the genetic information on Paeonia japonica remains limited. In this study, the chloroplast genome of P. japonica was sequenced using next-generation sequencing (NGS) technology and genome and phylogeny were analyzed using multiple tools. The chloroplast genome of P. japonica was 152,731 bp in length with an inverted repeat region of 26,656 bp, including a large single-copy region of 84,389 bp and a small single copy region of 17,030 bp. The P. japonica chloroplast genome included 113 genes comprising 80 protein-coding genes, 27 tRNA, and 5 rRNA genes. Phylogenetic analysis indicated that P. japonica and P. obovata share a close evolutionary relationship.
Collapse
Affiliation(s)
- Seo-Young Lim
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Ji-Hun Jang
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Hyun-Ju Lee
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Seong-Sik Park
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Sun-Ra Kim
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Kyeong-Min Lee
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Ji-Kyung Kim
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Ho Park
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Ho-Kyung Jung
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| |
Collapse
|
507
|
Xu L, Cao Y, Yang P, Ming J. The complete plastid genome of Lilium regale E.H.Wilson. Mitochondrial DNA B Resour 2021; 6:806-807. [PMID: 33763585 PMCID: PMC7954476 DOI: 10.1080/23802359.2021.1882913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lilium regale E.H.Wilson is a native lily species in western Sichuan of China and an important resource for lily breeding. In this study, the plastid genome of L. regale was assembled de novo using the next-generation sequencing data. The plastid genome of L. regale was 152,998 bp in length, with a typical quadripartite circle structure consisting of a small single-copy region of 17,529 bp, a large single-copy region of 82,375 bp, and a pair of inverted repeats of 26,547 bp each. A total of 137 different genes were predicted, including 84 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes, and 7 pseudogenes. The overall GC content of the plastid genome was 36.98%. Phylogenetic analysis revealed that L. regale is most closely related to Lilium leucanthum.
Collapse
Affiliation(s)
- Leifeng Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuwei Cao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Panpan Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Ming
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
508
|
Fang B, Xu Y, Yu J. The complete chloroplast genome sequence of Prunus salicina ‘Wushan plum’. Mitochondrial DNA B Resour 2021; 6:1243-1244. [PMID: 33829095 PMCID: PMC8008876 DOI: 10.1080/23802359.2021.1904802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Prunus salicina ‘Wushan plum’ is a local economic fruit crop. In this study, we reported the complete chloroplast genome sequence of P. salicina ‘Wushan plum’. The genome has a circular structure of 157,921 bp containing a large single-copy region (LSC) of 86,184 bp, a small copy region (SSC) of 19,031 bp, and two inverted repeats (IR) of 26,353 bp by each. It harbors 110 unique genes, including 78 protein-coding genes, 4 ribosomal RNA genes, and 28 transfer RNA genes. The phylogenomic analysis shows that P. salicina ‘Wushan plum’ is clustered with Prunus salicina.
Collapse
Affiliation(s)
- Bo Fang
- Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Yicen Xu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| |
Collapse
|
509
|
Yao JF, Zhang XF, Zhu ZX, Wang HF. Complete plastome sequence of Vernicia Montana Lour. (Euphorbiaceae): a deciduous tree species in southeast Asia. Mitochondrial DNA B Resour 2021; 6:1075-1076. [PMID: 33796744 PMCID: PMC7995848 DOI: 10.1080/23802359.2021.1899864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Vernicia montana Lour. is a deciduous tree species belonging to the family of Euphorbiaceae, distributed in southeast Asia. Here, we report and characterize the complete plastome of Vernicia montana Lour. The complete plastome is of 164,506 bp in length with a typical structure and gene content of angiosperm plastome, including two inverted repeat (IRs) regions of 27,965 bp, a large single-copy (LSC) region of 91,427 bp and a small single-copy (SSC) region of 17,149 bp. The plastome contains 130 genes, consisting of 81 protein-coding genes (six of which are repetitive in IR), 38 tRNA genes (seven of which are repetitive in IR), seven rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA) (three of which are repetitive in the IR), and four pseudogenes. The overall G/C content in the plastome of Vernicia montana Lour. is 35.8%. The complete plastome sequence of montana Lour. will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Euphorbiaceae.
Collapse
Affiliation(s)
- Jian-Feng Yao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Xiao-Feng Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| |
Collapse
|
510
|
Wang X, Zhang X, Li D, Hou J, Sheng L, Sun G, Zhu L, Chen Z. The complete chloroplast genome of Viburnum dilatatum (Adoxaceae). Mitochondrial DNA B Resour 2021; 6:997-998. [PMID: 33796714 PMCID: PMC7995874 DOI: 10.1080/23802359.2021.1891988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Viburnum dilatatum Thunb. is a large deciduous tree of Adoxaceae. In this study, the chloroplast genome sequence of V. dilatatum is 158,392 bp, consisting of a large single-copy (LSC) region with 87,070 bp, a small single-copy (SSC) region with 18,242 bp , and two inverted repeat (IR) regions with 26,540 bp. The GC content in the chloroplast genome of C. julianae is 38.1%. The chloroplast genome of V. dilatatum contains 126 genes, including 83 protein-coding genes, 39 tRNA genes, and 4 rRNA genes. Phylogenetic tree showed that V. dilatatum was clustered with V. utile.
Collapse
Affiliation(s)
- Xudong Wang
- School of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, PR China
| | - Xueqing Zhang
- China Construction Seventh Engineering Division Corp. Ltd, Zhengzhou, PR China
| | - Daojie Li
- China Construction Seventh Engineering Division Corp. Ltd, Zhengzhou, PR China
| | - Junshan Hou
- China Construction Seventh Engineering Division Corp. Ltd, Zhengzhou, PR China
| | - Leijie Sheng
- China Construction Seventh Engineering Division Corp. Ltd, Zhengzhou, PR China
| | - Guoyu Sun
- China Construction Seventh Engineering Division Corp. Ltd, Zhengzhou, PR China
| | - Longfei Zhu
- China Construction Seventh Engineering Division Corp. Ltd, Zhengzhou, PR China
| | - Zhuoqin Chen
- China Construction Seventh Engineering Division Corp. Ltd, Zhengzhou, PR China
| |
Collapse
|
511
|
Guo X, He L. The complete chloroplast genome of Ophiopogon bodinieri Levl. and its phylogenetic position. Mitochondrial DNA B Resour 2021; 6:1022-1024. [PMID: 33796725 PMCID: PMC7995887 DOI: 10.1080/23802359.2021.1895000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Ophiopogon bodinieri Levl. is an important turfgrass and ornamental cover plants which is widely used in urban garden construction in southern China. In this study, we sequenced the complete chloroplast genome of O.bodinieri on the Illumina HiSeq Platform. The chloroplast genome is 157,078 bp in length, with a typical quadripartite structure and consisting of a pair of inverted repeat (IR) regions (26,477 bp) separated by a large single copy (LSC) region (85,374 bp) and a small single copy (SSC) region (18,750 bp). It was predicted to contain a total of 132 genes, with an overall GC content of 38.63%. Phylogenetic analysis suggested O.bodinieri is closely relatedto Goodyera velutina, Anoectochilus emeiensis and Ludisia discolor.
Collapse
Affiliation(s)
- Xinchun Guo
- Key Laboratory of Poyang Lake Basin Agricultural Resource and Ecology of Jiangxi Province, College of Land Resource and Environment, Jiangxi Agricultural University, Nanchang, China
| | - Li He
- College of Life Science, Jinggangshan University, Ji’an, China
| |
Collapse
|
512
|
Gao LQ, Li YL, Zhang WG, Yang GY. The complete chloroplast genome of Phyllostachys edulis f. curviculmis (Bambusoideae): a newly ornamental bamboo endemic to China. Mitochondrial DNA B Resour 2021; 6:941-942. [PMID: 33796691 PMCID: PMC7971251 DOI: 10.1080/23802359.2021.1888663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Phyllostachys edulis (Bambusoideae) is a temperate woody bamboo with a long history of cultivation in China. Phyllostachys edulis f. curviculmis is the latest new forma that repored in 2018. Here, we performed the complete chloroplast genomes of P. edulis and P. edulis f. curviculmis using genome skimming. The length of two chloroplast genomes was 139,678 bp, and their GC contents were 38.9%. The sequences of each species contained 132 unique genes, including 39 tRNA, eight rRNA, and 85 protein-coding genes. Moreover, in subspecies-level, P. edulis ‘Pachyloen’ and P. edulis f. curviculmis are identical to P. edulis in the terms of chloroplast genome size, structure, and composition, further indicating their affinity.
Collapse
Affiliation(s)
- Li-Qin Gao
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, P. R. China
- Nanchang Business College, Jiangxi Agricultural University, Gongqingcheng, P. R. China
| | - Yong-Long Li
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Wen-Gen Zhang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Guang-Yao Yang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, P. R. China
| |
Collapse
|
513
|
Park SS, Jang JH, Lee KM, Lim SY, Seo JW, Kim SR, Jung HK, Cho HW. The complete chloroplast genome of Bupleurum euphorbioides, a traditional medicinal plant. Mitochondrial DNA B Resour 2021; 6:870-871. [PMID: 33796662 PMCID: PMC7971250 DOI: 10.1080/23802359.2021.1886006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bupleurum euphorbioides is a rare native plant attributed with analgesic, gallbladder-supportive, and other functions in China and the Republic of Korea. However, the complete chloroplast genome sequence of the native plant B. euphorbioides has not been determined. In this study, we sequenced the complete chloroplast genome sequence, and examined the molecular phylogeny and genetic information of B. euphorbioides. The total chloroplast genome of B. euphorbioides was 154,871 bp in length with a large single-copy region (85,089 bp), small single-copy region (17,714 bp), and pair of inverted repeats regions (26,034 bp). The chloroplast genome encoded a total of 176 genes, including 131 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic tree indicated that B. euphorbioides was most closely related to B. latissimum.
Collapse
Affiliation(s)
- Seong-Sik Park
- National Development Institute of Korean Medicine, Jangheung, South Korea
| | - Ji-Hun Jang
- National Development Institute of Korean Medicine, Jangheung, South Korea
| | - Kyung-Min Lee
- National Development Institute of Korean Medicine, Jangheung, South Korea
| | - Seo-Young Lim
- National Development Institute of Korean Medicine, Jangheung, South Korea
| | - Jae-Wan Seo
- National Development Institute of Korean Medicine, Jangheung, South Korea
| | - Sun-Ra Kim
- National Development Institute of Korean Medicine, Jangheung, South Korea
| | - Ho-Kyung Jung
- National Development Institute of Korean Medicine, Jangheung, South Korea
| | - Hyun-Woo Cho
- National Development Institute of Korean Medicine, Jangheung, South Korea
| |
Collapse
|
514
|
Wang H, Wang Y, Cheng H, Xue M, Wang J, Yue Z. The complete chloroplast genome of Schizonepeta tenuifolia (Benth.) Briq., a traditional Chinese herb. Mitochondrial DNA B Resour 2021; 6:907-908. [PMID: 33796676 PMCID: PMC7971225 DOI: 10.1080/23802359.2021.1886884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Schizonepeta tenuifolia (Benth.) Briq. is a traditional Chinese medicinal herb. The complete chloroplast genome sequence of S. tenuifolia was obtained by high-throughput sequencing platform. The chloroplast genome of S. tenuifolia is a circular form of 151,254 bp in length, with an average GC content of 37.85%. The genome contains a set of 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete chloroplast genome sequences indicates that S. tenuifolia has a close relationship with Dracocephalum palmatum. This study provides a molecular basis for the classification of S. tenuifolia.
Collapse
Affiliation(s)
- Hanping Wang
- College of Medicine, Xi'an International University, Xi’an, China
| | - Yan Wang
- Microbiology Institute of Shaanxi, Xi’an, China
| | - Huyin Cheng
- Shaanxi University of Chinese Medicine, Xi Xian New Area, China
| | - Mengju Xue
- College of Medicine, Xi'an International University, Xi’an, China
| | - Jinpei Wang
- College of Medicine, Xi'an International University, Xi’an, China
| | - Zhiyong Yue
- College of Medicine, Xi'an International University, Xi’an, China
| |
Collapse
|
515
|
Yu T, Ren SY, Wang XR, Xu L, Xu JH, Ding GT, Tang LM, Zhang DX, Guan WB. The complete chloroplast genome sequences of Dolichandrone spathacea (L. F.) K. Schum., a semi-mangrove plant. Mitochondrial DNA B Resour 2021; 6:1164-1165. [PMID: 33829081 PMCID: PMC8008931 DOI: 10.1080/23802359.2021.1901619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Ting Yu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, PR China
| | - Si-Yu Ren
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, PR China
| | - Xin-Rui Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, PR China
| | - Li Xu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, PR China
| | - Jiu-Heng Xu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, PR China
| | - Gong-Tao Ding
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, PR China
| | - Li-Ming Tang
- Forestry Department of Guangxi, Nanning, PR China;
| | - Dong-Xu Zhang
- Protected Agricultural Technology Development Center, Shanxi Datong University, Shanxi, PR China
| | - Wen-Bin Guan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, PR China
| |
Collapse
|
516
|
Han F, Li J, Yuan J, Yu J. The complete chloroplast genome sequence of Ficus beipeiensis (Moraceae), an endemic and endangered plant in China. Mitochondrial DNA B Resour 2021; 6:604-605. [PMID: 33659705 PMCID: PMC7899700 DOI: 10.1080/23802359.2020.1861556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Ficus beipeiensis S.S.Chang is an evergreen plant of Ficus from the family Moraceae. This is an endangered species endemic to China. In terms of economic value, F. beipeiensis are used as a native plant resource of urban landscaping in Chongqing, China. Here, we sequenced, assembled and annotated the chloroplast (cp) genome of F. beipeiensis, and aim to provide genetic resources for this endangered species. The length of cp genome was 160,595 bp, with a large single-copy region (LSC) of 88,683 bp and a small single-copy region (SSC) of 20,160 bp separated by a pair of inverted repeats (IRs) of 25,876 bp. It encodes 110 unique genes, including 76 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Besides, we reconstructed the phylogeny of Moraceae based on the whole cp genome sequences data set. Phylogenetic analysis shows that all analyzed Ficus species are clustered and form a monophyletic group. Antiaris is a sister group to Ficus. In our maximum likelihood (ML) tree, F. beipeiensis is closely related to F. racemose.
Collapse
Affiliation(s)
- Fang Han
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Jing Yuan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China.,Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| |
Collapse
|
517
|
Liu J, Mu W, Shi M, Zhao Q, Kong W, Xie H, Shi L. The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding. Front Pharmacol 2021; 12:607200. [PMID: 33664667 PMCID: PMC7921783 DOI: 10.3389/fphar.2021.607200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. & Hook. f. ex Franch. & Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.
Collapse
Affiliation(s)
- Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China.,Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Weishan Mu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Mengmeng Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Qing Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hongbo Xie
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| |
Collapse
|
518
|
Wang ZF, Liu TH, Cao HL. The complete chloroplast genome sequence of Begonia coptidifolia. Mitochondrial DNA B Resour 2021; 6:548-549. [PMID: 33628923 PMCID: PMC7889152 DOI: 10.1080/23802359.2021.1872434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/02/2021] [Indexed: 11/25/2022] Open
Abstract
Begonia (Begoniaceae) is a large, pantropically distributed genus, comprising more than 1900 species. Due to poorly available genome resources, the phylogeny of this species-rich genus is still challenged. B. coptidifolia is a newly discovered species of restricted distribution in Southern China, and its genetic relationship with the other Begonia species has not been reported. Therefore, in this study, we report for the first time its chloroplast genome for future phylogenetic analysis. The circular chloroplast genome of B. coptidifolia is 169,412 bp in length, with a GC content of 35.57%. Its large single-copy region is 75,937 bp, a small single-copy region is 18,362 bp, and two inverted repeat regions are 37,556 bp and 37,557 bp, respectively. The genome encodes 82 protein-coding genes, 8 ribosomal RNA genes, and 40 transfer RNA genes. Phylogenetic analysis indicated that B. coptidifolia is genetically closest to B. pulchrifolia.
Collapse
Affiliation(s)
- Zheng-Feng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ting-Hong Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Lin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| |
Collapse
|
519
|
Yan WJ, Yang TG, Qin R, Liu H. Complete chloroplast genome of Angelica keiskei (Umbelliferae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:536-537. [PMID: 33628918 PMCID: PMC7889118 DOI: 10.1080/23802359.2021.1873711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Angelica keiskei (Miq.) Koidz. is a perennial herbaceous plant belonging to the genus Angelica, Umbelliferae. As a plant with dual-purpose as food and medicine, it has the potential for the future development of high-value functional products. The complete chloroplast genome has a total size of 147,007 bp, consisting of two inverted repeats (IR, 18,508 bp, each), and separated by a large single-copy region (LSC, 92,415 bp) and a small single-copy region (SSC, 17,576 bp). Further annotation revealed the chloroplast genome contains 128 genes, including 84 protein-coding genes (80 PCG species), 36 tRNA genes (30 tRNA species), and 8 rRNA genes (4 rRNA species). A total of 83 simple sequence repeats (SSRs) were identified in the chloroplast genome. This chloroplast genome resource will be useful for the study of the evolution and genetic diversity of Angelica keiskei in the future.
Collapse
Affiliation(s)
- Wen-Jie Yan
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Tian-Ge Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities, Wuhan, China
| |
Collapse
|
520
|
Wang X, Liu H, Jing S, Liu Y. The complete chloroplast genome of Celtis julianae (Ulmaceae). Mitochondrial DNA B Resour 2021; 6:517-518. [PMID: 33628910 PMCID: PMC7889233 DOI: 10.1080/23802359.2021.1872445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/02/2021] [Indexed: 10/26/2022] Open
Abstract
Celtis julianae C.K. Schneid. is a large deciduous tree of Ulmaceae. In this study, the chloroplast genome sequence of C. julianae was 159,064 bp in length, consisting of a large single-copy (LSC) region with 86,139 bp, a small single-copy (SSC) region with 19,137 bp, and two inverted repeat regions (IRs) with 26,894 bp. The GC content in the chloroplast genome of C. julianae was 36.3%. The chloroplast genome of C. julianae contained 127 genes, including 86 protein-coding genes, 37 tRNA genes, and four rRNA genes. Phylogenetic tree showed that C. julianae was clustered with C. tetrandra.
Collapse
Affiliation(s)
- Xudong Wang
- School of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - Huadong Liu
- China Construction Seventh Engineering Division Corp. Ltd., Zhengzhou, China
| | - Sen Jing
- China Construction Seventh Engineering Division Corp. Ltd., Zhengzhou, China
| | - Yuhong Liu
- China Construction Seventh Engineering Division Corp. Ltd., Zhengzhou, China
| |
Collapse
|
521
|
Niu YF, Ni SB, Liu SH, Liu J. The complete chloroplast genome of Passiflora caerulea, a tropical fruit with a distinctive aroma. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:488-490. [PMID: 33628899 PMCID: PMC7889125 DOI: 10.1080/23802359.2021.1872442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Passiflora caerulea is native to brazil. In recent years, the edible, medicinal, and ornamental value of P. caerulea has stimulated its wide cultivation in Southeast Asian countries, especially China. Because the chloroplast genome is rich with information about the species evolution as well as its genetic relationship to other species, the P. caerulea chloroplast genome was sequenced, assembled, and annotated in this study. The P. caerulea chloroplast genome is 151,362 bp in total with an overall GC content of 37.03%. It has a quadripartite structure, includes a large single-copy region (LSC, 85,623 bp), a small single-copy region (SSC, 13,397 bp), and two inverted repeat regions (IRa and IRb, 26,180 bp combined). There are 131 genes in the P. caerulea chloroplast genome, including 79 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 7 pseudogenes. Phylogenetic analysis of 29 Passiflora spp. showed that P. caerulea is most closely related to P. edulis. These results provide a considerable foundation for P. caerulea conservation genetics research.
Collapse
Affiliation(s)
- Ying-Feng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Shu-Bang Ni
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Shi-Hong Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| |
Collapse
|
522
|
Jin Z, Jiang W, Yi D, Pang Y. The complete chloroplast genome sequence of Sainfoin ( Onobrychis viciifolia). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:496-498. [PMID: 33628902 PMCID: PMC7889117 DOI: 10.1080/23802359.2020.1871439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sainfoin (Onobrychis viciifolia) is one of the dominant legume forages distributed in Northern China. In our study, we assembled and annotated the structure of the complete chloroplast genome of sainfoin. The length of the circular genome is 122,102 bp. It contains 115 genes, including 79 protein-coding genes (68.7%), 31 tRNA genes (26.96%) and 5 rRNA genes (4.35%). The GC content of the total chloroplast genome of sainfoin is 34.58%. We construct the phylogenetic relationships between the chloroplast genome of sainfoin and the other 16 species by the Maximum likelihood (ML), and found sainfoin is most closely related to Hedysarum petrovii and Hedysarum taipeicum.
Collapse
Affiliation(s)
- Zhongzhiyue Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbo Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengxia Yi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhen Pang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
523
|
He Y, Wang R, Gai X, Lin P, Li Y, Wang J. The complete chloroplast genome of Thalictrum baicalense Turcz. ex Ledeb. Mitochondrial DNA B Resour 2021; 6:437-438. [PMID: 33628881 PMCID: PMC7889159 DOI: 10.1080/23802359.2020.1870896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Thalictrum baicalense Turcz. ex Ledeb. is a well-known herbaceous perennid that has been used as a traditional medicine to treat influenza, hepatitis, and detoxfeaction. In this study, we release and detail the complete chloroplast genome sequences of T. baicalense. The whole chloroplast genome was 155,859 bp in length and comprised 130 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes. The T. baicalense chloroplast genome had a GC content of 38.39%. The phylogenetic relationships inferred that T. baicalense, T. tenue, T. minus and T. petaloideum are closely related to each other within the genus Thalictrum.
Collapse
Affiliation(s)
- Yanfeng He
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Qinghai Nationalities University, Xining, China.,Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
| | - Ruinan Wang
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Qinghai Nationalities University, Xining, China.,Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
| | - Xiangyun Gai
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Qinghai Nationalities University, Xining, China.,Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
| | - Pengcheng Lin
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Qinghai Nationalities University, Xining, China.,Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, Xining, China
| | - Yongxi Li
- The College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China
| | - Jiuli Wang
- The College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China
| |
Collapse
|
524
|
Zheng F, Chen JB, Liu WR, Wang M. The complete chloroplast genome of an endangered species Apostasia ramifera (Orchidaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:470-471. [PMID: 33628892 PMCID: PMC7889234 DOI: 10.1080/23802359.2021.1872429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Apostasia ramifera S. C. Chen & K. Y. Lang 1986 is a Chinese endemic and endangered orchid. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of A. ramifera. The cp genome was 157,518 bp in length with a typical quadripartite structure, which was comprised of one large single-copy region (LSC, 86,353 bp) and one small single-copy region (SSC, 16,445 bp) separated by two inverted repeat regions (IRs, 27,360 bp). The cp genome encoded 133 genes, which included 87 protein-coding genes, 38 tRNAs and eight rRNAs. The average GC content of the genome is 35.8%. The phylogenetic analysis showed that A. ramifera was sister with A. wallichii and then nested in the other Apostasia species.
Collapse
Affiliation(s)
- Fang Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China;,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Jian-Bing Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China;,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Wei-Rong Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China;,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Meng Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China;,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| |
Collapse
|
525
|
Zhang G, Wang H, Jiang J, Wang Q, Li B, Shi L, Wei J. The complete chloroplast genome of Bupleurum marginatum var. stenophyllum (H. Wolff) Shan & Yin Li (Apiaceae), a new substitution for Chinese medicinal material, Bupleuri Radix (Chai hu). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:441-443. [PMID: 33659702 PMCID: PMC7872558 DOI: 10.1080/23802359.2020.1870899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The root of Bupleurum marginatum var. stenophyllum (H. Wolff) Shan & Yin Li (Apiaceae), a new substitution for the popular Chinese medicinal material, Bupleuri Radix (Chai hu), is not easily distinguishable via traditional methods. The complete chloroplast genome sequence of B. marginatum var. stenophyllum was characterized using next-generation sequencing and the de novo assembly method. The complete genome was 155,576 bp in length and contained two inverted repeat (IR) regions of 26,311 bp, a large single-copy (LSC) region of 85,351 bp, and a small single-copy (SSC) region of 17,603 bp. It encoded 113 unique genes consisting of 79 protein-coding genes (PCGs), 30 transfer RNA genes, and four ribosomal RNA genes. Importantly, three genes (petB, petD and rps16) with small exon, and one trans-splicing gene (rps12) were correctly annotated. The overall GC content of the B. marginatum var. stenophyllum chloroplast genome is 37.7%. The phylogenetic analyses indicated that B. marginatum var. stenophyllum was closely related to B. marginatum. Moreover, many genetic information sites were available for distinguishing B. marginatum var. stenophyllum from the official ‘Chai hu’ plant sources, B. scorzonerifolium Willd. and B. chinense DC.
Collapse
Affiliation(s)
- Gaixia Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Jiemei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiuling Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoli Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
526
|
Fu LF, Zhang ZX. Complete chloroplast genome sequence of Procris crenata C.B.Rob (Urticaceae). Mitochondrial DNA B Resour 2021; 6:458-459. [PMID: 33628887 PMCID: PMC7889184 DOI: 10.1080/23802359.2020.1871436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/20/2020] [Indexed: 11/17/2022] Open
Abstract
The complete chloroplast (cp) genome of Procris crenata C.B.Rob was reported. The cp genome was 154,124 bp in length and contained two inverted repeats (IRs) of 25,626 bp, which were separated by large single-copy and small single-copy of 84,599 bp and 18,273 bp, respectively. The GC content was 36.5%. A total of 113 functional genes were encoded, comprising 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. This is the first reported plastid genome in Procris (Urticaceae), which will be useful data for resolving the relationship within the family.
Collapse
Affiliation(s)
- Long-Fei Fu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing, China
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Zhi-Xiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing, China
| |
Collapse
|
527
|
Wang ZF, Qin QM, Cao HL. The complete chloroplast genome of Aganope dinghuensis (Fabaceae). Mitochondrial DNA B Resour 2021; 6:460-461. [PMID: 33628888 PMCID: PMC7889246 DOI: 10.1080/23802359.2020.1871437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/19/2020] [Indexed: 11/05/2022] Open
Abstract
Aganope is a genus in the family Fabaceae, with only 11 species. They are distributed throughout Asia and Africa. Aganope dinghuensis, a newly reported species, is native to China with a restricted distribution. We, therefore, report its complete chloroplast genome for better future conservation. The chloroplast genome of A. dinghuensis is 143,690 bp, with a GC content of 35.32%. In the genome, a pair of inverted repeat regions of 13,015 bp each, a large single-copy region of 98,824 bp, and a small single-copy region of 18,836 bp were identified. Genome annotation identified 115 genes, comprising 74 protein-coding genes, 8 ribosomal RNA genes, and 33 transfer RNA genes. Repeat analysis indicates that the chloroplast genome of A. dinghuensis contains 126 simple sequence repeats (SSR), of which the majority are A/T mononucleotides. Phylogenetic analysis revealed that A. dinghuensis is a sister to the clade that includes Indigofera tinctoria, Desmodium uncinatum, Sarcodum scandens, Wisteria brachybotrys, and Callerya nitida.
Collapse
Affiliation(s)
- Zheng-Feng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Qiao-Mei Qin
- Guangdong Eco-engineering Polytechnic, Guangzhou, China
| | - Hong-Lin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| |
Collapse
|
528
|
Sima YK, Wu T, Chen SY, Ma HF, Hao JB, Fu YP, Zhu YF. The complete chloroplast genome sequence of Michelia balansae var. balansae (Aug. Candolle) Dandy, a timber and spices species in Magnoliaceae. Mitochondrial DNA B Resour 2021; 6:465-467. [PMID: 33628890 PMCID: PMC7889223 DOI: 10.1080/23802359.2021.1872427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/02/2021] [Indexed: 10/28/2022] Open
Abstract
Michelia balansae var. balansae (Aug. Candolle) Dandy is a timber and spices species in Magnoliaceae, native to China and Vietnam. In this paper, the complete chloroplast genome (cpDNA) and basic annotated information were reported and its phylogenetic relationship with other species in Magnoliaceae was analyzed. The size of chloroplast genome of M. balansae var. balansae is 160,134 bp, which exhibited a typical quadripartite structure comprising a large single-copy (LSC) region of 88,161 bp and a small single-copy (SSC) region of 18,845 bp separated by a pair identical inverted repeat regions (IRs) of 26,564 bp each. The chloroplast genome contains 131 genes, including 86 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that M. balansae var. balansae is most affinal to M. montana and they form a nomophyletic group with other 14 Michelia species. This Michelia clade is sister to the Aromadendron clade with high support. All genera mentioned in this analysis are nomophyletic under the system of Magnoliaceae by Sima and Lu.
Collapse
Affiliation(s)
- Yong-Kang Sima
- Yunnan Academy of Forestry & Grassland Science, Kunming, Yunnan, China
| | - Tao Wu
- Yunnan Academy of Forestry & Grassland Science, Kunming, Yunnan, China
| | - Shao-Yu Chen
- Yunnan Academy of Forestry & Grassland Science, Kunming, Yunnan, China
| | - Hui-Fen Ma
- Yunnan Academy of Forestry & Grassland Science, Kunming, Yunnan, China
| | - Jia-Bo Hao
- Yunnan Academy of Forestry & Grassland Science, Kunming, Yunnan, China
| | - Yu-Pin Fu
- Yunnan Academy of Forestry & Grassland Science, Kunming, Yunnan, China
| | - Yun-Feng Zhu
- Yunnan Academy of Forestry & Grassland Science, Kunming, Yunnan, China
| |
Collapse
|
529
|
Qu WR, Jiao PP, Jiang X, Zhang SH, Yang TG, Li ZJ, Wu ZH. Complete chloroplast genome sequence of Sphaerophysa salsula (Leguminosae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:399-401. [PMID: 33659692 PMCID: PMC7872530 DOI: 10.1080/23802359.2020.1869618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Sphaerophysa salsula (Pall.) DC. is a perennial herbaceous plant belonging to the genus Sphaerophysa, Galegeae, Leguminosae, and is mainly distributed in dry areas in Central Asia and Northwest China. The complete chloroplast genome with a total size of 123,300 bp was reported in this study. Further annotation revealed the chloroplast genome contains 109 genes, including 76 protein coding genes, 29 tRNA genes, and four rRNA genes. A total of 107 simple sequence repeats (SSRs) from mononucleotide to hexa-nucleotide repeat motif were identified in the chloroplast genome. This information will be useful for study on the evolution and genetic diversity of Sphaerophysa salsula in the future.
Collapse
Affiliation(s)
- Wen-Rui Qu
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.,College of Life Science, Tarim University, Alar, China
| | - Pei-Pei Jiao
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.,College of Life Science, Tarim University, Alar, China.,College of Life Science and Technology of Huazhong Agricultural University, Wuhan, China
| | - Xi Jiang
- College of Plant Science, Tarim University, Alar, China
| | - Shan-He Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.,College of Life Science, Tarim University, Alar, China
| | - Tian-Ge Yang
- College of Life Sciences, Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, China
| | - Zhi-Jun Li
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.,College of Life Science, Tarim University, Alar, China
| | - Zhi-Hua Wu
- College of Life Sciences, Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, China
| |
Collapse
|
530
|
Jiang ZB, Zhai JT, Jiao PP, Yang TG, Wu ZH, Li ZJ. Complete chloroplast genome sequence of Populus euphratica from PacBio Sequel platform. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:378-380. [PMID: 33659684 PMCID: PMC7872525 DOI: 10.1080/23802359.2020.1869605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Populus euphratica Oliv., one of tall arbors growing in desert areas, has great stress resistance. The complete chloroplast genome was reported in this study using the PacBio Sequel Platform. The chloroplast genome with a total size of 157,881 bp consisted of two inverted repeats (IRs) (27,666 bp) separated by a large single-copy region (85,906 bp) and a small single-copy region (16,643 bp). Further annotation revealed the chloroplast genome contains 111 genes, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. The information of the chloroplast genome will be useful for study on the evolution of P. euphratica in the future.
Collapse
Affiliation(s)
- Zhen-Bo Jiang
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, PR China.,Desert Poplar Research Center, Tarim University, Alar, PR China.,College of Life Science, Tarim University, Alar, PR China
| | - Jun-Tuan Zhai
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, PR China.,Desert Poplar Research Center, Tarim University, Alar, PR China.,College of Life Science, Tarim University, Alar, PR China
| | - Pei-Pei Jiao
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, PR China.,Desert Poplar Research Center, Tarim University, Alar, PR China.,College of Life Science, Tarim University, Alar, PR China
| | - Tian-Ge Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, PR China
| | - Zhi-Hua Wu
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, PR China.,Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, PR China
| | - Zhi-Jun Li
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, PR China.,Desert Poplar Research Center, Tarim University, Alar, PR China.,College of Life Science, Tarim University, Alar, PR China
| |
Collapse
|
531
|
Jiao PP, Jiang X, Qu WR, Zhang SH, Yang TG, Wu ZH. Complete chloroplast genome sequence of Thermopsis turkestanica Gand. (Leguminosae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:335-336. [PMID: 33659669 PMCID: PMC7872544 DOI: 10.1080/23802359.2020.1867017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Thermopsis turkestanica Gand. is a perennial herbaceous plant belonging to the genus Thermopsis, Leguminosae, and is mainly distributed in dry areas. Most of the species in this genus have high medicinal value. The complete chloroplast genome was reported in this study. The chloroplast genome with a total size of 149,551 bp consists of two inverted repeats (IRs, 24,159 bp) separated by a large single-copy region (LSC, 83,692 bp) and a small single-copy region (SSC, 17,541 bp). Further annotation revealed the chloroplast genome contains 110 genes, including 77 protein coding genes, 29 tRNA genes, and four rRNA genes. This information will be useful for study on the evolution and genetic diversity of Thermopsis turkestanica in the future.
Collapse
Affiliation(s)
- Pei-Pei Jiao
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.,College of Life Science, Tarim University, Alar, China.,College of Life Science and Technology of Huazhong Agricultural University, Wuhan, China
| | - Xi Jiang
- College of Plant Science, Tarim University, Alar, China
| | - Wen-Rui Qu
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.,College of Life Science, Tarim University, Alar, China
| | - Shan-He Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.,College of Life Science, Tarim University, Alar, China
| | - Tian-Ge Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Zhi-Hua Wu
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Xinjiang Production and Construction Corps, Tarim University, Alar, China.,Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| |
Collapse
|
532
|
Zhang Y, Zhang R, Deng C, Yang J, Deng G. The complete chloroplast genome sequence of Ficus altissima (Moraceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:299-301. [PMID: 33659654 PMCID: PMC7872538 DOI: 10.1080/23802359.2020.1863874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ficus altissima plays an important role on biodiversity in tropical forests. In this study, the complete chloroplast genome sequence and the genome features of F. altissima were analyzed using the Illumina NovaSeq platform. The whole chloroplast genome sequence of F. altissima is 160,251 including a large single-copy region (LSC, 88,468 bp), a small single-copy region (SSC, 20,009 bp), and a pair of repeat regions (IRs, 25,887 bp, each). Further gene annotation revealed the chloroplast genome contains 124 genes, including 79 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 82 simple sequence repeats (SSRs) were identified in the chloroplast genome. Phylogenetic development was analyzed based on F. altissima with other species of Moraceae. This information will be useful for study on the evolution and genetic diversity of F. altissima in the future.
Collapse
Affiliation(s)
- Yuan Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China.,College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Ruli Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China.,College of Forestry, Southwest Forestry University, Kunming, China
| | - Chongli Deng
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China.,College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Junwen Yang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China.,College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Guobin Deng
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China.,College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| |
Collapse
|
533
|
Dong F, Lin Z, Lin J, Ming R, Zhang W. Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. PLANTS 2021; 10:plants10020283. [PMID: 33540810 PMCID: PMC7912957 DOI: 10.3390/plants10020283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023]
Abstract
Rambutan (Nephelium lappaceum L.) is an important fruit tree that belongs to the family Sapindaceae and is widely cultivated in Southeast Asia. We sequenced its chloroplast genome for the first time and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding genes, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis suggested that ccsA, clpP, rpoA, rps12, psbJ and rps19 were under positive selection, which might reflect specific adaptations of N. lappaceum to its particular living environment. Comparative chloroplast genome analyses from nine species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the large single-copy (LSC) and small single-copy (SSC) regions. The phylogenetic analysis showed that N. lappaceum chloroplast genome has the closest relationship with that of Pometia tomentosa. The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.
Collapse
Affiliation(s)
- Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Zhicong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
| | - Wenping Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
| |
Collapse
|
534
|
Li Y, Zhou M, Wang L, Wang J. The characteristics of the chloroplast genome of the Michelia chartacea (Magnoliaceae). Mitochondrial DNA B Resour 2021; 6:493-495. [PMID: 33628901 PMCID: PMC7889203 DOI: 10.1080/23802359.2020.1871432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this study, the complete chloroplast genome of Michelia chartacea B. L. Chen & S. C. Yang was 160,138 bp in length. It includes a large single-copy (LSC) region of 88,164 bp, a small single-copy region (SSC) of 18,824 bp, and with a pair of inverted repeats (IRs) of 26,575 bp. The GC content in the chloroplast genome was 39.23%. In total, 130 genes in the chloroplast genome of Michelia chartacea were annotated, including 83 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that M. chartacea was closely related with M. martini and M. maudiae, forming a clade included in Michelia.
Collapse
Affiliation(s)
- Yanyan Li
- Pingdingshan University, Pingdingshan, Henan, China
| | - Meng Zhou
- Pingdingshan University, Pingdingshan, Henan, China
| | - LingMin Wang
- Pingdingshan University, Pingdingshan, Henan, China
| | - Junqing Wang
- Pingdingshan University, Pingdingshan, Henan, China
| |
Collapse
|
535
|
Yue Z, Wang Y, Zhou B, Wang H. The complete chloroplast genome of Isodon rubescens, a traditional Chinese herb. Mitochondrial DNA B Resour 2021; 6:337-338. [PMID: 33659670 PMCID: PMC7872541 DOI: 10.1080/23802359.2020.1860704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Isodon rubescens (Hemsley) H. Hara is a kind of traditional medical herb which can be used for cancer treatment. In this study, the complete chloroplast genome sequence of I. rubescens was assembled. Its complete circular chloroplast DNA length was 152,761 bp. The genome was made up of a large single-copy region of 83,655 bp, a small single-copy region of 17,660 bp, and a pair of inverted repeat regions of 25,723 bp. The genome totally encoded 129 genes, containing 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that I. rubescens had a close relationship with basil (Ocimum basilicum).
Collapse
Affiliation(s)
- Zhiyong Yue
- College of Medicine, Xi'an International University, Xi’an, Shaanxi, China
| | - Yan Wang
- Microbiology Institute of Shaanxi, Xi’an, Shaanxi, China
| | - Baozhen Zhou
- College of Medicine, Xi'an International University, Xi’an, Shaanxi, China
| | - Hanping Wang
- College of Medicine, Xi'an International University, Xi’an, Shaanxi, China
| |
Collapse
|
536
|
Zhang G, Wang H, Yin X, Kong W, Wang Q, Chen Y, Wei J, Liu J, Guo X. Characterization of the complete chloroplast genome of Bupleurum hamiltonii N. P. Balakr. (Apiaceae) and its phylogenetic implications. Mitochondrial DNA B Resour 2021; 6:447-449. [PMID: 33628883 PMCID: PMC7889215 DOI: 10.1080/23802359.2020.1870902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Bupleurum hamiltonii has a thin, wood, grayish-yellow root and is reputed to possess medicinal value. This study employs the de novo method using high-throughput sequencing data to assemble the complete chloroplast genome for this species. The total B. hamiltonii genome is 155,320 bp in length, containing a large single-copy region of 85,280 bp, a small single-copy region of 17,468 bp, a pair of inverted repeat regions of 26,286 bp, and has a GC content of 37.8%. The genome encodes 113 unique genes, of which there are 79 protein-coding, 30 tRNA, and four rRNA genes. In addition, 18 genes contained introns, petB, petD, and rpl16 are coded for by two exons, and rps12 is identified as a trans-splicing gene. Phylogenetic analysis results strongly suggest that B. hamiltonii is closely related to B. marginatum. This study provides valuable genetic information to facilitate reliable identification.
Collapse
Affiliation(s)
- Gaixia Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Xin Yin
- Chengde Academy of Agricultural and Forestry Sciences, Chengde, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiuling Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Chen
- College of Continuing Education, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Xinwei Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
537
|
Du W, Jiang W, Yi D, Pang Y. The complete chloroplast genome of Galega officinalis L. Mitochondrial DNA B Resour 2021; 6:663-665. [PMID: 33763542 PMCID: PMC7928000 DOI: 10.1080/23802359.2021.1878961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Galega officinalis L. is a perennial herb of the Fabaceae family. The flowers of G. officinalis L. are colorful and suitable for ornamental purposes. It can be used as a food complement for animals and humans, and it could promote lactation in animals and humans. In this study, we obtained the complete chloroplast genome of G. officinalis L. and found it is 125,086 bp in length. The GC content of this genome is 34.18%. Among the 112 unique genes in the chloroplast genome of G. officinalis L., 30 tRNA, 4 rRNA and 78 protein-coding genes were successfully annotated. We constructed the maximum likelihood (ML) tree with 26 species, and concluded that G. officinalis is phylogenetically closely related to the genus of Cicer, Glycine and Desmodium.
Collapse
Affiliation(s)
- Wenxuan Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbo Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengxia Yi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhen Pang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
538
|
Xu X, Wang D. Comparative Chloroplast Genomics of Corydalis Species (Papaveraceae): Evolutionary Perspectives on Their Unusual Large Scale Rearrangements. FRONTIERS IN PLANT SCIENCE 2021; 11:600354. [PMID: 33584746 PMCID: PMC7873532 DOI: 10.3389/fpls.2020.600354] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/21/2020] [Indexed: 05/08/2023]
Abstract
The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed Corydalis to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced Corydalis plastomes that represent all the three subgenera of Corydalis, we detected (1) two independent relocations of the same five genes (trnV-UAC-rbcL) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the atpH gene in Corydalis saxicola or the trnK-UUU gene in both Corydalis davidii and Corydalis hsiaowutaishanensis; (2) relocation of the rps16 gene from the LSC region to the inverted repeat (IR) region in Corydalis adunca; (3) uniform inversion of an 11-14 kb segment (ndhB-trnR-ACG) in the IR region of all the four Corydalis species (the same below); (4) expansions (>10 kb) of IR into the small single-copy (SSC) region and corresponding contractions of SSC region; and (5) extensive pseudogenizations or losses of 13 genes (accD, clpP, and 11 ndh genes). In addition, we also found that the four Corydalis plastomes exhibited elevated GC content in both gene and intergenic regions and high number of dispersed repeats. Phylogenomic analyses generated a well-supported topology that was consistent with the result of previous studies based on a few DNA markers but contradicted with the morphological character-based taxonomy to some extent. This study provided insights into the evolution of plastomes throughout the three Corydalis subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of Corydalis.
Collapse
Affiliation(s)
- Xiaodong Xu
- School of Life Sciences, Central China Normal University, Key Laboratory for Geographical Process Analysis and Simulation, Wuhan, China
| | - Dong Wang
- School of Life Sciences, Central China Normal University, Key Laboratory for Geographical Process Analysis and Simulation, Wuhan, China
- Bio-Resources Key Laboratory of Shaanxi Province, Shaanxi University of Technology, Hanzhong, China
| |
Collapse
|
539
|
Jiang W, Ma L, Yi D, Pang Y. The complete chloroplast genome sequence of Lotus corniculatus L. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:189-190. [PMID: 33537439 PMCID: PMC7832577 DOI: 10.1080/23802359.2020.1860708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Lotus corniculatus L., a member of the Fabaceae family, is considered one of the most agriculturally important forage plants, owing to its anti-bloating properties; its ability to grow in low-fertility, acidic, and high-salinity soils; and high nutritional value. In this study, we obtained the complete chloroplast genome of L. corniculatus by Illumina sequencing and GetOrganelle assembly pipeline. The whole chloroplast genome of L. corniculatus is 150,700 bp in length, and has a typical circular structure with four parts: a large single-copy region (LSC 82,117 bp), a small single-copy region (SSC 18,275 bp), and a pair of inverted repeat regions (25,154 bp for both IRa and IRb). The overall GC content is 36.03%. The plastome has 109 unique genes, consisting of 78 protein-coding genes, 27 unique tRNA gene, and 4 unique rRNA genes. Based on the protein-coding gene sequences from 17 species, we reconstructed a maximum likelihood (ML) tree. The phylogenetic result shows that L. corniculatus has a closer relationship with Lotus japonicas.
Collapse
Affiliation(s)
- Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengxia Yi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
540
|
Wang Y, Wang H, Zhou B, Yue Z. The complete chloroplast genomes of Lycopus lucidus and Agastache rugosa, two herbal species in tribe Mentheae of Lamiaceae family. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:89-90. [PMID: 33521278 PMCID: PMC7819123 DOI: 10.1080/23802359.2020.1847617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Lamiaceae is one of the largest families in the kingdom Plantae, including lots of traditional Chinese herbs. Lycopus lucidus and Agastache rugosa are two Lamiaceae species, which are most frequently used in Chinese traditional medicine. In the current study, the complete chloroplast genome sequences of two species were assembled. Their circular DNA lengths were 152,096 and 151,922 bp respectively. Both genomes were made up of a large single-copy region, a small single-copy region, and a pair of inverted repeat regions. Each genome totally encoded 133 genes, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that both species belong to the Mentheae tribe of the Lamiaceae family.
Collapse
Affiliation(s)
- Yan Wang
- Microbiology Institute of Shaanxi, Xi'an, Shaanxi, China
| | - Hanping Wang
- College of Medicine, Xi'an International University, Xi'an, Shaanxi, China
| | - Baozhen Zhou
- College of Medicine, Xi'an International University, Xi'an, Shaanxi, China
| | - Zhiyong Yue
- College of Medicine, Xi'an International University, Xi'an, Shaanxi, China
| |
Collapse
|
541
|
Cui H, Zhu Z, Lu Z, Ding Z, Zhang C, Luan F. The complete chloroplast genome sequence of the Sechium edule (Jacq.) Swartz. (Cucurbitaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:97-98. [PMID: 33490597 PMCID: PMC7808746 DOI: 10.1080/23802359.2020.1847614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sechium edule (Jacq.) Swartz is an important vegetable with both food and medicinal values. The complete chloroplast genome sequence of S. edule has been reported in this study. The total genome size is 154,558 bp in length and contains a pair of inverted repeats (IRs) of 19,128 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 98,806 and 17,496 bp, respectively. A total of 122 genes were predicted including 78 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. Further, the phylogenetic analysis confirmed that S. edule belongs to the family Cucurbitaceae. The complete chloroplast genome of S. edule would play a significant role in the development of molecular markers for plant phylogenetic and population genetic studies.
Collapse
Affiliation(s)
- Haonan Cui
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, PR China.,Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, PR China
| | - Zicheng Zhu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, PR China.,Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, PR China
| | - Zhaokai Lu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, PR China.,Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, PR China
| | - Zhuo Ding
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, PR China.,Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, PR China
| | - Chen Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, PR China.,Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, PR China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, PR China.,Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, PR China
| |
Collapse
|
542
|
Li J, Tang J, Zeng S, Han F, Yuan J, Yu J. Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea. BMC PLANT BIOLOGY 2021; 21:25. [PMID: 33413130 PMCID: PMC7792329 DOI: 10.1186/s12870-020-02793-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/09/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis. RESULTS The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. CONCLUSION Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.
Collapse
Affiliation(s)
- Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jianmin Tang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Siyuan Zeng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Fang Han
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jing Yuan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716, China.
| |
Collapse
|
543
|
Deng G, Zhang R, Yang J, Deng C, Zhang Y. Characterization of the complete chloroplast genome of medical plant Curculigo orchioides Gaertn. (Amaryllidaceae). Mitochondrial DNA B Resour 2021; 6:285-287. [PMID: 33659650 PMCID: PMC7872582 DOI: 10.1080/23802359.2020.1863875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Curculigo orchioides Gaertn. distributed in subtropical regions of Asia including southern China and India. The plant is used as a traditional medicine in China for the treatment of menorrhagia, osteoporosis, and other gynecological problems. The complete chloroplast genome was reported in this study using the Illumina NovaSeq platform. The whole genome of this species was 157,472 bp in length, with a total GC content of 37.44%. The large single copy (LSC) was 86,507 bp, the small single copy (SSC) was 16,867 bp, and both of the two inverted repeats (IRs) were 27,049 bp, respectively. A total of 132 unique genes were identified, among which are 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The phylogenetic analysis revealed that C. orchioides was highly clustered with C. capitulata. Our study will provide useful fundamental data for further phylogenetic and evolutionary studies of C. orchioides.
Collapse
Affiliation(s)
- Guobin Deng
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Ruli Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
- College of Forestry, Southwest Forestry University, Kunming, China
| | - Junwen Yang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Chongli Deng
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Yuan Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| |
Collapse
|
544
|
Wang L, Liang J, Sa W, Wang L. Sequencing and comparative analysis of the chloroplast genome of Ribes odoratum provide insights for marker development and phylogenetics in Ribes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:81-92. [PMID: 33627964 PMCID: PMC7873140 DOI: 10.1007/s12298-021-00932-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/10/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Ribes odoratum, commonly known as clove currant, is a perennial deciduous shrub noted for its long-lasting fragrant flowers and edible fruits. Owing to its ornamental values, this species has been widely used in city gardening and urban landscaping. Here, the complete cp genome of R. odoratum was de novo assembled for the first time. The plastome is 157,152 bp in length, with a GC content of 38.2%. The cp genome featured a typical quadripartite structure, consisting of a pair of inverted repeat regions of 25,961 bp, separated by a large single copy region of 86,896 bp, and a small single copy region of 18,333 bp. A total of 131 genes were annotated in the plastome, including 86 protein coding genes, 37 tRNA genes, and 8 rRNA genes. 56 SSRs were identified, among which, 82.35% were located in the intergenic regions. A strong A/T bias in base composition was observed in these cpSSRs. In addition, 49 repeats of different sizes and types were also found in the plastome. Through comparison, seven divergence hotspots were identified between the cp genomes of R. odoratum and R. fasciculatum var. chinense. Sequences of these divergent regions could be developed as potential markers for species delimitation in further studies. We re-investigated the relationship aomong 32 Saxifragales species through plastome-based phylogenywhich revealed that R. odoratum as a sister of R. fasciculatum var. chinense. Thus, our study provides genomic resources and valuable reference for marker development and phylogenomics in Ribes. SUPPLEMENTARY INFORMATION The online version of this article (10.1007/s12298-021-00932-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Le Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi’ning, 810016 China
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xi’ning, 810016 China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xi’ning, 810016 China
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xi’ning, 810016 Qinghai China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi’ning, 810016 China
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xi’ning, 810016 China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xi’ning, 810016 China
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xi’ning, 810016 Qinghai China
| | - Wei Sa
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi’ning, 810016 China
| | - Li Wang
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xi’ning, 810016 China
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xi’ning, 810016 Qinghai China
| |
Collapse
|
545
|
Rasheed S, Zaidi S, Azim MK. The chloroplast genome sequence of Momordica charantia L. (bitter gourd). GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
546
|
Chen X, Cai L, Zhang Y, Su W, Li B, Zhou Q, Zhu Q. The complete chloroplast genome sequence of the Dioscorea esculenta (Lour.) Burkill (Dioscoreaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3804-3806. [PMID: 33367107 PMCID: PMC7703703 DOI: 10.1080/23802359.2020.1832593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Dioscorea esculenta (Lour.) Burkill is an essential tuber crop with pharmacological effects in the family Dioscoreaceae. The complete chloroplast genome of D. esculenta was determined in this study. The total genome size is 153, 437 bp in length and demonstrates a typical quadripartite structure containing a large single copy (LSC, 83,628 bp) and a small single copy (SSC, 18,893 bp), separated by a pair of inverted repeats (IRa, IRb) of 25,458 bp. The GC content of the complete chloroplast genome sequence is 37.07%. A total of 131 genes were predicted including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree analysis of 25 species belonging to the genus Dioscorea indicated that D. esculenta and D. sansibarensis were clustered into one branch.
Collapse
Affiliation(s)
- Xin Chen
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Lijuan Cai
- Nanchang Business College, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Yu Zhang
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Wenzheng Su
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Bicong Li
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Qinghong Zhou
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Qianglong Zhu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| |
Collapse
|
547
|
Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes. PLANTS 2020; 9:plants9111605. [PMID: 33218207 PMCID: PMC7699153 DOI: 10.3390/plants9111605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 12/28/2022]
Abstract
Biebersteiniaceae and Nitrariaceae, two small families, were classified in Sapindales recently. Taxonomic and phylogenetic relationships within Sapindales are still poorly resolved and controversial. In current study, we compared the chloroplast genomes of five species (Biebersteinia heterostemon, Peganum harmala, Nitraria roborowskii, Nitraria sibirica, and Nitraria tangutorum) from Biebersteiniaceae and Nitrariaceae. High similarity was detected in the gene order, content and orientation of the five chloroplast genomes; 13 highly variable regions were identified among the five species. An accelerated substitution rate was found in the protein-coding genes, especially clpP. The effective number of codons (ENC), parity rule 2 (PR2), and neutrality plots together revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported (Nitrariaceae (Biebersteiniaceae + The Rest)) relationships in Sapindales. Our findings can provide useful information for analyzing phylogeny and molecular evolution within Biebersteiniaceae and Nitrariaceae.
Collapse
|
548
|
Wang L, Liang J, Shang Q, Sa W, Wang L. The complete plastome of Sorbaria kirilowii: genome structure, comparative analysis, and phylogenetic implications. Mol Biol Rep 2020; 47:9677-9687. [PMID: 33159676 DOI: 10.1007/s11033-020-05976-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/03/2020] [Indexed: 11/25/2022]
Abstract
Sorbaria kirilowii is a deciduous perennial admired for its showy white blossoms. Though of importance for horticultural purposes, the plastomic study concerning this species is still lacking. Here, the plastome of S. kirilowii was de novo assembled using the high-throughput sequencing data. The complete plastome assembly of S. kirilowii was 160,810 bp in length, with a GC content of 36.03%. It featured a typical quadripartite structure, containing a pair of inverted repeats (IRs; 26,338 bp) separated by a large single-copy (LSC; 88,762 bp) and a small single-copy (SSC, 19,372 bp). In total, 132 genes were annotated in the plastome, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Furthermore, 63 SSRs, most of which were AT-rich, were identified in the cp genome of S. kirilowii. 71.7% of the cpSSRs were shown to be located in the intergenic regions. In addition, 49 repeats of varying sizes and types were also identified in the plastome. Through comparison, eight divergence hotspots were identified between the plastome of S. kirilowii and S. sorbifolia var. stellipila. These variable regions could potentially be developed into molecular markers for species delimitation or phylogenetics in future studies. We re-investigated the relationship among 17 Rosaceae species using the plastomic sequences, and S. kirilowii was shown to be a sister to S. sorbifolia var. stellipila. Overall, this study provides plastomic resources which could facilitate marker development and phylogenomics of Rosaceae.
Collapse
Affiliation(s)
- Le Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, 810016, China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, 810016, China
| | - Qianhan Shang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, 810016, China
| | - Wei Sa
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, 810016, China
| | - Li Wang
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xi'ning, 810016, China. .,Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xi'ning, 810016, Qinghai, China.
| |
Collapse
|
549
|
Zheng Y, Li J, Chen H, Huang L. The complete chloroplast genome sequence of Hemerocallis fulva. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3543-3544. [PMID: 33458234 PMCID: PMC7782359 DOI: 10.1080/23802359.2020.1829126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Hemerocallis fulva L. is a traditional Chinese medicine. The flowers of H. fulva are used in ethnic medicine to treat various diseases, including certain central nervous system diseases. In this study, we characterized the complete chloroplast genome of H. fulva. It is 156,059 bp in length and encodes 87 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The phylogenomic analysis showed that the H. fulva and species of Anemarrhena asphodeloides Bunge, Liriope muscari, and Liriope spicata were clustered together. This chloroplast genome sequencing offers genetic background for conservation and phylogenetic studies.
Collapse
Affiliation(s)
- Yan Zheng
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi
| | - Jingling Li
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Southwest University, Chongqing, China
| | - Haimei Chen
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Linfang Huang
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| |
Collapse
|
550
|
Tan W, Gao H, Jiang W, Zhang H, Yu X, Liu E, Tian X. The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes. Sci Rep 2020; 10:16309. [PMID: 33005000 PMCID: PMC7529812 DOI: 10.1038/s41598-020-73392-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/07/2020] [Indexed: 11/09/2022] Open
Abstract
Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.
Collapse
Affiliation(s)
- Wei Tan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Han Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Weiling Jiang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Huanyu Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Erwei Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
| |
Collapse
|