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Gan J, Li Y, Tang D, Guo B, Li D, Cao F, Sun C, Yu L, Yan Z. The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus. Genes (Basel) 2023; 14:genes14040929. [PMID: 37107687 PMCID: PMC10138119 DOI: 10.3390/genes14040929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/06/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Gynostemma is an important medicinal and food plant of the Cucurbitaceae family. The phylogenetic position of the genus Gynostemma in the Cucurbitaceae family has been determined by morphology and phylogenetics, but the evolutionary relationships within the genus Gynostemma remain to be explored. The chloroplast genomes of seven species of the genus Gynostemma were sequenced and annotated, of which the genomes of Gynostemma simplicifolium, Gynostemma guangxiense and Gynostemma laxum were sequenced and annotated for the first time. The chloroplast genomes ranged from 157,419 bp (Gynostemma compressum) to 157,840 bp (G. simplicifolium) in length, including 133 identical genes: 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. Phylogenetic analysis showed that the genus Gynostemma is divided into three primary taxonomic clusters, which differs from the traditional morphological classification of the genus Gynostemma into the subgenus Gynostemma and Trirostellum. The highly variable regions of atpH-atpL, rpl32-trnL, and ccsA-ndhD, the repeat unilts of AAG/CTT and ATC/ATG in simple sequence repeats (SSRs) and the length of overlapping regions between rps19 and inverted repeats(IRb) and between ycf1 and small single-copy (SSC) were found to be consistent with the phylogeny. Observations of fruit morphology of the genus Gynostemma revealed that transitional state species have independent morphological characteristics, such as oblate fruit and inferior ovaries. In conclusion, both molecular and morphological results showed consistency with those of phylogenetic analysis.
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Affiliation(s)
- Jiaxia Gan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Ying Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Deying Tang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong 666100, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Doudou Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Feng Cao
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Chao Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Liying Yu
- Guangxi Botanical Garden of Medicinal Plant, Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Nanning 530023, China
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Zhang J, Huang H, Qu C, Meng X, Meng F, Yao X, Wu J, Guo X, Han B, Xing S. Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.). PLANTA 2021; 255:26. [PMID: 34940902 DOI: 10.1007/s00425-021-03812-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
The Albizia julibrissin chloroplasts have a classical chloroplast genome structure, containing 93 coding genes and 34 non-coding genes. Our research provides basic data for plant phylogenetic evolutionary studies. There is limited genomic information available for the important Chinese herb Albizia julibrissin Durazz. In this study, we constructed the chloroplast (Cp) genome of A. julibrissin. The length of the assembled Cp genome was 175,922 bp consisting of four conserved regions: a 5145 bp small single-copy (SSC) region, a 91,323 bp large single-copy (LSC) region, and two identical length-inverted repeat (IR) regions (39,725 bp). This Cp genome included 34 non-coding RNAs and 93 unique genes, the former contains 30 transfer and 4 ribosomal RNA genes. Gene annotation indicated some of the coding genes (82) in the A. julibrissin Cp genome classified in the Leguminosae family, with some to other related families (11). The results show that low GC content (36.9%) and codon bias towards A- or T-terminal codons may affect the frequency of gene codon usage. The sequence analysis identified 30 forward, 18 palindrome, and 1 reverse repeat > 30 bp length, and 149 simple sequence repeats (SSR). Fifty-five RNA editing sites in the Cp of A. julibrissin were predicted, most of which are C-to-U conversions. Analysis of the reverse repeat expansion or contraction and divergence area between several species, including A. julibrissin, was performed. The phylogenetic tree revealed that A. julibrissin was most closely related to Albizia odoratissima and Albizia bracteata, followed by Samanea saman, forming an evolutionary branch with Mimosa pudica and Leucaena trichandra. The research results are helpful for breeding and genetic improvement of A. julibrissin, and also provide valuable information for understanding the evolution of this plant.
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Affiliation(s)
- Jing Zhang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Huizhen Huang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, 421008, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-Aging, Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, Minneapolis, 55108, USA
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiaoyan Yao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China
| | - Xiaohu Guo
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Bangxing Han
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, West Anhui University, Lu'an, 237012, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, 230012, China.
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Zhang P, Xu W, Lu X, Wang L. Analysis of codon usage bias of chloroplast genomes in Gynostemma species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2727-2737. [PMID: 35035132 PMCID: PMC8720125 DOI: 10.1007/s12298-021-01105-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/13/2021] [Accepted: 11/20/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED Gynostemma plants are important Chinese medicinal material and economic crops. Codon usage analysis is a good way to understand organism evolution and phylogeny. There is no report yet about analysis of codon usage bias of chloroplast genomes in Gynostemma species. In this study, the chloroplast genomes in nine Gynostemma species were analyzed systematically to explore the factors affecting the formation of codon usage bias. The codon usage indicators were analyzed. Multivariate statistical analysis including analysis of neutrality plot, effective number of codons plot, parity rule 2 plot and correspondence were performed. Composition analysis of codons showed that the frequency of GC in chloroplast genes of all nine Gynostemma species was less than 50%, and the protein-coding sequences of chloroplast genes preferred to end with A/T at the third codon position. The chloroplast genes had an overall weak codon usage bias. A total of 29 high frequency codons and 12 optimal codons were identified. These could provide useful information in optimizing and modifying codons thus improving the gene expression of Gynostemma species. The results of multivariate analysis showed that the codon usage patterns were not only affected by single one factor but multiple factors. Mutation pressure, natural selection and base composition might have an influence on the codon usage patterns while natural selection might be the main determinant. The study could provide a reference for organism evolution and phylogeny of Gynostemma species and help to understand the patterns of codons in chloroplast genomes in other plant species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01105-z.
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Affiliation(s)
- Peipei Zhang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 Jiangsu China
| | - Wenbo Xu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 Jiangsu China
| | - Xu Lu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 Jiangsu China
| | - Long Wang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198 Jiangsu China
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Huang X, Tan W, Li F, Liao R, Guo Z, Shi T, Gao Z. The chloroplast genome of Prunus zhengheensis: Genome comparative and phylogenetic relationships analysis. Gene 2021; 793:145751. [PMID: 34062257 DOI: 10.1016/j.gene.2021.145751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/06/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
Abstract
Prunus zhengheensis is a novel species originated in Fujian province, China. However, there is no further information available on its classification and molecular biology study. In this study, we first report the complete chloroplast (cp) genome sequence of P. zhengheensis. The cp genome of P. zhengheensis is 158,106 bp and GC content is 36.73%, is a circular structure composed of LSC (large single copy), SSC (small single copy), and IR (inverted repeat) regions, with the size of the three regions being 86,321 bp, 18,999 bp and 26,393 bp, respectively. The cp genome of P. zhengheensis contains 130 genes, and 242 SSRs are identified in the cp genome. The comparative analysis of cp genomes in eight Prunus plants demonstrates the subtle divergences occur in the protein-coding gene rps18, rps12, psbF, rpl33, matK, and rbcL, and that the KA/KS nucleotide substitution ratio of the ndhF of P. zhengheensis and P. armeniaca is 1.79636. The phylogenetic results indicate that the P. zhengheensis is closely related to P. mume, compared to other species of Prunus. Our research results provide the important genomic information for molecular phylogeny of P. zhengheensis.
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Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Li
- Jilin Academy of Agricultural Sciences, Jilin 136100, China.
| | - Ruyu Liao
- Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
| | - Zhongren Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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