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Wang Y, Jiang D, Guo K, Zhao L, Meng F, Xiao J, Niu Y, Sun Y. Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species. BMC Genom Data 2023; 24:3. [PMID: 36624369 PMCID: PMC9830715 DOI: 10.1186/s12863-023-01104-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The Phenomenon of codon usage bias exists in the genomes of prokaryotes and eukaryotes. The codon usage pattern is affected by environmental factors, base mutation, gene flow and gene expression level, among which natural selection and mutation pressure are the main factors. The study of codon preference is an effective method to analyze the source of evolutionary driving forces in organisms. Epimedium species are perennial herbs with ornamental and medicinal value distributed worldwide. The chloroplast genome is self-replicating and maternally inherited which is usually used to study species evolution, gene expression and genetic transformation. RESULTS The results suggested that chloroplast genomes of Epimedium species preferred to use codons ending with A/U. 17 common high-frequency codons and 2-6 optimal codons were found in the chloroplast genomes of Epimedium species, respectively. According to the ENc-plot, PR2-plot and neutrality-plot, the formation of codon preference in Epimedium was affected by multiple factors, and natural selection was the dominant factor. By comparing the codon usage frequency with 4 common model organisms, it was found that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae were suitable exogenous expression receptors. CONCLUSION The evolutionary driving force in the chloroplast genomes of 10 Epimedium species probably comes from mutation pressure. Our results provide an important theoretical basis for evolutionary analysis and transgenic research of chloroplast genes.
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Affiliation(s)
- Yingzhe Wang
- grid.449428.70000 0004 1797 7280College of Pharmacy, Jining Medical University, Rizhao, Shandong China ,grid.440665.50000 0004 1757 641XSchool of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, Jilin China
| | - Dacheng Jiang
- grid.440665.50000 0004 1757 641XSchool of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, Jilin China
| | - Kun Guo
- grid.440665.50000 0004 1757 641XSchool of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, Jilin China
| | - Lei Zhao
- grid.440665.50000 0004 1757 641XSchool of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, Jilin China
| | - Fangfang Meng
- grid.440665.50000 0004 1757 641XSchool of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, Jilin China
| | - Jinglei Xiao
- grid.440665.50000 0004 1757 641XSchool of Pharmaceutical Sciences, Changchun University of Chinese Medicine, Changchun, Jilin China
| | - Yuan Niu
- Lanzhou Agro-Technical Research and Popularization Center, Lanzhou, Gansu China
| | - Yunlong Sun
- grid.449428.70000 0004 1797 7280College of Pharmacy, Jining Medical University, Rizhao, Shandong China
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Wang Z, Cai Q, Xia H, Han B, Li M, Wang Y, Zhu M, Jiao C, Wang D, Zhu J, Yuan W, Zhu D, Xu C, Wang H, Zhou M, Zhang X, Shi J, Chen J. Genome-Wide Identification and Comparative Analysis of WOX Genes in Four Euphorbiaceae Species and Their Expression Patterns in Jatropha curcas. Front Genet 2022; 13:878554. [PMID: 35846114 PMCID: PMC9280045 DOI: 10.3389/fgene.2022.878554] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
The WUSCHEL-related homeobox (WOX) proteins are widely distributed in plants and play important regulatory roles in growth and development processes such as embryonic development and organ development. Here, series of bioinformatics methods were utilized to unravel the structural basis and genetic hierarchy of WOX genes, followed by regulation of the WOX genes in four Euphorbiaceae species. A genome-wide survey identified 59 WOX genes in Hevea brasiliensis (H. brasiliensis: 20 genes), Jatropha curcas (J. curcas: 10 genes), Manihot esculenta (M. esculenta: 18 genes), and Ricinus communis (R. communis: 11 genes). The phylogenetic analysis revealed that these WOX members could be clustered into three close proximal clades, such as namely ancient, intermediate and modern/WUS clades. In addition, gene structures and conserved motif analyses further validated that the WOX genes were conserved within each phylogenetic clade. These results suggested the relationships among WOX members in the four Euphorbiaceae species. We found that WOX genes in H. brasiliensis and M. esculenta exhibit close genetic relationship with J. curcas and R. communis. Additionally, the presence of various cis-acting regulatory elements in the promoter of J. curcas WOX genes (JcWOXs) reflected distinct functions. These speculations were further validated with the differential expression profiles of various JcWOXs in seeds, reflecting the importance of two JcWOX genes (JcWOX6 and JcWOX13) during plant growth and development. Our quantitative real-time PCR (qRT-PCR) analysis demonstrated that the JcWOX11 gene plays an indispensable role in regulating plant callus. Taken together, the present study reports the comprehensive characteristics and relationships of WOX genes in four Euphorbiaceae species, providing new insights into their characterization.
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Affiliation(s)
- Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Qianwen Cai
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Haimeng Xia
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Bingqing Han
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minhui Li
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Yue Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minhui Zhu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Chunyan Jiao
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Dandan Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Junjie Zhu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenya Yuan
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Di Zhu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Congcong Xu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Hongyan Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minghui Zhou
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Xie Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jinhui Chen,
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Xia C, Wang M, Guan Y, Li J. Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships. Front Genet 2022; 13:878182. [PMID: 35711937 PMCID: PMC9194378 DOI: 10.3389/fgene.2022.878182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Aconitum is an important medicinal group of the Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. There are about 350 Aconitum species globally and about 170 species in China. It is challenging to identify the species in morphology, and the lack of molecular biology information hinders the identification and rational utilization of the germplasm of this genus. Therefore, it is necessary to increase the molecular data of Aconitum species. This paper acquired the complete chloroplast (CP) genome sequence of ten medicinal plants of Aconitum species from Yunnan by Illumina paired-end (PE) sequencing technology and compared it with other species in the same family and genus. These CP genomes exhibited typical circular quadripartite structure, and their sizes ranged from 155,475 (A. stylosum) to 155,921 bp (A. vilmoinianum), including a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRs). Their gene content, order, and GC content (38.1%) were similar. Moreover, their number of genes ranged from 129 (A. vilmoinianum) to 132 (A. ramulosum), including 83 to 85 protein-coding genes (PCGs), 37 tRNA genes (tRNAs), eight rRNA genes (rRNAs), and two pseudogenes. In addition, we performed repeated sequence analysis, genomic structure, and comparative analysis using 42 Aconitum chloroplast genomes, including ten Aconitum chloroplast genomes and other sequenced Aconitum species. A total of 48–79 simple sequence repeats (SSRs) and 17 to 77 long repeat sequences were identified. IR regions showed higher variability than the SSC region and LSC region. Seven mutational hotspots were screened out, including trnK-UUU-trnQ-UGG, psbD, ndhJ-ndhK, clpP, psbH-petB, ycf1, and trnA-UGC-trnI-GAU, respectively. The phylogenetic trees of ten Aconitum species and other Aconitum species revealed that the complete CP genome was beneficial in determining the complex phylogenetic relationships among Aconitum species. This study provides a potential molecular marker and genomic resource for phylogeny and species identification of Aconitum species and an important reference and basis for Ranunculaceae species identification and phylogeny.
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Affiliation(s)
- Conglong Xia
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, China.,College of Pharmacy, Dali University, Dali, China
| | - Manjiong Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, China
| | - Yunhui Guan
- College of Pharmacy, Dali University, Dali, China
| | - Jian Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, China.,College of Pharmacy, Dali University, Dali, China
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Wang Z, Zhu J, Yuan W, Wang Y, Hu P, Jiao C, Xia H, Wang D, Cai Q, Li J, Wang C, Zhang X, Chen Y, Wang Z, Ou Z, Xu Z, Shi J, Chen J. Genome-wide characterization of bZIP transcription factors and their expression patterns in response to drought and salinity stress in Jatropha curcas. Int J Biol Macromol 2021; 181:1207-1223. [PMID: 33971233 DOI: 10.1016/j.ijbiomac.2021.05.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 11/18/2022]
Abstract
The basic leucine zipper (bZIP) family is one of the largest families of transcription factors (TFs) in plants and is responsible for various functions, including regulating development and responses to abiotic/biotic stresses. However, the roles of bZIPs in the regulation of responses to drought stress and salinity stress remain poorly understood in Jatropha curcas L., a biodiesel crop. In the present study, 50 JcbZIP genes were identified and classified into ten groups. Cis-element analysis indicated that JcbZIP genes are associated with abiotic stress. Gene expression patterns and quantitative real-time PCR (qRT-PCR) showed that four JcbZIP genes (JcbZIPs 34, 36, 49 and 50) are key resistance-related genes under both drought and salinity stress conditions. On the basis of the results of cis-element and phylogenetic analyses, JcbZIP49 and JcbZIP50 are likely involved in responses to drought and salinity stress; moreover, JcbZIP34 and JcbZIP36 might also play important roles in seed development and response to abiotic stress. These findings advance our understanding of the comprehensive characteristics of JcbZIP genes and provide new insights for functional validation in the further.
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Affiliation(s)
- Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jin Zhu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Wenya Yuan
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Ying Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Peipei Hu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Chunyan Jiao
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Haimeng Xia
- School of Biosciences, University of Nottingham, Sutton Bonington 999020, UK
| | - Dandan Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qianwen Cai
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Jie Li
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Chenchen Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Xie Zhang
- Institute of Botany, Hunan Academy of Forestry, Changsha 410004, China
| | - Yansong Chen
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zhaoxia Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zulan Ou
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zhongdong Xu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Jisen Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jinhui Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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