Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea
In order to enrich the understanding of the genetic basis of the genus Pleurozia purpurea, the codon usage bias (CUB) in the mitochondrial genome of Pleurozia purpurea and its main influencing factors were investigated. Firstly, protein-coding sequences were screened based on the complete mitochondr...
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Hebei University of Science and Technology
2025-02-01
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| Series: | Journal of Hebei University of Science and Technology |
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| author | Mengxue DU Xin ZHANG Jie GAO Sheng BI Jiewei HAO Lina ZHANG |
| author_facet | Mengxue DU Xin ZHANG Jie GAO Sheng BI Jiewei HAO Lina ZHANG |
| author_sort | Mengxue DU |
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| description | In order to enrich the understanding of the genetic basis of the genus Pleurozia purpurea, the codon usage bias (CUB) in the mitochondrial genome of Pleurozia purpurea and its main influencing factors were investigated. Firstly, protein-coding sequences were screened based on the complete mitochondrial genome of Pleurozia purpurea. Then, CodonW and EMBOSS explorer were utilized to calculate various metrics for each gene, including GC content, effective number of codons (ENC), codon adaptation index (CAI), and relative synonymous codon usage (RSCU). Finally, correlation analysis between parameters was analyzed and plotted using R software. The results show that: 1) A total of 31 protein-coding sequences are identified from the mitochondrial genome of Pleurozia purpurea, with an average GC content of 38.17% and a GC content of 32.28% for the third base of codons, respectively. The average values for ENC and CAI are 50.29 and 0.17, indicating a preference for codons ending with A/U bases and a relatively weak CUB; 2) ENC exhibits significantly positive correlations with GCall, GC3, and the length of amino acid encoding genes, indicating significant influences of GC content and gene length on CUB; 3) Analyses including neutrality plot, ENC-plot and PR2-plot indicate that mutation pressure and natural selection jointly shaped the CUB, with mutation being the most important influencing factor; 4) A total of 23 optimal codons are selected, most of which end with A/U. Therefore, the CUB in the mitochondrial genome of Pleurozia purpurea is relatively weak, influenced primarily by mutational pressure, and by factors such as natural selection, base composition, and gene length. The research results can provide reference for evolutionary studies of mitochondrial genomes in bryophytes. |
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| institution | Kabale University |
| issn | 1008-1542 |
| language | zho |
| publishDate | 2025-02-01 |
| publisher | Hebei University of Science and Technology |
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| series | Journal of Hebei University of Science and Technology |
| spelling | doaj-art-a6a43a919bfd4093a0b9ebc315f7e4ed2025-01-17T06:48:06ZzhoHebei University of Science and TechnologyJournal of Hebei University of Science and Technology1008-15422025-02-01461919910.7535/hbkd.2025yx01010b202501010Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpureaMengxue DU0Xin ZHANG1Jie GAO2Sheng BI3Jiewei HAO4Lina ZHANG5Ministry of Education Key Laboratory for Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants,Hainan University,Haikou,Hainan 570228,ChinaMinistry of Education Key Laboratory for Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants,Hainan University,Haikou,Hainan 570228,ChinaMinistry of Education Key Laboratory for Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants,Hainan University,Haikou,Hainan 570228,ChinaMinistry of Education Key Laboratory for Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants,Hainan University,Haikou,Hainan 570228,ChinaMinistry of Education Key Laboratory for Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants,Hainan University,Haikou,Hainan 570228,ChinaMinistry of Education Key Laboratory for Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants,Hainan University,Haikou,Hainan 570228,ChinaIn order to enrich the understanding of the genetic basis of the genus Pleurozia purpurea, the codon usage bias (CUB) in the mitochondrial genome of Pleurozia purpurea and its main influencing factors were investigated. Firstly, protein-coding sequences were screened based on the complete mitochondrial genome of Pleurozia purpurea. Then, CodonW and EMBOSS explorer were utilized to calculate various metrics for each gene, including GC content, effective number of codons (ENC), codon adaptation index (CAI), and relative synonymous codon usage (RSCU). Finally, correlation analysis between parameters was analyzed and plotted using R software. The results show that: 1) A total of 31 protein-coding sequences are identified from the mitochondrial genome of Pleurozia purpurea, with an average GC content of 38.17% and a GC content of 32.28% for the third base of codons, respectively. The average values for ENC and CAI are 50.29 and 0.17, indicating a preference for codons ending with A/U bases and a relatively weak CUB; 2) ENC exhibits significantly positive correlations with GCall, GC3, and the length of amino acid encoding genes, indicating significant influences of GC content and gene length on CUB; 3) Analyses including neutrality plot, ENC-plot and PR2-plot indicate that mutation pressure and natural selection jointly shaped the CUB, with mutation being the most important influencing factor; 4) A total of 23 optimal codons are selected, most of which end with A/U. Therefore, the CUB in the mitochondrial genome of Pleurozia purpurea is relatively weak, influenced primarily by mutational pressure, and by factors such as natural selection, base composition, and gene length. The research results can provide reference for evolutionary studies of mitochondrial genomes in bryophytes.https://xuebao.hebust.edu.cn/hbkjdx/article/pdf/b202501010?st=article_issuemolecular genetics; the genus pleurozia purpurea; codon usage bias; mitochondrial genomes; optimal codon |
| spellingShingle | Mengxue DU Xin ZHANG Jie GAO Sheng BI Jiewei HAO Lina ZHANG Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea Journal of Hebei University of Science and Technology molecular genetics; the genus pleurozia purpurea; codon usage bias; mitochondrial genomes; optimal codon |
| title | Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea |
| title_full | Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea |
| title_fullStr | Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea |
| title_full_unstemmed | Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea |
| title_short | Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea |
| title_sort | analysis of codon usage bias in the mitochondrial genome of pleurozia purpurea |
| topic | molecular genetics; the genus pleurozia purpurea; codon usage bias; mitochondrial genomes; optimal codon |
| url | https://xuebao.hebust.edu.cn/hbkjdx/article/pdf/b202501010?st=article_issue |
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