Codon usage pattern of the ancestor of green plants revealed through Rhodophyta
Abstract Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that althou...
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09586-w |
| _version_ | 1797453838969470976 |
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| author | Huipeng Yao Tingting Li Zheng Ma Xiyuan Wang Lixiao Xu Yuxin Zhang Yi Cai Zizhong Tang |
| author_facet | Huipeng Yao Tingting Li Zheng Ma Xiyuan Wang Lixiao Xu Yuxin Zhang Yi Cai Zizhong Tang |
| author_sort | Huipeng Yao |
| collection | DOAJ |
| description | Abstract Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future. |
| first_indexed | 2024-03-09T15:28:40Z |
| format | Article |
| id | doaj.art-d0f7e17e360d48cc926965a9f99cd474 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:28:40Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-d0f7e17e360d48cc926965a9f99cd4742023-11-26T12:25:30ZengBMCBMC Genomics1471-21642023-09-0124111210.1186/s12864-023-09586-wCodon usage pattern of the ancestor of green plants revealed through RhodophytaHuipeng Yao0Tingting Li1Zheng Ma2Xiyuan Wang3Lixiao Xu4Yuxin Zhang5Yi Cai6Zizhong Tang7College of Life Science, Sichuan Agriculture UniversityCollege of Life Science, Sichuan Agriculture UniversityCollege of Life Science, Sichuan Agriculture UniversityCollege of Life Science, Sichuan Agriculture UniversityCollege of Life Science, Sichuan Agriculture UniversityCollege of Life Science, Sichuan Agriculture UniversityCollege of Life Science, Sichuan Agriculture UniversityCollege of Life Science, Sichuan Agriculture UniversityAbstract Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.https://doi.org/10.1186/s12864-023-09586-wRhodophytaOptimal codonsCodon usage biasTranslational accuracytRNA modification |
| spellingShingle | Huipeng Yao Tingting Li Zheng Ma Xiyuan Wang Lixiao Xu Yuxin Zhang Yi Cai Zizhong Tang Codon usage pattern of the ancestor of green plants revealed through Rhodophyta BMC Genomics Rhodophyta Optimal codons Codon usage bias Translational accuracy tRNA modification |
| title | Codon usage pattern of the ancestor of green plants revealed through Rhodophyta |
| title_full | Codon usage pattern of the ancestor of green plants revealed through Rhodophyta |
| title_fullStr | Codon usage pattern of the ancestor of green plants revealed through Rhodophyta |
| title_full_unstemmed | Codon usage pattern of the ancestor of green plants revealed through Rhodophyta |
| title_short | Codon usage pattern of the ancestor of green plants revealed through Rhodophyta |
| title_sort | codon usage pattern of the ancestor of green plants revealed through rhodophyta |
| topic | Rhodophyta Optimal codons Codon usage bias Translational accuracy tRNA modification |
| url | https://doi.org/10.1186/s12864-023-09586-w |
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