Codon usage provide insights into the adaptation of rice genes under stress condition
Plants experience different stresses, i.e., abiotic, or biotic, and to combat them, plants re-program the expression of growth-, metabolism-, and resistance-related genes. These genes differ in their synonymous codon usage frequency and show codon usage bias. Here, we investigated the correlation am...
| Autores principales: | , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164000 |
| _version_ | 1855519164948545536 |
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| author | Tyagi, Swati Kabade, Pramod Gorakhanath Gnanapragasam, Niranjani Singh, Uma Maheshwar Gurjar, Anoop Kishor Singh Rai, Ashutosh Sinha, Pallavi Kumar, Arvind Singh, Vikas Kumar |
| author_browse | Gnanapragasam, Niranjani Gurjar, Anoop Kishor Singh Kabade, Pramod Gorakhanath Kumar, Arvind Rai, Ashutosh Singh, Uma Maheshwar Singh, Vikas Kumar Sinha, Pallavi Tyagi, Swati |
| author_facet | Tyagi, Swati Kabade, Pramod Gorakhanath Gnanapragasam, Niranjani Singh, Uma Maheshwar Gurjar, Anoop Kishor Singh Rai, Ashutosh Sinha, Pallavi Kumar, Arvind Singh, Vikas Kumar |
| author_sort | Tyagi, Swati |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Plants experience different stresses, i.e., abiotic, or biotic, and to combat them, plants re-program the expression of growth-, metabolism-, and resistance-related genes. These genes differ in their synonymous codon usage frequency and show codon usage bias. Here, we investigated the correlation among codon usage bias, gene expression, and underlying mechanisms in rice under abiotic and biotic stress conditions. The results indicated that genes with higher expression (up- or downregulated) levels had high GC content (≥60%), a low effective number of codon usage (≤40), and exhibited strong biases towards the codons with C/G at the third nucleotide position, irrespective of stress received. TTC, ATC, and CTC were the most preferred codons, while TAC, CAC, AAC, GAC, and TGC were moderately preferred under any stress (abiotic or biotic) condition. Additionally, downregulated genes are under mutational pressure (R2 ≥ 0.5) while upregulated genes are under natural selection pressure (R2 ≤ 0.5). Based on these results, we also identified the possible target codons that can be used to design an optimized set of genes with specific codons to develop climate-resilient varieties. Conclusively, under stress, rice has a bias towards codon usage which is correlated with GC content, gene expression level, and gene length. |
| format | Journal Article |
| id | CGSpace164000 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1640002025-12-08T10:29:22Z Codon usage provide insights into the adaptation of rice genes under stress condition Tyagi, Swati Kabade, Pramod Gorakhanath Gnanapragasam, Niranjani Singh, Uma Maheshwar Gurjar, Anoop Kishor Singh Rai, Ashutosh Sinha, Pallavi Kumar, Arvind Singh, Vikas Kumar abiotic stress biotic stress gene expression codons growth metabolism mutation genomics genetics Plants experience different stresses, i.e., abiotic, or biotic, and to combat them, plants re-program the expression of growth-, metabolism-, and resistance-related genes. These genes differ in their synonymous codon usage frequency and show codon usage bias. Here, we investigated the correlation among codon usage bias, gene expression, and underlying mechanisms in rice under abiotic and biotic stress conditions. The results indicated that genes with higher expression (up- or downregulated) levels had high GC content (≥60%), a low effective number of codon usage (≤40), and exhibited strong biases towards the codons with C/G at the third nucleotide position, irrespective of stress received. TTC, ATC, and CTC were the most preferred codons, while TAC, CAC, AAC, GAC, and TGC were moderately preferred under any stress (abiotic or biotic) condition. Additionally, downregulated genes are under mutational pressure (R2 ≥ 0.5) while upregulated genes are under natural selection pressure (R2 ≤ 0.5). Based on these results, we also identified the possible target codons that can be used to design an optimized set of genes with specific codons to develop climate-resilient varieties. Conclusively, under stress, rice has a bias towards codon usage which is correlated with GC content, gene expression level, and gene length. 2023-01-06 2024-12-19T12:53:19Z 2024-12-19T12:53:19Z Journal Article https://hdl.handle.net/10568/164000 en Open Access MDPI Tyagi, Swati; Kabade, Pramod Gorakhanath; Gnanapragasam, Niranjani; Singh, Uma Maheshwar; Gurjar, Anoop Kishor Singh; Rai, Ashutosh; Sinha, Pallavi; Kumar, Arvind and Singh, Vikas Kumar. 2023. Codon usage provide insights into the adaptation of rice genes under stress condition. IJMS, Volume 24 no. 2 p. 1098 |
| spellingShingle | abiotic stress biotic stress gene expression codons growth metabolism mutation genomics genetics Tyagi, Swati Kabade, Pramod Gorakhanath Gnanapragasam, Niranjani Singh, Uma Maheshwar Gurjar, Anoop Kishor Singh Rai, Ashutosh Sinha, Pallavi Kumar, Arvind Singh, Vikas Kumar Codon usage provide insights into the adaptation of rice genes under stress condition |
| title | Codon usage provide insights into the adaptation of rice genes under stress condition |
| title_full | Codon usage provide insights into the adaptation of rice genes under stress condition |
| title_fullStr | Codon usage provide insights into the adaptation of rice genes under stress condition |
| title_full_unstemmed | Codon usage provide insights into the adaptation of rice genes under stress condition |
| title_short | Codon usage provide insights into the adaptation of rice genes under stress condition |
| title_sort | codon usage provide insights into the adaptation of rice genes under stress condition |
| topic | abiotic stress biotic stress gene expression codons growth metabolism mutation genomics genetics |
| url | https://hdl.handle.net/10568/164000 |
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