Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition.
abiotic stress
codon usage bias
gene expression
mutational pressure
natural selection
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
06 Jan 2023
06 Jan 2023
Historique:
received:
08
10
2022
revised:
14
12
2022
accepted:
17
12
2022
entrez:
21
1
2023
pubmed:
22
1
2023
medline:
25
1
2023
Statut:
epublish
Résumé
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 (R
Identifiants
pubmed: 36674611
pii: ijms24021098
doi: 10.3390/ijms24021098
pmc: PMC9861248
pii:
doi:
Substances chimiques
Codon
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Department of Biotechnology
ID : BT/PR32853/AGill/103/1159/2019
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