ArticlePloS one2020
Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 30 citations in OpenAlex.
- System level identification and multidimensional analysis of hub genes reveal complex regulatory networks underlying human iPSC differentiation into motor neurons.Biochemistry and biophysics reports · 2026Article
- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Integrating multi-omic data to identify key genes and pathways involved in rice bacterial leaf streak disease.Scientific reports · 2025Article
- Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.Genome biology and evolution · 2025Article
- Epigenetics and plant hormone dynamics: a functional and methodological perspective.Journal of experimental botany · 2024Review
- Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species.Plants (Basel, Switzerland) · 2024Article
- Codon-optimization in gene therapy: promises, prospects and challenges.Frontiers in bioengineering and biotechnology · 2024Review
- Review
- Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition.International journal of molecular sciences · 2023Article
- Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species.Frontiers in plant science · 2023Article
- Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant (Frontiers in plant science · 2023Article
- Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice.Frontiers in plant science · 2023Article
- Plastomes ofInternational journal of molecular sciences · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Comprehensive analysis of coding sequence architecture features and gene expression inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We studied the correlation of synonymous codon usage (SCU) on gene expression levels under drought stress in rice. Sixty genes related to drought stress (with high, intermediate and low expression) were selected from rice meta-analysis data and various codon usage indices such as the effective number of codon usage (ENC), codon adaptation index (CAI) and relative synonymous codon usage (RSCU) were calculated. We found that in genes highly expressing under drought 1) GC content was higher, 2) ENC value was lower, 3) the preferred codons of some amino acids changed and 4) the RSCU ratio of GC-end codons relative to AT-end codons for 18 amino acids increased significantly compared with those in other genes. We introduce ARSCU as the Average ratio of RSCUs of GC-end codons to AT-end codons in each gene that could significantly separate high-expression genes under drought from low-expression genes. ARSCU is calculated using the program ARSCU-Calculator developed by our group to help predicting expression level of rice genes under drought. An index above ARSCU threshold is expected to indicate that the gene under study may belong to the "high expression group under drought". This information may be applied for codon optimization of genes for rice genetic engineering. To validate these findings, we further used 60 other genes (randomly selected subset of 43233 genes studied for their response to drought stress). ARSCU value was able to predict the level of expression at 88.33% of the cases. Using third set of 60 genes selected amongst high expressing genes not related to drought, only 31.65% of the genes showed ARSCU value of higher than the set threshold. This indicates that the phenomenon we described in this report may be unique for drought related genes. To justify the observed correlation between CUB and high expressing genes under drought, possible role of tRNA post transcriptional modification and tRFs was hypothesized as possible underlying biological mechanism.
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