ArticleMolecular genetics and genomics : MGG2015
Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice (Oryza sativa L.).
Article in Molecular genetics and genomics : MGG, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 20 citations in OpenAlex.
- Genome-wide analysis of codon usage in sesame (Heliyon · 2022Article
- Mutation profiling of a limbless pig reveals genome-wide regulation of RNA processing related to bone development.Journal of applied genetics · 2021Article
- Genome-wide expression changes mediated by A-to-I RNA editing correlate with hepatic oncogenesis.Translational cancer research · 2021Article
- Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis.Molecular genetics and genomics : MGG · 2021Article
- Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana.BMC ecology and evolution · 2021Article
- Synonymous mutations that regulate translation speed might play a non-negligible role in liver cancer development.BMC cancer · 2021Article
- Cost-efficiency tradeoff is optimized in various cancer types revealed by genome-wide analysis.Molecular genetics and genomics : MGG · 2021Article
- 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 analysis of codon usage betweenMitochondrial DNA. Part B, Resources · 2020Article
- Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection.Nature ecology & evolution · 2020Article
- Codon usage and codon pair patterns in non-grass monocot genomes.Annals of botany · 2017Review
- New insights into the interplay between codon bias determinants in plants.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
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3 authors at 1 institution in 1 country.
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Abstract
Alternative splicing plays important roles in diverse aspects of plant development, metabolism, and stress responses. However, the regulatory mechanisms of alternative splicing of genes still remain incompletely elucidated, especially in plants. In this study, the synonymous codon usage pattern of alternatively spliced (AS) genes in rice was firstly explored using the combination of correspondence analysis (CA), internal CA, correlation and ANOVA analyses. The results show that alternatively and non-alternatively spliced (non-AS) genes have similar tendency for overall codon usage, but exhibit significant difference in 58 out of 64 codons. AS and non-AS genes are both under strong purifying selection, but the former ones have significant lower mutation rate and are prone to be enriched towards the chromosomal ends. In the group of AS genes, the variability in synonymous codon usage between genes is mainly due to the variations in GC content, CDS length, as well as gene functions. Mutational bias that accounts for 25.85 % of the total codon usage variability plays a major role in shaping the codon usage pattern of AS genes. In contrast, no obvious evidence is found for the contributions of translational selection, AS types, the conservation of AS events, and numbers of AS variants to the codon usage divergence between AS genes. These findings may be useful for further understanding the mechanisms of origination, differentiation and regulation of alternatively spliced genes in plants.
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