ArticleBMC ecology and evolution2021
Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana.
Article in BMC ecology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 14 citations in OpenAlex.
- Comprehensive Codon Usage Analysis Across Diverse Plant Lineages.Biochemical genetics · 2026Article
- Fine mapping of a major QTL, qECQ8, for rice taste quality.BMC plant biology · 2024Article
- Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene.BMC ecology and evolution · 2024Article
- Liver cancer-specific mutations in functional domains of ADAR2 lead to the elevation of coding and non-coding RNA editing in multiple tumor-related genes.Molecular genetics and genomics : MGG · 2024Article
- SARS-CoV-2 continuously optimizes its codon usage to adapt to human lung environment.Journal of applied genetics · 2023Article
- Evidence Supporting That C-to-U RNA Editing Is the Major Force That Drives SARS-CoV-2 Evolution.Journal of molecular evolution · 2023Article
- uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response.Journal of molecular evolution · 2022Article
- Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals.Journal of molecular evolution · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Comparative genomic analysis of a naturally born serpentized pig reveals putative mutations related to limb and bone development.BMC genomics · 2021Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSynonymous mutations do not alter the amino acids and therefore are regarded as neutral for a long time. However, they do change the tRNA adaptation index (tAI) of a particular codon (independent of its context), affecting the tRNA availability during translation. They could also change the isoaccepting relationship with its neighboring synonymous codons in particular context, which again affects the local translation process. Evidence of selection pressure on synonymous mutations has emerged.
resultsThe proposed selection patterns on synonymous mutations are never formally and systematically tested in plant species. We fully take advantage of the SNP data from 1,135 A. thaliana lines, and found that the synonymous mutations that increase tAI or the isoaccepting mutations in isoaccepting codon context tend to have higher derived allele frequencies (DAF) compared to other synonymous mutations of the opposite effects.
conclusionsSynonymous mutations are not strictly neutral. The synonymous mutations that increase tAI or the isoaccepting mutations in isoaccepting codon context are likely to be positively selected. We propose the concept of context-dependent and -independent selection on synonymous mutations. These concepts broaden our knowledge of the functional consequences of synonymous mutations, and should be appealing to phytologists and evolutionary biologists.
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