ArticleBMC genomics2020
Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- 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
- Genome expression analysis of basic helix-loop-helix transcription factors in Sea buckthorn (Frontiers in plant science · 2024Article
- Identification of hub genes regulating isoflavone accumulation in soybean seedsFrontiers in plant science · 2023Article
- Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber).G3 (Bethesda, Md.) · 2022Article
- Comparative genomic analysis of a naturally born serpentized pig reveals putative mutations related to limb and bone development.BMC genomics · 2021Article
- Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (International journal of molecular sciences · 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
- Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana.BMC genetics · 2020Article
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2 authors.
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Abstract
backgroundSynonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and consequently affect the local translation rate. Intuitively, one may hypothesize that those synonymous mutations which increase the tAI values are favored by natural selection.
resultsWe use the maize (Zea mays) genome to test our assumption. The first supporting evidence is that the tAI-increasing synonymous mutations have higher fixed-to-polymorphic ratios than the tAI-decreasing ones. Next, the DAF (derived allele frequency) or MAF (minor allele frequency) of the former is significantly higher than the latter. Moreover, similar results are obtained when we investigate CAI (codon adaptation index) instead of tAI.
conclusionThe synonymous mutations in the maize genome are not strictly neutral. The tAI-increasing mutations are positively selected while those tAI-decreasing ones undergo purifying selection. This selection force might be weak but should not be automatically ignored.
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