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.
Highlights
Synonymous mutations are able to change the transfer RNA (tRNA) adaptation index (tAI) of a codon and affect the local translation rate
Another impact of synonymous mutations is the change in tRNA adaptation index [6], a terminology which described the tRNA availability of a codon
To ensure that the orthologous sites in wheat or carrot are not polymorphic, we downloaded RNA-seq data of roots generated from the corresponding species and mapped the RNA-seq reads to the reference Coding sequence (CDS) and discarded all the potential polymorphic sites (Methods)
Summary
Synonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and affect the local translation rate. As understood by the broad researchers, synonymous mutations do not change the amino acid (AA) sequences They are still subjected to natural selection [1,2,3]. A few synonymous mutations occurring in the proper place could affect mRNA splicing [4, 5]. Another impact of synonymous mutations is the change in tRNA adaptation index (tAI) [6], a terminology which described the tRNA availability of a codon.
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