Abstract
Synonymous codons are widely selected for various biological mechanisms in both prokaryotes and eukaryotes. Recent evidence suggests that microRNA (miRNA) function may affect synonymous codon choices near miRNA target sites. To better understand this, we perform genome-wide analysis on synonymous codon usage around miRNA target sites in four plant genomes. We observed a general trend of increased site accessibility around miRNA target sites in plants. Guanine-cytosine (GC)-poor codons are preferred in the flank region of miRNA target sites. Within-genome analyses show significant variation among miRNA targets in species. GC content of the target gene can partly explain the variation of site accessibility among miRNA targets. miRNA targets in GC-rich genes show stronger selection signals than those in GC-poor genes. Gene's codon usage bias and the conservation level of miRNA and its target also have some effects on site accessibility, but the expression level of miRNA or its target and the mechanism of miRNA activity do not contribute to site accessibility differences among miRNA targets. We suggest that synonymous codons near miRNA targets are selected for efficient miRNA binding and proper miRNA function. Our results present a new dimension of natural selection on synonymous codons near miRNA target sites in plants, which will have important implications of coding sequence evolution.
Highlights
Mutations at synonymous codon sites are normally assumed to be evolutionarily neutral because these mutations don’t change its encoded protein sequences (Yang and Nielsen, 2000)
To eliminate the false positives of low expression levels caused by sequencing errors, we only considered mRNAs or miRNAs with 4 or more tags in a tissue as valid Massively Parallel Signature Sequencing (MPSS) data (Wright, et al, 2004)
Synonymous codons are selected for increased site accessibility in plants
Summary
Mutations at synonymous codon sites are normally assumed to be evolutionarily neutral because these mutations don’t change its encoded protein sequences (Yang and Nielsen, 2000). Under this assumption, functional sites in protein coding sequences are identified by comparing non-‐synonymous substitution rate with synonymous substitution rate (Yang and Bielawski, 2000). The inclusion of synonymous codon selection has made more accurate inferences in evolutionary analysis of protein coding sequences (Nielsen, et al, 2007; Yang and Nielsen, 2008; Zhou, et al, 2010)
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