Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants

Zhen Qin,Mengcheng Wang,Guangmin Xia,Zhengqiu Cai

doi:10.1186/1471-2164-14-56

Zhen Qin, Mengcheng Wang + Show 2 more

Open Access

https://doi.org/10.1186/1471-2164-14-56

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Abstract

BackgroundEvidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. However, the relationship (if any) between SCUB and intron number as well as exon position is at present rather unclear.ResultsTo explore this relationship, the sequences of a set of genes containing between zero and nine introns was extracted from the published genome sequences of three algal species, one moss, one fern and six angiosperms (three monocotyledonous species and three dicotyledonous species). In the algal genomes, the frequency of synonymous codons of the form NNG/NNC (codons with G and C at the third position) was positively related to intron number, but that of NNA/NNT was inversely correlated; the opposite was the case in the land plant genomes. The frequency of NNC/NNG was higher and that of NNA/NNT lower in two terminal exons than in the interstitial exons in the land plant genes, but the rule showed to be opposite in the algal genes. SCUB patterns in the interstitial and two terminal exons mirror the different evolutionary relationships between these plant species, while the first exon shows the highest level of conservation is therefore concluded to be the one which experiences the heaviest selection pressure. The phenomenon of SCUB may also be related to DNA methylation induced conversion of CG to AT.ConclusionsThese data provide some evidence of linkage between SCUB, the evolution of introns and DNA methylation, which brings about a new perspective for understanding how genomic variation is created during plant evolution.

Highlights

Evidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron
The frequencies of most NNAs and NNTs were inversely related to intron number, while the relationship was largely opposite for most NNCs and NNGs
In the land plant sequences, the frequencies of NNAs and NNTs were positively correlated with intron number but the opposite was the case for NNCs and NNGs

Summary

Introduction

Evidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. The evolution of SCs is Evidence has been assembled to suggest a relationship between intron and SCUB (see review by [1]). Indel events necessarily entail prior DNA breakage and refusion, processes associated with genomic shock [9,10], a consequence of which can be the induction of local single nucleotide polymorphisms. Just as is the case for indels, the gain/loss of introns potentially induces genomic shock and its attendant consequences [11]. The propensity for intron gain/loss is related both to intron number and the intron’s position within the gene [12], so there is reason to suspect that SCUB may in turn be related to these variables

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