Research Article

Analysis of synonymous codon usage in FAD7 genes from different plant species

Published: February 13, 2015
Genet. Mol. Res. 14 (1) : 1414-1422 DOI: 10.4238/2015.February.13.20

Abstract

In this study, the codon bias of the FAD7 genes among 10 different plant species was analyzed to identify general patterns of codon usage in the FAD7 genes. Our results showed that U-ended or A-ended codons were preferentially used in FAD7 for dicots, whereas G-ended or C-ended codons were preferentially used in FAD7 for monocots. An ENC-plot showed that some other factors may influence the codon usage of FAD7, except mutation bias in plant species. A correlation analysis between the codon adaptation index and GC or GC3s contents demonstrated that the codon usage bias of the FAD7 gene in plant species could be influenced by the gene expression level. The cluster analysis of relative synonymous codon usage values and phylogenetic trees of protein sequences for FAD7 genes confirm that the codon preference of FAD7 is influenced by genetic relationships. Moreover, Arabidopsis thaliana and Nicotiana tabacum were predicted to be the most appropriate expression hosts for the FAD7 genes from dicots, and Zea mays may be suitable for the expression of the FAD7 genes from monocots. Our results provide useful insights into the evolutionary relationships of plant species.

In this study, the codon bias of the FAD7 genes among 10 different plant species was analyzed to identify general patterns of codon usage in the FAD7 genes. Our results showed that U-ended or A-ended codons were preferentially used in FAD7 for dicots, whereas G-ended or C-ended codons were preferentially used in FAD7 for monocots. An ENC-plot showed that some other factors may influence the codon usage of FAD7, except mutation bias in plant species. A correlation analysis between the codon adaptation index and GC or GC3s contents demonstrated that the codon usage bias of the FAD7 gene in plant species could be influenced by the gene expression level. The cluster analysis of relative synonymous codon usage values and phylogenetic trees of protein sequences for FAD7 genes confirm that the codon preference of FAD7 is influenced by genetic relationships. Moreover, Arabidopsis thaliana and Nicotiana tabacum were predicted to be the most appropriate expression hosts for the FAD7 genes from dicots, and Zea mays may be suitable for the expression of the FAD7 genes from monocots. Our results provide useful insights into the evolutionary relationships of plant species.

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