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Comparative analysis of synonymous codon usage patterns among six chloroplast genomes of wide taxonomic range species

Babak Latif, Rasoul Mohammadi Najafabadi, Mokhtar Jalali Javaran, Hamid Rajabi Memari, Houshang Alizadeh

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J. Bio. Env. Sci.4(3), 279-288, March 2014

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Abstract

It is important to understand general patterns of codon usage in chloroplast genomes. In the present study, codon usage patterns in chloroplast genomes of wide taxonomic range organisms namely Adiantum capillus-veneris, Arabidopsis thaliana, Chlorella vulgaris, Glycine max, Pinus koraiensis, and Triticum aestivum were analyzed using multivariate statistical analysis. The results indicated that the GC content at the third position of codons was low in the six investigated chloroplast genomes. There was a significant positive correlation between gene expression level, assessed by CAI values, and the position of genes along axis 1. On the other hand, there was a negative correlation between CAI and GC3s in the chloroplast genomes, which indicated that the gene expression level was the main factor in shaping codon usage, whereas mutational bias played a minor role in determining codon usage bias. Furthermore, gene length played a crucial role in codon usage bias of chloroplast genome in C. vulgaris and G. max and hydrophobicity of each protein played an important role in A. thaliana, C. vulgaris, and P. koraiensis. In addition, optimal codons of the chloroplast genomes were defined which may be usable to introduce point mutation, design of degenerate primers, investigate molecular evolution, and heterologous gene expression in the chloroplast genome.

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Comparative analysis of synonymous codon usage patterns among six chloroplast genomes of wide taxonomic range species

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