Comparative analysis of codon usage and tRNA in mitochondrial genomes of Gallus gallus

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Codon usage in mitochondrial genes of 11 Gallus gallus and two Anatidae species was analysed to determine the general patterns in codon choice of Gallus gallus species. C3 contents were higher in Gallus gallus than in mammalian mitochondrial genomes that encode protein codon positions. The high C3 contents of Gallus gallus might be the result of relatively strong mutational bias that occurred in the lineage of the Gallus gallus species. A and C ending codons were detected as the "preferred" codons in Gallus gallus and Anatidae. The NNR codon families are dominated by the A-ending codons, the NNY codon families are dominated by the C-ending codons and the NNN codon families are dominated by the A-ending or the C-ending codons. A comparison of the relative synonymous codon usage (RSCU) and synonymous codon families (SCF) of tRNA and proteins was made, and two groups can be classified by SCF. The codon usage in Gallus gallus species indicates that codons containing A or C at the third position are used preferentially, regardless of whether corresponding tRNAs are encoded in the mtDNA. In both Gallus gallus and Anatidae species mtDNA, codon usage biases are highly related to CC-ending binucleotide condons.


Document Type: Research Article


Publication date: August 1, 2009

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