Analysis of synonymous codon usage patterns in different plant mitochondrial genomes |
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Authors: | Meng Zhou Xia Li |
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Institution: | (1) Department of Bioinformatics, Harbin Medical University, Harbin, 150086, China |
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Abstract: | Codon usage in mitochondrial genome of the six different plants was analyzed to find general patterns of codon usage in plant
mitochondrial genomes. The neutrality analysis indicated that the codon usage patterns of mitochondrial genes were more conserved
in GC content and no correlation between GC12 and GC3. T and A ending codons were detected as the preferred codons in plant
mitochondrial genomes. The Parity Rule 2 plot analysis showed that T was used more frequently than A. The ENC-plot showed that although a majority of the points with low ENC values were lying below the expected curve, a few genes lied on the expected curve. Correspondence analysis of relative synonymous
codon usage yielded a first axis that explained only a partial amount of variation of codon usage. These findings suggest
that natural selection is likely to be playing a large role in codon usage bias in plant mitochondrial genomes, but not only
natural selection but also other several factors are likely to be involved in determining the selective constraints on codon
bias in plant mitochondrial genomes. Meantime, 1 codon (P. patens), 6 codons (Z. mays), 9 codons (T. aestivum), 15 codons (A. thaliana), 15 codons (M. polymorpha) and 15 codons (N. tabacum) were defined as the preferred codons of the six plant mitochondrial genomes. |
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