Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species |
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Authors: | Qingpo Liu Qingzhong Xue |
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Institution: | (1) Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, 310 029 Hangzhou, China |
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Abstract: | A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm
speciesOryza sativa, Zea mays, Triticum aestivum andArabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in
chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The
results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon
usage bias of nuclear genes inO. sativa, Z. mays, andT. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence
analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of
chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have
predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These
findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from
its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines
were found more frequently than purines at the synonymous codon position of optimal codons. |
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Keywords: | codon usage bioinformatics chloroplast plant genome |
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