Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species.

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dc.contributor.authorLiu, Qingpoen_US
dc.contributor.authorXue, Qingzhongen_US
dc.date.accessioned2005-04-07en_US
dc.date.accessioned2009-06-02T07:23:49Z
dc.date.available2005-04-07en_US
dc.date.available2009-06-02T07:23:49Z
dc.date.issued2005-04-07en_US
dc.description.abstractA detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm species Oryza sativa, Zea mays, Triticum aestivum and Arabidopsis 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 in O. sativa, Z. mays, and T. 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.en_US
dc.description.affiliationDepartment of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, 310029 Hangzhou, People's Republic of China. liuqp@genomics.org.cnen_US
dc.identifier.citationLiu Q, Xue Q. Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. Journal of Genetics. 2005 Apr; 84(1): 55-62en_US
dc.identifier.urihttps://imsear.searo.who.int/handle/123456789/114425
dc.language.isoengen_US
dc.source.urihttps://www.ias.ac.in/jgenet/index.htmlen_US
dc.subject.meshArabidopsis --geneticsen_US
dc.subject.meshBase Compositionen_US
dc.subject.meshChloroplasts --geneticsen_US
dc.subject.meshCodonen_US
dc.subject.meshGenome, Planten_US
dc.subject.meshNuclear Proteins --geneticsen_US
dc.subject.meshOryza sativa --geneticsen_US
dc.subject.meshPlant Proteins --geneticsen_US
dc.subject.meshSelection (Genetics)en_US
dc.subject.meshTriticum --geneticsen_US
dc.subject.meshZea mays --geneticsen_US
dc.titleComparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species.en_US
dc.typeComparative Studyen_US
dc.typeJournal Articleen_US
dc.typeResearch Support, Non-U.S. Gov'ten_US
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