Codon Usage in the Chloroplast Genome of Rice ( Oryza sativa L ssp japonica )

The codon usage in the genome is usually influenced by many factors A correspondence analysis was performed for exploring the effects of several important factors on codon usage in the complete chloroplast genome sequences of Nipponbare The results showed that there were significant correlations ( r =0 785 ** and -0 804 ** ) between the gene position on first axis and gene expression level, with both the assessments (Codon Adaptation Index,CAI and GC3s values ), whereas a strongly negative correlation ( r = -0 917 ** ) between CAI and GC3s values, indicating that the natural selection on gene expression level was the major factor affecting the codon usage of Nipponbare, and that highly expressed genes had a stronger preference for codons with T or A at the third nucleotide position From a lower positive correlation between GC content and ENC ( r =0 344 ** ), and lower negative correlations between GC content and CAI, axis 1 coordinates ( r = -0 422 ** and -0 421 ** , respectively), we could conclude that the GC content in coding region gave a less contribution to codon usage bias than that to gene expression level The results of correlation analysis and variance analysis showed that gene lengths did not significantly affected genomic codon usage bias, which was probably related to those ORFs with unidentified function The replication transcription selection had a far less influence on the codon usage of a gene Through an analysis of both the high expression codon and high frequency codon, we defined 12 codons from 12 amino acids as the major preference codons in cv Nipponbare