Abstract:

【Objective】The codon usage bias in Gossypium hirsutum chloroplast genome was analyzed to find the factors affecting the formation of codon bias. 【Method】 Codon of fifty genes which were selected from the chloroplast genome sequence of Gossypium hirsutum were studied. Mobyle and other softwares were used to calculate different parameters for the codon usage.【Result】G+C content of the third position in the codons is the lowest among the three positions. The GC3 has a low correlation coefficient (0.14) to the GC12 which is insignificant, whereas GC1 and GC2 have a significant correlation coefficient. ENC ratio of most genes ranged from -0.05 to 0.05. In the corresponding analysis, the first axis shows 10.27% variation. The correlation coefficients for axis1 with GC3 and ENC are 0.223 and -0.147, respectively, and both are insignificant. 【Conclusion】The codon usage bias is formed under effect of mutation and selection, as well as other factors. Genes in function group possibly have the similar factor for the codon formation. The third positions for all codon are preferred to pyrimidine and the most preferred codons end with A and T.

Key words: Gossypium hirsutum, codon bias, GC contents, preferred codon