Codon Usage Bias and Cluster Analysis on Chloroplastic Genes from Seven Crop Species

doi:10.3969/j.issn.1000-7091.2012.04.011

Abstract

Abstract: The analysis of coded characters of crop chloroplast genes is benefit to the genetic engineering design of chloroplast,and the efficient and stable expression of exotic genes in recipient crops. In this study,the codon us- age bias of genes encoded by chloroplast DNA in 7 field crops were analyzed by means of several softwares. Results showed that there was little difference among the characters of chloroplast-coded genes among the 7 crops, which held a higher content of A and lower content of G and C. However, there were significant differences in the base composition of the third codon. The codons in the 3 dicotyledon crops were preferred to end with C, and second with T,while the other 4 gramineous crops preferred the codons ended with prior T, and second with C. There were 26 preferable codons used in the 4 gramineous crops and 25 in the 3 dicotyledon plants,among which 22 codons were totally same between the 2 kinds of crops. The cluster analysis based on RSCU value showed that the codon usage bias in the genes encoded by chloroplast was related to the plant species, indicating that the cluster analysis of RSCU in chloroplast genes could be used as a complementary method for the systematic developmental analysis.

Key words: Crop, Chloroplastic gene, Codon usage bias, Cluster analysis

CLC Number:

Q349.55

CHAO Yue-en, CHANG Yang, WANG Mei-fang, HE Sheng-lian, ZHAO Xian-lin, LEI Zhen-sheng. Codon Usage Bias and Cluster Analysis on Chloroplastic Genes from Seven Crop Species[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2012, 27(4): 60-64. doi: 10.3969/j.issn.1000-7091.2012.04.011.

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