Analysis of Codon Bias on Clostridium Perfringens Del1 Genome

Abstract

Abstract. Clostridium perfringens is a conditional pathogen, which widely exists in the nature water, soil, intestinal tract, and serious threat to public health and safety. In this study, the codon usage of Clostridium perfringens was examined. CDS sequences of 2744 high confidence protein coding genes were selected from Clostridium perfringens Genome Database. Their GC content of these genes ranged from 14.7% to 41.9%, with the average of 29.9% for whole genome. The frequency of G or C in the third position of synonymous codon was 25.6%, which was lower than that of A or T. The effective number of codon(ENC) of Clostridium perfringens genome ranged from 26.9 to 61.0,with the average of 39.9. Clostridium perfringens prefer codons ending in A/T. The ENC values of each gene significantly positive correlated with its C3s, G3s, GC3s and GC content (r=0.674, 0.738, 0.780 and 0.368, respectively, p<0.01). However, ENC showed significant negative correlations with T3s, respectively, p<0.01). A total of 27 optimal codons were found from Clostridium perfringens genome, all of which the third position of synonymous codon was A or T.