Prediction of gene expression and codon usage in human parasitic helminths

Codon usage bias refers to the differences in the occurrence frequency of synonymous codons. To understand the patterns of codon usage in mitochondrial genes we used bioinformatic approaches to analyze the protein coding sequences of W. bancrofti and S. haematobium as no work was reported earlier. It was found that the ENC value ranged from 43 to 60 with a mean of 46.91 in W. bancrofti but varied from 49 to 60 with a mean of 45.17 in S. haematobium, respectively. In W. bancrofti a significant positive correlation was found between ENC and GC3% (r = 0.826**, p < 0.01), but in S. haematobium significant correlation was found between ENC and GC3% (r = 0.983**, p < 0.01). Principal component analysis suggests that the pattern of codon usage significantly differed between W. bancrofti and S. haematobium. Neutrality plot reveals that natural selection played a major role while mutation pressure played a minor role in codon usage pattern in the mitochondrial protein coding genes of W. bancrofti and S. haematobium. Various factors namely nucleotide composition, natural selection and mutation pressure affected the codon usage pattern.