Analysis of synonymous codon usage in the Cas1 gene of Riemerella anatipestifer

Object: The study herein was aimed to provide a comprehensive analysis of synonymous codon usage in Riemerella anatipestifer (RA) Cas1 gene and a comparative study of the codon usage bias between RA and other 11 reference strains within the Flavobacteriaceae family. Methods: Using bioinformatics method, the values of relative synonymous codon usage (RSCU), the effective number of codons (ENc), G+C content at the 3rd codon position (GC3s), and the codon adaptation index (CAI) was computed with the help of CHIPS, CUSP, and CAI programs of EMBOSS. Result: The results suggested that Cas1 genes in RA and its 11 reference strains applied the relatively similar pattern of codon usage with similar sequence length, CAI, and ENc values, and all of them were lowly expressed genes. The codon bias pattern of Cas1 genes in RA and its reference strains was closely related to their gene function. The plots of ENc versus GC3s indicated that the genetic heterogeneity of these genes observed herein was constrained by GC composition. Besides, RA Cas1 gene preferred A or/and T ending codons to G or/and C ending codons, and the bias corresponded to high A+T content in RA cas1 gene. GC compositional constraint was found to be a major determinant of codon usage in RA Cas1 gene. Additionally, The comparison of the codon preference of RA Cas1 gene with those of E. coli, yeast, and human, revealed that codon usage varied among different organisms and the codon usage pattern of RA Cas1 gene was similar to that of yeast. Accordingly, it can be speculated that yeast was a well suited host for heterologous expression of RA Cas1 gene. Conclusion: Bioinformatics analysis plays an important role in research of genes. And using bioinformatics method, the paper provides a foundational understanding of the molecular evolution and function of RA Cas1 gene, as well as contributes significantly to guiding the further study of the gene.