Analysis of synonymous codon usage in the mfs_1 gene of Riemerella anatipestifer

Abstract

The analysis on codon usage bias of major facilitator superfamily mfs_1 gene of Riemerella anatipestifer (RA) may improve our understanding of the evolution and pathogenesis of RA and provide a basis for understanding the relevant mechanism for biased usage of synonymous codons and for selecting appropriate expression systems to improve the expression of target genes. All of these analysis results of synonymous codon usage in major facilitator superfamily mfs_1 gene were finished by kinds of bioinformatics analysis software such as CodonW version 1.4, The European Molecular Biology Open Software Suite (EMBOSS) Chips online service program, Clustal-X and MEGA software, at the same time, including some online website. The information you needed would be listed after you submitting the right format of the sequence of major facilitator superfamily mfs_1 gene. In this paper, the codon usage bias of major facilitator superfamily mfs_1 genes of RA and 16 other bacteriums were analyzed. The results showed that codon of major facilitator superfamily mfs_1 gene of RA were strong bias toward the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed, and the effective number of codons used in a gene plot revealed that the genetic heterogeneity in major facilitator superfamily mfs_1 gene of bacteriums was constrained by the G +C content. The phylogenic analysis suggested that RA was evolutionarily closer to Flavobacterium indicum GPTSA100-9 and Sphingobacterium spiritivorum ATCC 33300 contig00111. There were 31 codons showing distinct usage differences between RA and yeast, 38 between RA and Homo sapiens, but only 35 codons between RA and Escherichia coli. Therefore the Escherichia coli expression system may be more suitable for the expression of RA genes.