Abstract
Riemerella anatipestifer (RA) belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC3 (p > 0.05). Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA.
Highlights
Riemerella anatipestifer (RA), belonging to the Flavobacteriaceae family, is a non-spore-forming, rod-shaped, and atrichous Gram-negative bacterium [1]
In bacteria with extreme genomic GC compositions, synonymous codon usage could be dominated by strong compositional bias [32].What is more, the mutation is universally biased towards AT in bacteria [33,34]
Our study reveals that codon usage bias in RA is slightly biased, and there is no significant difference between the strains in codon usage
Summary
Riemerella anatipestifer (RA), belonging to the Flavobacteriaceae family, is a non-spore-forming, rod-shaped, and atrichous Gram-negative bacterium [1]. It can cause a contagious disease in domestic ducks, geese, turkeys, and various other wild birds. More than 21 serovars have been identified [2]. No cross-protection has been observed with inactivated bacterins made from different serotypes of RA [3]. RA can cause large economic losses in the duck industry over the world. Codon usage bias (CUB) of genes generally exists in prokaryotes and eukaryotes. Except Trp (UGG) and Met (ATG) can allow more than one codon (called synonymous codon). Tmheethhoigdh. eTrhReShCiUghvearluReS,CsUuggveaslutien,gsmugogreestfirnegqumenotrecofdreoqnuuensatge, wacsordeopnreusseangtee,dwwaisthredparrekseenrtsehdadweisthofdraerdke. rInshRaidemeseroefllareadn.aItnipeRsiteimfeerr(eRllaAa)ngaetnipoemstiefesr, c(RodAo)ngsenenodmiensg, in A ocordUonhsaevnedhinigghienrARSoCr UU hvaavlueehtihgahnercRoSdCoUnsveanludeintghainn cGodoornCs.ending in G or C
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