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Int. J. Mol. Sci. 2016, 17(8), 1304; doi:10.3390/ijms17081304

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

1
Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
2
Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
3
China Rural Technology Development Center, Beijing 100045, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Patrick C. Y. Woo
Received: 25 June 2016 / Revised: 31 July 2016 / Accepted: 2 August 2016 / Published: 10 August 2016
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
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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. View Full-Text
Keywords: Riemerella anatipestifer; codon usage bias; natural selection; highly expressed gene Riemerella anatipestifer; codon usage bias; natural selection; highly expressed gene
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Liu, J.; Zhu, D.; Ma, G.; Liu, M.; Wang, M.; Jia, R.; Chen, S.; Sun, K.; Yang, Q.; Wu, Y.; Chen, X.; Cheng, A. Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer. Int. J. Mol. Sci. 2016, 17, 1304.

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