title: Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer.
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.
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. eaeas12@163.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. eaeas12@163.com.
authors: Jibin
authors: J
authors: Liu
authors: Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. zdk24@sicau.edu.cn.
authors: Dekang
authors: D
authors: Zhu
authors: China Rural Technology Development Center, Beijing 100045, China. maguangpeng1977@163.com.
authors: Guangpeng
authors: G
authors: Ma
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. liumafengra@163.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. liumafengra@163.com.
authors: Mafeng
authors: M
authors: Liu
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. mshwang@163.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. mshwang@163.com.
authors: Mingshu
authors: M
authors: Wang
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. cqrc_jry@163.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. cqrc_jry@163.com.
authors: Renyong
authors: R
authors: Jia
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. sophia_cs@163.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. sophia_cs@163.com.
authors: Shun
authors: S
authors: Chen
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. 18981613263@163.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. 18981613263@163.com.
authors: Kunfeng
authors: K
authors: Sun
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. yangqiao721521@sina.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. yangqiao721521@sina.com.
authors: Qiao
authors: Q
authors: Yang
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. yingzi_no1@126.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. yingzi_no1@126.com.
authors: Ying
authors: Y
authors: Wu
authors: Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. chenxy_24@sina.cn.
authors: Xiaoyue
authors: X
authors: Chen
authors: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. chenganchun@vip.163.com.|Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. chenganchun@vip.163.com.
authors: Anchun
authors: A
authors: Cheng
mesh_terms: D003062:Codon / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D009154:Mutation; D060494:Riemerella / Q000235:genetics*; D012641:Selection, Genetic / Q000235:genetics
chemical_list: D003062:Codon
keywords: Riemerella anatipestifer; codon usage bias; highly expressed gene; natural selection