ArticleInternational journal of molecular sciences2016
Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer.
Article in International journal of molecular sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
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- Comparative Genomics Insights Into the Evolutionary Disparities Between Nitroplast-Evolved Ecotype UCYN-A2 and Its Closest Relative UCYN-A1.Ecology and evolution · 2025Article
- The complete mitogenome of Hyalomma anatolicum: novel insights into the phylogenetics of Hyalomma.Parasitology research · 2025Article
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- The complete mitochondrial genome of Eulaelaps huzhuensis (Mesostigmata: Haemogamasidae).Experimental & applied acarology · 2023Article
- Ten Plastomes ofBiology · 2022Article
- Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis.BMC plant biology · 2022Article
- Evolution of codon usage inFrontiers in veterinary science · 2022Article
- Analysis of codon usage bias of lumpy skin disease virus causing livestock infection.Frontiers in veterinary science · 2022Article
- Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2.Scientific reports · 2021Article
- Identification of the Natural Transformation Genes inFrontiers in microbiology · 2021Article
- Characterization of the complete mitochondrial genome of Amblyomma ovale, comparative analyses and phylogenetic considerations.Experimental & applied acarology · 2020Article
- Cas1 and Cas2 From the Type II-C CRISPR-Cas System ofFrontiers in cellular and infection microbiology · 2018Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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