Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine ...

The degeneracy of the genetic code allows for multiple codons to encode the same amino acid. However, alternative codons and amino acids are used unevenly among genes, a phenomenon termed codon-usage bias. Genes regulating amino acid biosynthesis of Salinibacter ruber, an extremely halophilic bacterium were studied in order to determine the synonymous codon usage patterns. Factors responsible f...

Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple compl...

ABST RACT In this study, we analyzed the synonymous codon usage bias in porcine epidemic diarrhea virus genome. The effective number of codons (ENC) and the relative synonymous codon usage (RSCU) values are used to estimate codon usage variation. The plot of ENC values against GC3s and correlation analysis revealed that mutational pressure rather than translational selection is the main factor ...

A comparative analysis of the codon usage bias in the newly discovered dUTPase gene (Assigned Accession No.: DQ486149) of the duck enteritis virus (DEV) and the dUTPase gene of 32 reference herpesviruses was performed. The results indicated that the DEV dUTPase gene encodes a protein of 477 amino acids, which includes five conserved motifs with a 3–1–2–4–5 arrangement. The codon adaptation inde...

As one of the most ancient tree species, the codon usage pattern analysis of Ginkgo biloba is a useful way to understand its evolutionary and genetic mechanisms. Several studies have been conducted on angiosperms, but seldom on gymnosperms. Based on RNA-Seq data of the G. biloba transcriptome, amount to 17,579 unigenes longer than 300 bp were selected and analyzed from 68,547 candidates. The co...

We have analyzed codon usage patterns of 70 sequenced genes from different Lactobacillus species. Codon usage in lactobacilli is highly biased. Both inter-species and intra-species heterogeneity of codon usage bias was observed. Codon usage in L. acidophilus is similar to that in L. helveticus, but dissimilar to that in L. bulgaricus, L. casei, L. pentosus and L. plantarum. Codon usage in the l...

This data article contains data related to the article "Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions" by Subramanian and Sarkar, Genomics, 2015 (10.1016/j.ygeno.2015.05.009). The data comprises of sequence-based measures that quantify the effect of codon usage across genomes. The dat...

In unicellular organisms, synonymous codon bias is correlated with the level of gene expression [1]. The codon bias becomes stronger in genes with higher expression levels. It becomes weaker but still remains in genes with lower expression levels. The bias means that synonymous codons are not used at random. In highly expressed genes, the synonymous codon usage is mainly determined by an abunda...