ArticlePloS one2012
Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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77 citing papers in PubMed, 173 citations in OpenAlex.
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- Comparative Analysis of Codon Usage Bias in Transcriptomes of Eight Species of Formicidae.Genes · 2025Article
- Insights into the mitochondrial genome structure and phylogenetic placement of Theileria velifera in comparison to other apicomplexan parasites.Scientific reports · 2025Article
- TAILcaller: an R package for analyzing differences in poly(A) tail length for Oxford Nanopore RNA sequencing.Bioinformatics advances · 2025Article
- Comparative chloroplast genomes and phylogenetic analysis of theFrontiers in plant science · 2025Article
- Compare Analysis of Codon Usage Bias of Nuclear Genome in Eight Sapindaceae Species.International journal of molecular sciences · 2024Article
- Mitochondrial genomes of Macropsini (Hemiptera: Cicadellidae: Eurymelinae): Structural features, codon usage patterns, and phylogenetic implications.Ecology and evolution · 2024Article
- Comparative structure and evolution of the organellar genomes of Padina usoehtunii (Dictyotales) with the brown algal crown radiation clade.BMC genomics · 2024Article
- Article
- The Patterns of Codon Usage between Chordates and Arthropods are Different but Co-evolving with Mutational Biases.Molecular biology and evolution · 2024Article
- Relative synonymous codon usage and codon pair analysis of depression associated genes.Scientific reports · 2024Article
- Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias.Acta biochimica Polonica · 2024Article
- Comparative and phylogenetic analyses based on the complete chloroplast genome ofFrontiers in plant science · 2024Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundCodon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene. Although genome sequencing of multiple species of dipteran and hymenopteran insects have been completed only a few of these species have been analyzed for codon usage bias. METHODS AND PRINCIPAL
findingsHere, we use bioinformatics approaches to analyze codon usage bias and codon context patterns in a genome-wide manner among 15 dipteran and 7 hymenopteran insect species. Results show that GAA is the most frequent codon in the dipteran species whereas GAG is the most frequent codon in the hymenopteran species. Data reveals that codons ending with C or G are frequently used in the dipteran genomes whereas codons ending with A or T are frequently used in the hymenopteran genomes. Synonymous codon usage orders (SCUO) vary within genomes in a pattern that seems to be distinct for each species. Based on comparison of 30 one-to-one orthologous genes among 17 species, the fruit fly Drosophila willistoni shows the least codon usage bias whereas the honey bee (Apis mellifera) shows the highest bias. Analysis of codon context patterns of these insects shows that specific codons are frequently used as the 3'- and 5'-context of start and stop codons, respectively.
conclusionsCodon bias pattern is distinct between dipteran and hymenopteran insects. While codon bias is favored by high GC content of dipteran genomes, high AT content of genes favors biased usage of synonymous codons in the hymenopteran insects. Also, codon context patterns vary among these species largely according to their phylogeny.
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