ArticleG3 (Bethesda, Md.)2021
Codon usage bias and dinucleotide preference in 29 Drosophila species.
Article in G3 (Bethesda, Md.), 2021. 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, 22 citations in OpenAlex.
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- Analysis and comparison of chloroplast genome codon usage patterns in five accessions of Toxicodendron vernicifluum.BMC genomics · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.PLoS biology · 2026Article
- Comparative Genomics of the Testacea Group of Drosophila Reveals Introgression and Variation in Chromosome Size and Structure.Genome biology and evolution · 2025Article
- Sex-biased duplicates are rapidly generated duringbioRxiv : the preprint server for biology · 2025Article
- Differences in morphological characteristics, photosynthetic capacity and Chloroplast genomes reveal molecular markers to distinguish Angelica sinensis, A. acutiloba and A. gigas.BMC plant biology · 2025Article
- Deciphering the genomic characters of Ptygonotus chinghaiensis, a high-altitude grasshopper endemic to the Qinghai-Tibet Plateau, using low-coverage short-read sequencing.BMC genomics · 2025Article
- Dinucleotide preferences underlie apparent codon preference reversals in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Codon-Usage Bias and Genomic Architecture of 79 Psoriasis-Susceptibility Genes: Implications for Expression Efficiency and Therapeutic Targeting.Psoriasis (Auckland, N.Z.) · 2025Article
- Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.BMC genomics · 2024Article
- Genome-wide identification, molecular evolution and gene expression of P450 gene family in Cyrtotrachelus buqueti.BMC genomics · 2024Article
- Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias.Acta biochimica Polonica · 2024Article
- The first complete mitochondrial genome of the genusParasitology · 2023Article
- In silico analysis of NAC gene family in the mangrove plant Avicennia marina provides clues for adaptation to intertidal habitats.Plant molecular biology · 2023Article
- Analysis of synonymous codon usage patterns in mitochondrial genomes of nineFrontiers in microbiology · 2023Article
- Protein-protein interaction and non-interaction predictions using gene sequence natural vector.Communications biology · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon usage bias, where certain codons are used more frequently than their synonymous counterparts, is an interesting phenomenon influenced by three evolutionary forces: mutation, selection, and genetic drift. To better understand how these evolutionary forces affect codon usage bias, an extensive study to detect how codon usage patterns change across species is required. This study investigated 668 single-copy orthologous genes independently in 29 Drosophila species to determine how the codon usage patterns change with phylogenetic distance. We found a strong correlation between phylogenetic distance and codon usage bias and observed striking differences in codon preferences between the two subgenera Drosophila and Sophophora. As compared to the subgenus Sophophora, species of the subgenus Drosophila showed reduced codon usage bias and a reduced preference specifically for codons ending with C, except for codons with G in the second position. We found that codon usage patterns in all species were influenced by the nucleotides in the codon's 2nd and 3rd positions rather than the biochemical properties of the amino acids encoded. We detected a concordance between preferred codons and preferred dinucleotides (at positions 2 and 3 of codons). Furthermore, we observed an association between speciation, codon preferences, and dinucleotide preferences. Our study provides the foundation to understand how selection acts on dinucleotides to influence codon usage bias.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.