ArticleBMC plant biology2022
Codon usage patterns across seven Rosales species.
Article in BMC plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
- Comparative mitogenomics of six Thrips species reveals conserved architecture, repeat variation, and nucleotide composition bias.Genetica · 2026Article
- Mitochondrial genome of Iodes seguinii reveals repeat-mediated recombination and phylogenetic insights in Icacinaceae.BMC genomics · 2026Article
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- The First Complete Mitochondrial Genome ofCurrent issues in molecular biology · 2026Article
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- Codon usage bias and selective constraints in Gentianales mitogenomes.BMC genomics · 2026Article
- Structural divergence and molecular adaptation ofFrontiers in plant science · 2026Article
- Sequence dynamics and plastome evolution: decoding the complete chloroplast genome of Oenothera drummondii and comparative analysis within Oenothera (Onagraceae).Functional & integrative genomics · 2025Article
- Codon Usage Bias Analysis in the Chloroplast Genome ofCurrent issues in molecular biology · 2025Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
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- Comprehensive analysis of complete chloroplast genome sequence of Morina L.Scientific reports · 2025Article
- Analysis of synonymous codon usage bias of Lassa virus.Virus research · 2025Article
- Analysis of heavy metal tolerance and genomics in an indigenous Kurthia strain from Kulik River reveals multi-metal resistance and dominance of selection pressure on codon usage patterns.Archives of microbiology · 2025Article
- Codon usage analysis in selected virulence genes of Staphylococcal species.Current genetics · 2025Article
- Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution.BMC genomics · 2025Article
- Complete mitochondrial genome ofFrontiers in genetics · 2025Article
- The organelle genomes of the endangered seagrassFrontiers in plant science · 2025Article
- Compare Analysis of Codon Usage Bias of Nuclear Genome in Eight Sapindaceae Species.International journal of molecular sciences · 2024Article
- Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae).BMC plant biology · 2024Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundCodon usage bias (CUB) analysis is an effective method for studying specificity, evolutionary relationships, and mRNA translation and discovering new genes among various species. In general, CUB analysis is mainly performed within one species or between closely related species and no such study has been applied among species with distant genetic relationships. Here, seven Rosales species with high economic value were selected to conduct CUB analysis.
resultsThe results showed that the average GC1, GC2 and GC3 contents were 51.08, 40.52 and 43.12%, respectively, indicating that the A/T content is more abundant and the Rosales species prefer A/T as the last codon. Neutrality plot and ENc plot analysis revealed that natural selection was the main factor leading to CUB during the evolution of Rosales species. All 7 Rosales species contained three high-frequency codons, AGA, GTT and TTG, encoding Arg, Val and Leu, respectively. The 7 Rosales species differed in high-frequency codon pairs and the distribution of GC3, though the usage patterns of closely related species were more consistent. The results of the biclustering heat map among 7 Rosales species and 20 other species were basically consistent with the results of genome data, suggesting that CUB analysis is an effective method for revealing evolutionary relationships among species at the family or order level. In addition, chlorophytes prefer using G/C as ending codon, while monocotyledonous and dicotyledonous plants prefer using A/T as ending codon.
conclusionsThe CUB pattern among Rosales species was mainly affected by natural selection. This work is the first to highlight the CUB patterns and characteristics of Rosales species and provides a new perspective for studying genetic relationships across a wide range of species.
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