ArticleMolecular biotechnology2011
Synonymous codon usage, GC(3), and evolutionary patterns across plastomes of three pooid model species: emerging grass genome models for monocots.
Article in Molecular biotechnology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 71 citations in OpenAlex.
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- Phylogenetic and comparative analyses of Hydnora abyssinica plastomes provide evidence for hidden diversity within Hydnoraceae.BMC ecology and evolution · 2023Article
- Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships.BMC plant biology · 2022Article
- Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau.BMC plant biology · 2022Article
- Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae).Biology · 2022Article
- Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns.Frontiers in neuroscience · 2022Article
- Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus.Pathogens (Basel, Switzerland) · 2021Article
- Peculiarities of the inverted repeats in the complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2021Article
- Exploiting codon usage identifies intensity-specific modifiers of Ras/MAPK signaling in vivo.PLoS genetics · 2020Article
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- DNA methylation changes in clonally propagated oil palm.Plant cell reports · 2020Article
- The Plastid Genome of Deschampsia cespitosa (Poaceae).Molecules (Basel, Switzerland) · 2019Article
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Authors and funding
4 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have analyzed factors affecting the codon usage pattern of the chloroplasts genomes of representative species of pooid grass family. Correspondence analysis of relative synonymous codon usages (RSCU) showed that genes on secondary axis were correlated with their GC(3S) values (all r > 0.3, p < 0.05), indicating mutational bias as an important selective force that shaped the variation in the codon usage among chloroplast genes. The Nc-plot showed that although a majority of the points with low-Nc values were lying below the expected curve, a few genes lied on the expected curve. Nc plot clearly showed that mutational bias plays a major role in codon biology across the monocot plastomes. The hydrophobicity and aromaticity of encoded proteins of each species were found to be other factors of codon usage variation. In the view of above light, besides natural selection, several other factors also likely to be involved in determining the selective constraints on codon bias in plastomes of pooid grass genomes. In addition, five codons (B. distachyon), seven codons (H. vulgare), and four codons (T. aestivum) were identified as optimal codons of the three grass chloroplasts. To identify genes evolving under positive selection, rates of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) were computed for all groups of orthologous gene pairs.
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