Analysis of codon usage bias reveals optimal codons in Elaeis guineensis

Aditama, Redi; Tanjung, Zulfikar Achmad; Sudania, Widyartini Made; Nugroho, Yogo Adhi; Utomo, Condro; Liwang, Tony

doi:10.13057/biodiv/d211138

Cited by 4 publications

(4 citation statements)

References 39 publications

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“…Natural selection and other factors played a dominant role in codon preference. This was consistent with findings in Ginkgo biloba , Elaeis guineensis , and Morus notabilis [ 43 , 46 , 47 ]. The analysis of codon variation sources revealed that multiple factors influenced codon usage preference in the three coffee species, with natural selection and other factors being the determining factors.…”

Section: Discussionsupporting

confidence: 92%

“…cerevisiae is frequently used in eukaryotic systems [ 41 ]. Selecting receptors with small differences in codon preference is important for successful expression of exogenous genes and achieving high expression levels [ 43 , 46 , 47 ]. In our study, by comparing the codon usage frequencies of the three coffee genes with those of A. thaliana , N. tabacum , E. coli , and, S. cerevisiae , the codon frequency of the three kinds of coffee had slightly difference from that of N. tabacum and S. cerevisiae .…”

Section: Discussionmentioning

confidence: 99%

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An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

Xiang

Xiao

et al. 2023

BMC Genom Data

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Background The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation. Results Analysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes. Conclusion This study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

Xiang

Xiao

et al. 2023

BMC Genom Data

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“…In conclusion, natural selection played a dominant role in determining codon usage bias in the chloroplast genomes of the nine forage legumes, followed by mutational pressure. This finding is similar to previous studies on the chloroplast genes of P. sativum (Bhattacharyya et al 2019 ), Medicago truncatula (Song et al 2018 ), and Elaeis guineensis (Aditama et al 2020 ).…”

Section: Discussionsupporting

confidence: 92%

Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes

Xiao,

Hu,

et al. 2024

Physiol Mol Biol Plants

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Leguminosae is one of the three largest families of angiosperms after Compositae and Orchidaceae. It is widely distributed and grows in a variety of environments, including plains, mountains, deserts, forests, grasslands, and even waters where almost all legumes can be found. It is one of the most important sources of starch, protein and oil in the food of mankind and also an important source of high-quality forage material for animals, which has important economic significance. In our study, the codon usage patterns and variation sources of the chloroplast genome of nine important forage legumes were systematically analyzed. Meanwhile, we also constructed a phylogenetic tree based on the whole chloroplast genomes and protein coding sequences of these nine forage legumes. Our results showed that the chloroplast genomes of nine forage legumes end with A/T bases, and seven identical high-frequency (HF) codons were detected among the nine forage legumes. ENC-GC3s mapping, PR2 analysis, and neutral analysis showed that the codon bias of nine forage legumes was influenced by many factors, among which natural selection was the main influencing factor. The codon usage frequency showed that the Nicotiana tabacum and Saccharomyces cerevisiae can be considered as receptors for the exogenous expression of chloroplast genes of these nine forage legumes. The phylogenetic relationships of the chloroplast genomes and protein coding genes were highly similar, and the nine forage legumes were divided into three major clades. Among the clades Melilotus officinalis was more closely related to Medicago sativa, and Galega officinalis was more closely related to Galega orientalis. This study provides a scientific basis for the molecular markers research, species identification and phylogenetic studies of forage legumes.

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“…In this study, the CDSs from six B. distachyon inbred lines were used to analyze codon usage bias and the factors influencing the patterns. The bimodal distribution of the GC content and the negative correlation between the CG-skew and the number of hydrogen bonds in the codons positioned at the 5 -ends of the CDSs were detected in the six lines, indicating that GC content plays a major role in codon usage bias [37,38].…”

Section: Discussionmentioning

confidence: 93%

Analysis of Codon Usage Patterns of Six Sequenced Brachypodium distachyon Lines Reveals a Declining CG Skew of the CDSs from the 5′-ends to the 3′-ends

Jian-Yong

Lin

Mao

2021

Genes

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Brachypodium distachyon, a new monocotyledonous model plant, has received wide attention in biological research due to its small genome and numerous genetic resources. Codon usage bias is an important feature of genes and genomes, and it can be used in transgenic and evolutionary studies. In this study, the nucleotide compositions and patterns of codon usage bias were calculated using Codon W. Additionally, an ENC plot, Parity rule 2 and correspondence analyses were used to explore the major factors influencing codon usage bias patterns. The numbers of hydrogen bonds and skews were used to analyze the GC trend in the 5′-ends of the coding sequences. The results showed that minor differences in the codon usage bias patterns were revealed by the ENC plot, Parity rule 2 and correspondence analyses. The analyses of the CG-skew and the number of hydrogen bonds showed a declining trend in the number of cytosines at the 5′-ends of the CDSs (from the 5′-ends to the 3′-ends), indicating that GC may play a major role in codon usage bias. In addition, our results laid a foundation for the study of codon usage bias patterns in Brachypodium genus and suggested that the GC plays a major role in determining these patterns.

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Analysis of codon usage bias reveals optimal codons in Elaeis guineensis

Cited by 4 publications

References 39 publications

An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes

Analysis of Codon Usage Patterns of Six Sequenced Brachypodium distachyon Lines Reveals a Declining CG Skew of the CDSs from the 5′-ends to the 3′-ends

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