Analysis of Codon Usage Bias in the &lt;i&gt;Platycarya&lt;/i&gt; Chloroplast Genome

Wang, Xiaoshuang; Wang, Yanqing; Li, Shihong; Liu, Yingliang; Zhu, Bin

doi:10.5376/tgmb.2021.11.0001

Cited by 3 publications

(2 citation statements)

References 20 publications

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“…In the chloroplast genomes of the six plants examined in this study, Arg and Leu were found to be more frequently used. Among amino acids with a total codon count below 2,000, Cys exhibited the lowest frequency, aligning with patterns observed in terrestrial plants like Allium mongolicum Regel 66 and Psammosilene tunicoides W.C. Wu et C.Y. Wu 67 .…”

Section: Disscussionsupporting

confidence: 77%

Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes

Feng,

Zheng,

Jiang

et al. 2024

Sci Rep

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The subfamily Polygonoideae encompasses a diverse array of medicinal and horticultural plants that hold significant economic value. However, due to the lack of a robust taxonomy based on phylogenetic relationships, the classification within this family is perplexing, and there is also a scarcity of reports on the chloroplast genomes of many plants falling under this classification. In this study, we conducted a comprehensive analysis by sequencing and characterizing the complete chloroplast genomes of six Polygonoideae plants, namely Pteroxygonum denticulatum, Pleuropterus multiflorus, Pleuropterus ciliinervis, Fallopia aubertii, Fallopia dentatoalata, and Fallopia convolvulus. Our findings revealed that these six plants possess chloroplast genomes with a typical quadripartite structure, averaging 162,931 bp in length. Comparative chloroplast analysis, codon usage analysis, and repetitive sequence analysis demonstrated a high level of conservation within the chloroplast genomes of these plants. Furthermore, phylogenetic analysis unveiled a distinct clade occupied by P. denticulatum, while P. ciliinrvis displayed a closer relationship to the three plants belonging to the Fallopia genus. Selective pressure analysis based on maximum likelihood trees showed that a total of 14 protein-coding genes exhibited positive selection, with psbB and ycf1 having the highest number of positive amino acid sites. Additionally, we identified four molecular markers, namely petN-psbM, psal-ycf4, ycf3-trnS-GGA, and trnL-UAG-ccsA, which exhibit high variability and can be utilized for the identification of these six plants.

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Section: Disscussionsupporting

confidence: 77%

Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes

Feng,

Zheng,

Jiang

et al. 2024

Sci Rep

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“…Analyzing codon usage patterns is important for the study of gene expression levels, protein structures and translation rates in organisms (Wang et al, 2023). Codon usage preference is an adaptive choice formed by species during long-term natural selection and evolutionary processes, which is mainly influenced by gene mutation pressure and natural selection pressure (Sueoka et al, 1988).…”

Section: Gc Content Analysismentioning

confidence: 99%

Analysis of Codon Preferences in Medicago ruthenica based on Transcriptome Data

Peng,

Mu,

et al. 2024

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Background: The study investigated codon usage bias in Medicago ruthenica transcriptome coding sequences, aiming to lay the foundation for optimizing codon composition and enhancing heterologous gene expression in Medicago ruthenica. Methods: In this research, Medicago ruthenica was used as the research material and 11,581 high-quality transcript gene sequences were selected from transcriptome data. Codon usage patterns and preferences were analyzed using software such as CodonW, R and Excel. Result: The study revealed that the effective number of codons (ENC) ranged from 28.8 to 61.0. The average GC content of codons in expressed genes of Medicago ruthenica was 0.40 and the average GC content of the third nucleotide position of synonymous codons (GC3s) was 0.33. Analysis through ENC-plot, neutrality plot and bias analysis suggested that codon usage bias in the Medicago ruthenica transcriptome may be the result of a combination of factors including selection and mutation. Fifteen optimal codons were selected, with ten ending in ‘A’ and five ending in ‘U’, indicating a preference for ‘A/U’ ending codons in the Medicago ruthenica transcriptome. The frequency of codon usage in Medicago ruthenica was compared to five other organisms, including Arabidopsis thaliana, Glycine max, Nicotiana tabacum, yeast and Escherichia coli, revealing significant differences with E. coli and relatively smaller differences with Nicotiana tabacum.

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Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae)

Zhou

Nie

et al. 2023

Physiol Mol Biol Plants

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Analysis of Codon Usage Bias in the <i>Platycarya</i> Chloroplast Genome

Cited by 3 publications

References 20 publications

Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes

Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes

Analysis of Codon Preferences in Medicago ruthenica based on Transcriptome Data

Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae)

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