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, Wang; Lin, Yichen; Mao, Xi

doi:10.3390/genes12101467

Cited by 8 publications

(6 citation statements)

References 44 publications

(69 reference statements)

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“…We established the graphic with A3/(A3 + T3) as the y-axis and G3/(G3 + C3) as the x-axis [ 48 ]. The points around the central point (A = T, G = C) illustrate the degree and direction of base deviation [ 49 ]. The center point means that there is no deviation between natural selection and mutation pressure.…”

Section: Methodsmentioning

confidence: 99%

Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species

et al. 2023

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Background The Phenomenon of codon usage bias exists in the genomes of prokaryotes and eukaryotes. The codon usage pattern is affected by environmental factors, base mutation, gene flow and gene expression level, among which natural selection and mutation pressure are the main factors. The study of codon preference is an effective method to analyze the source of evolutionary driving forces in organisms. Epimedium species are perennial herbs with ornamental and medicinal value distributed worldwide. The chloroplast genome is self-replicating and maternally inherited which is usually used to study species evolution, gene expression and genetic transformation. Results The results suggested that chloroplast genomes of Epimedium species preferred to use codons ending with A/U. 17 common high-frequency codons and 2–6 optimal codons were found in the chloroplast genomes of Epimedium species, respectively. According to the ENc-plot, PR2-plot and neutrality-plot, the formation of codon preference in Epimedium was affected by multiple factors, and natural selection was the dominant factor. By comparing the codon usage frequency with 4 common model organisms, it was found that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae were suitable exogenous expression receptors. Conclusion The evolutionary driving force in the chloroplast genomes of 10 Epimedium species probably comes from mutation pressure. Our results provide an important theoretical basis for evolutionary analysis and transgenic research of chloroplast genes.

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Section: Methodsmentioning

confidence: 99%

Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species

et al. 2023

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“…Moreover, the average values of A3 + T3 and G3 + C3 were calculated as 0.5696 and 0.4304, respectively. These findings indicate an imbalance in codon usage between A + T and G + C at the third codon position, suggesting the influence of factors beyond mutation, natural selection pressure 41,42 , on codon usage patterns in GmWRKY transcription factors.…”

Section: Pr2-bias Plot Analysismentioning

confidence: 90%

“…PR2-plot analysis 24,25 positions the center point to indicate balanced base content, where A = T and G = C, suggesting an equilibrium between mutation pressure and natural selection 33 . Any deviation from this equilibrium implies a significant influence of natural selection on the gene compared to mutational pressure 25,[39][40][41] . In this study, the PR2 plot analysis revealed a tendency of occupancy toward the lower left or lower right region along the ordinate axis (A < T), with a comparable distribution on both sides of the abscissa axis (Figure 5).…”

Section: Pr2-bias Plot Analysismentioning

confidence: 99%

Natural Selection Primarily Shaping Codon Usage Bias in Glycine max (soybean) WRKY Genes

Sinha,

Jana,

Pramanik

et al. 2024

Preprint

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Background: Codon usage biases in genomes emerge from the interaction of two prominent evolutionary factors: mutational pressure and natural selection. Studying codon usage bias facilitates the understanding of the fundamental evolutionary mechanisms influencing genetic structure. Glycine max (soybean) holds considerable agricultural and industrial significance as a widely cultivated crop. Despite the pivotal role of WRKY transcription factors in plant regulation and stress responses, investigations of these transcription factors in Glycine max are limited, providing an opportunity to probe evolutionary trends within this gene family. Results: Examination of the base composition of the Glycine max WRKY genes revealed an average GC content of 44.85% and an average GC3 content of 42.01%, indicating a preference for A/T(U)-ending codons. Relative synonymous codon usage (RSCU) analysis identified 27 codons with RSCU > 1, predominantly ending with A and U bases. The effective number of codons (NC) ranged from 42.17 to 61, with codon adaptation index (CAI) values ranging from 0.713 to 0.904, suggesting a phenomenon of weak codon bias yet high expression levels in WRKY genes. Neutrality analysis indicated a significantly weak correlation between GC12 and GC3, while NC plot analysis revealed the predominant role of natural selection in shaping the codon usage pattern. Parity rule 2 plot (PR2) analysis highlighted disproportionate usage of AT and GC bases. One optimal codon was identified. Conclusion: Natural selection is the primary driving force of codon usage preferences in Glycine max WRKY genes. These findings provide new insights into the genetic landscape and evolutionary mechanisms of translational efficiency in Glycine max, contributing to the enhancement of genetic resources in soybeans.

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“…According to PR2, the center of the coordinate is A = T and G = C, indicating the absence of mutation pressure or natural selection on the codons. If there is mutation pressure or selection bias, the values deviate from the center (off-center) and the PCGs are unevenly distributed ( Wang et al 2021 ).…”

Section: Methodsmentioning

confidence: 99%

First report of the complete mitochondrial genome of 3 beetles (Coleoptera: Scarabaeidae) harming Gastrodia elata (Asparagales: Orchidaceae)

Long,

Zhu,

Yang

et al. 2024

Journal of Insect Science

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Gastrodia elata Blume, a valuable traditional Chinese medicine with significant clinical and nutritional importance, is a fungal heterotrophic orchid. We present the first report of the mitochondrial genome structure and characteristics of 3 Scarabaeidae pests affecting G. elata: Sophrops peronosporus Gu & Zhang, Anomala rufiventris Kollar & Redtenbacher, and Callistethus plagiicollis Fairmaire. Each mitogenome contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region, with no gene rearrangements observed. All 21 tRNAs, except trnS1 that lacks a dihydrouridine, had a stable cloverleaf secondary structure. Maximum likelihood and Bayesian inference analyses based on the 13 PCGs produced 2 topologically similar phylogenetic trees, both of with high nodal support. Larvae of these Scarabaeidae pests cause substantial damage by gnawing on the tubers and roots of G. elata, leading to reduced yield and compromised quality. These findings contribute to phylogenetic studies of Scarabaeidae, expand knowledge of G. elata pests, and offer valuable reference materials for their identification and control.

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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

Cited by 8 publications

References 44 publications

Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species

Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species

Natural Selection Primarily Shaping Codon Usage Bias in Glycine max (soybean) WRKY Genes

First report of the complete mitochondrial genome of 3 beetles (Coleoptera: Scarabaeidae) harming Gastrodia elata (Asparagales: Orchidaceae)

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