Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species

Wang, Zhanjun; Cai, Qianwen; Wang, Yue; Li, Min-Hui; Wang, Chenchen; Wang, Zhaoxia; Chen, Jiao; Xu, Congcong; Wang, Hongyan; Zhang, Zhaoliang

doi:10.3389/fgene.2022.824610

Cited by 36 publications

(34 citation statements)

References 53 publications

(72 reference statements)

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“…Consequently, AT is strongly favored at the third bases of codons in the Saxifragales plastid genes, suggesting that selection pressure is responsible for the CUB patterns. Additionally, our findings revealed that ten genes in Saxifragales had GC1 > 0.5 and two genes had GC2 > 0.5, which is different from other studies where GC1, GC2, and GC3 values of plastid genes were all less than 0.5 [ 36 , 62 , 84 , 85 ]. Most notably, as proposed by Morton and So [ 86 ], stronger codon adaptation in plastid genes would lead to higher GC contents in the first and second bases of codons.…”

Section: Discussioncontrasting

confidence: 99%

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Han

Zhou

et al. 2023

Genes

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Saxifragales is a 15-family order of early-divergent Eudicots with a rich morphological diversity and an ancient rapid radiation. Codon usage bias (CUB) analyses have emerged as an essential tool for understanding the evolutionary dynamics in genes. Thus far, the codon utilization patterns had only been reported in four separate genera within Saxifragales. This study provides a comprehensive assessment of the codon manipulation based on 50 plastid genes, covering 11 constituent families at a larger sampling scale. Our results first showed a high preference for AT bases and AT-ending codons. We then used effective number of codons (ENC) to assess a range of codon bias levels in the plastid genes. We also detected high-informative intrafamilial differences of ENC in three families. Subsequently, parity rule 2 (PR2) plot analyses revealed both family-unique and order-shared bias patterns. Most importantly, the ENC plots and neutrality analyses collectively supported the dominant roles of selection in the CUB of Saxifragales plastid genes. Notably, the phylogenetic affinities inferred by both ML and BI methods were consistent with each other, and they all comprised two primary clades and four subclades. These findings significantly enhance our understanding of the evolutionary processes of the Saxifrage order, and could potentially inspire more CUB analyses at higher taxonomic levels.

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Section: Discussioncontrasting

confidence: 99%

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Han

Zhou

et al. 2023

Genes

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“…In terms of nucleotide composition at three codon positions (GC1s, GC2s, and GC3s), together with the codon bias index N c and RSCU values, Quercus chloroplasts showed no significant differences between genomes but significant differences between genes within the genomes. Codon usage in chloroplast genomes of Theaceae species was found to be similar between species and prefer A/T ending codons [ 61 ], in accordance with the results of 16 Fagaceae chloroplast genomes [ 27 ] and the results of our investigation. We found that codon usage was consistent between oak chloroplast genomes, and that most A- and T-ending codons had relatively higher RSCU values and were therefore preferred for use.…”

Section: Discussionsupporting

confidence: 89%

Comprehensive Analysis of Codon Usage in Quercus Chloroplast Genome and Focus on psbA Gene

Sheng

Liu

Xia

et al. 2022

Genes

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Quercus (oak) is an important economic and ecological tree species in the world, and it is the necessary feed for oak silkworm feeding. Chloroplasts play an important role in green plants but the codon usage of oak chloroplast genomes is not fully studied. We examined the codon usage of the oak chloroplast genomes in detail to facilitate the understanding of their biology and evolution. We downloaded all the protein coding genes of 26 non-redundant chloroplast reference genomes, removed short ones and those containing internal stop codons, and finally retained 50 genes shared by all genomes for comparative analyses. The base composition, codon bias, and codon preference are not significantly different between genomes but are significantly different among genes within these genomes. Oak chloroplast genomes prefer T/A-ending codons and avoid C/G-ending codons, and the psbA gene has the same preference except for the codons encoding amino acid Phe. Complex factors such as context-dependent mutations are the major factors affecting codon usage in these genomes, while selection plays an important role on the psbA gene. Our study provided an important understanding of codon usage in the oak chloroplast genomes and found that the psbA gene has nearly the same codon usage preference as other genes in the oak chloroplasts.

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“…This was consistent with previous studies. Chloroplast genomes in other plants, such as Camellia amplexicaulis [ 24 ], Panicum incomtum [ 25 ], Oryza australiensis [ 26 ], Euphorbia esula [ 27 ], etc., also tended to use codons ending with A/U. According to the RSCU analysis, it was found that most of the frequently used codons (RSCU > 1) were A/U-ending, whereas the less frequently used codons (RSCU< 1) were G/C-ending.…”

Section: Discussionmentioning

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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Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species

Cited by 36 publications

References 53 publications

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Comprehensive Analysis of Codon Usage in Quercus Chloroplast Genome and Focus on psbA Gene

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

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