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

Li, Changle; Zhou, Lu; Nie, Jiangbo; Wu, Songping; Li, Wei; Liu, Yonghong; Liu, Yulin

doi:10.1007/s12298-023-01289-6

Cited by 10 publications

(5 citation statements)

References 66 publications

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“…In general, natural selection is the main factor affecting codon usage bias in the cp genes of T. costata. It has been detected as a major factor influencing the codon usage bias in the cp genomes of several groups and species, for instance, in Mesona chinensis [55], Elaeagnus [56], Gynostemma [50], Juglandaceae [49], and Euphorbiaceae [53]. It has been reported that codon preference affects gene expression by regulating the accuracy and efficiency of gene translation [57].…”

Section: Codon Usage Bias In T Costata Cp Genomementioning

confidence: 99%

“…The study of codon usage patterns can determine the best codon to design gene expression vectors for increasing the expression of target genes [61]. Furthermore, in Gynostemma, it was found that the phylogenetic tree constructed using the RSCU clustering method was more suitable for analyzing evolutionary relationships than sequence data [56]. Detecting the codon usage pattern and optimal codon in the T. costata cp genome may be crucial in exploring species evolution and enhancing exogenous gene expression.…”

Section: Codon Usage Bias In T Costata Cp Genomementioning

confidence: 99%

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Structural Characterization of Trivalvaria costata Chloroplast Genome and Molecular Evolution of rps12 Gene in Magnoliids

Ping

Wang

2023

Forests

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Chloroplasts (cp) are important organelles in plant cells that have been widely used in phylogenetic, molecular evolution, and gene expression studies due to their conserved molecular structure. In this study, we obtained the complete cp genome of Trivalvaria costata (Annonaceae) and analyzed its structural characteristics. Additionally, we analyzed the rps12 gene in the phylogenetic framework of magnoliids. The T. costata cp genome comprises 1,662,002 bp and contains 132 genes. We detected 48 simple sequence repeats (SSRs) and identified 29 high-frequency codons as well as 8 optimal codons. Our multiple analyses show that codon usage bias is mainly influenced by natural selection. For the first time, we found the rps12 gene to be entirely located in the IR region (in Annona). In groups with exon 1 located in the single-copy (SC) region and exons 2–3 located in the inverted repeat (IR) region, the transition rate and synonymous substitution rate of exon 1 were higher than those of exons 2–3. Adaptive evolution identified a positive selection site (116) located in the 310-helix region, suggesting that the rps12 gene may undergo adaptive changes during the evolutionary history of magnoliids. This study enhances our knowledge regarding genetic information on T. costata and provides support for reduced substitution rates in the IR region.

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Section: Codon Usage Bias In T Costata Cp Genomementioning

confidence: 99%

Section: Codon Usage Bias In T Costata Cp Genomementioning

confidence: 99%

Structural Characterization of Trivalvaria costata Chloroplast Genome and Molecular Evolution of rps12 Gene in Magnoliids

Ping

Wang

2023

Forests

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“…The codon usage bias in chloroplast genomes may arise from a combination of natural selection and genetic mutation, which is important to investigate this phenomenon as it provides insights into the evolutionary processes and functional constraints shaping the genetic code of chloroplasts 39 . The relative frequency of synonymous codons in the coding sequence of M. pubescens cp demonstrated that all genes were represented by 19,850 codons.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome of Mussaenda pubescens and phylogenetic analysis

Zhou,

Tao,

Long

et al. 2024

Sci Rep

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The chloroplast (cp) genome sequence of Mussaenda pubescens, a promising resource that is used as a traditional medicine and drink, is important for understanding the phylogenetic relationships among the Mussaenda family and genetic improvement and reservation. This research represented the first comprehensive description of the morphological characteristics of M. pubescens, as well as an analysis of the complete cp genome and phylogenetic relationship. The results indicated a close relationship between M. pubescens and M. hirsutula based on the morphological characteristics of the flower and leaves. The cp was sequenced using the Illumina NovaSeq 6000 platform. The results indicated the cp genome of M. pubescens spanned a total length of 155,122 bp, including a pair of inverted repeats (IRA and IRB) with a length of 25,871 bp for each region, as well as a large single-copy (LSC) region and a small single-copy (SSC) region with lengths of 85,370 bp and 18,010 bp, respectively. The results of phylogenetic analyses demonstrated that species within the same genus displayed a tendency to group closely together. It was suggested that Antirhea, Cinchona, Mitragyna, Neolamarckia, and Uncaria might have experienced an early divergence. Furthermore, M. hirsutula showed a close genetic connection to M. pubescens, with the two species having partially overlapping distributions in China. This study presents crucial findings regarding the identification, evolution, and phylogenetic research on Mussaenda plants, specifically targeting M. pubescens.

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“…It has been proposed that organellar genes exhibit AT-richness and bias toward A- or T-ending codons in their genomes [ 37 – 39 ]. Extensive studies on the codon preference of the cp genomes have been published for a wide variety of organisms, for instance, Oryza plants [ 40 ], Elaeagnus plants [ 41 ], Epimedium plants [ 42 ], Euphorbiaceae species [ 39 ], Asteraceae species [ 43 ], and Theaceae species [ 44 ], among others. Nevertheless, the status of plant mitogenomes has not been well surveyed.…”

Section: Discussionmentioning

confidence: 99%

Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina

Zhang,

Wang,

Zhang

et al. 2024

BMC Genom Data

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Background Hemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and ornamental value. The phenomenon of codon usage bias (CUB) is prevalent in various genomes and provides excellent clues for gaining insight into organism evolution and phylogeny. Comprehensive analysis of the CUB of mitochondrial (mt) genes can provide rich genetic information for improving the expression efficiency of exogenous genes and optimizing molecular-assisted breeding programmes in H. citrina. Results Here, the CUB patterns in the mt genome of H. citrina were systematically analyzed, and the possible factors shaping CUB were further evaluated. Composition analysis of codons revealed that the overall GC (GCall) and GC at the third codon position (GC3) contents of mt genes were lower than 50%, presenting a preference for A/T-rich nucleotides and A/T-ending codons in H. citrina. The high values of the effective number of codons (ENC) are indicative of fairly weak CUB. Significant correlations of ENC with the GC3 and codon counts were observed, suggesting that not only compositional constraints but also gene length contributed greatly to CUB. Combined ENC-plot, neutrality plot, and Parity rule 2 (PR2)-plot analyses augmented the inference that the CUB patterns of the H. citrina mitogenome can be attributed to multiple factors. Natural selection, mutation pressure, and other factors might play a major role in shaping the CUB of mt genes, although natural selection is the decisive factor. Moreover, we identified a total of 29 high-frequency codons and 22 optimal codons, which exhibited a consistent preference for ending in A/T. Subsequent relative synonymous codon usage (RSCU)-based cluster and mt protein coding gene (PCG)-based phylogenetic analyses suggested that H. citrina is close to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in evolutionary terms, reflecting a certain correlation between CUB and evolutionary relationships. Conclusions There is weak CUB in the H. citrina mitogenome that is subject to the combined effects of multiple factors, especially natural selection. H. citrina was found to be closely related to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in terms of their evolutionary relationships as well as the CUB patterns of their mitogenomes. Our findings provide a fundamental reference for further studies on genetic modification and phylogenetic evolution in H. citrina.

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

Cited by 10 publications

References 66 publications

Structural Characterization of Trivalvaria costata Chloroplast Genome and Molecular Evolution of rps12 Gene in Magnoliids

Structural Characterization of Trivalvaria costata Chloroplast Genome and Molecular Evolution of rps12 Gene in Magnoliids

The complete chloroplast genome of Mussaenda pubescens and phylogenetic analysis

Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina

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