Analysis of codon usage patterns in “Lonicerae Flos” (Lonicera macranthoides Hand. -Mazz.) based on transcriptome data

Liu, Sisi; Qiao, Zhongquan; Wang, Xiaoming; Zeng, Huijie; Li, Yongxin; Cai, Neng; Chen, Yi

doi:10.1016/j.gene.2019.04.065

Cited by 19 publications

(13 citation statements)

References 35 publications

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“…The results above indicated that the R. palmatum genes were preferred to A/U-ending synonymous codons which was inconsistent with Triticum aestivum ( Zhang et al, 2007 ), Oryza sativa ( Liu et al, 2004 ) and Zea mays ( Liu et al, 2010 ) that preferred to G/C-ending synonymous. Our result was consistent with the study of codon usage patterns in Lonicera macranthoides which was also biased to A/U-ending synonymous codons ( Liu et al, 2019 ).…”

Section: Resultssupporting

confidence: 92%

“…Moreover, the ratio of A/U-ended codons and G/C-ended codons for the most frequently used codons is 22:8. The result was consistent with that of nucleotide composition above and the phenomenon was also similar to other species with richer AT contents, namely Kluyveromyces lactis , Saccharomyces cerevisiae and Pichia pastoris ( Peixoto, Fernandez & Musto, 2004 ; Liu et al, 2019 ).…”

Section: Discussionsupporting

confidence: 90%

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Analysis of synonymous codon usage of transcriptome database inRheum palmatum

Huo

Liu²,

et al. 2021

PeerJ

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Background Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. Methods In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. Results The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.

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Section: Resultssupporting

confidence: 92%

Section: Discussionsupporting

confidence: 90%

Analysis of synonymous codon usage of transcriptome database inRheum palmatum

Huo

Liu²,

et al. 2021

PeerJ

Self Cite

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“…The results above indicated that the R. palmatum genes were preferred to A/U-ending synonymous codons which was inconsistent with Triticum aestivum (Zhang et al, 2007), Oryza sativa (Liu et al, 2004) and Zea mays (Liu et al, 2010) that preferred to G/C-ending synonymous. Our result was consistent with the study of codon usage patterns in Lonicera macranthoides which was also biased to A/U-ending synonymous codons (Liu et al, 2019).…”

Section: Effects Of Gene Expression Levelsupporting

confidence: 92%

Table 2: Correlation analysis of R. palmatum gene-related parameters.

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“…Among 18 amino acids that were encoded by synonymous codon in G. luofuense , A‐ending codons were more ideal than the U‐ending codons. In addition, G‐ending codons were more preferred than C‐ending codons, which corresponded to angiosperms but neither dicots nor monocots (Liu et al., 2019; Murray et al., 1989). Moreover, the GC content of three positions had significant differences among the novel and known transcripts.…”

Section: Discussionmentioning

confidence: 99%

Codon usage pattern analysis of Gnetum luofuense (Gnetales) based on transcriptome data

Deng¹,

Liu²,

Song³

et al. 2020

Agronomy Journal

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The Gnetum genus is an important medical, grain, and oil crop with ambiguous phylogenetic placement in seed plants. In the current study, full-length transcripts from G. luofuense L. leaves were utilized for codon usage pattern analysis.For this, a total of 30,666 full-length transcripts were used for analysis after data filtering. The GC content of all transcripts was 44.75%, with GC1 being the highest at 50.98%. Eighteen codons were identified as optimal codons, and 16 codons ending with A/U, indicating a higher frequency of A/T codon usage. Advanced analyses indicated that other factors, such as natural selection, play an important role in shaping the codon usage patterns in Gnetum. This study will be beneficial for understanding both the evolutionary mechanisms as well as the history of Gnetum genus.

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Analysis of codon usage patterns in “Lonicerae Flos” (Lonicera macranthoides Hand. -Mazz.) based on transcriptome data

Cited by 19 publications

References 35 publications

Analysis of synonymous codon usage of transcriptome database inRheum palmatum

Analysis of synonymous codon usage of transcriptome database inRheum palmatum

Table 2: Correlation analysis of R. palmatum gene-related parameters.

Codon usage pattern analysis of Gnetum luofuense (Gnetales) based on transcriptome data

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