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Transcriptomic analysis of codon usage patterns and gene expression characteristics in leafy spurge.

Zhanjun Wang1,2,3, Jie Li1, Xuyuan Liu4

  • 1School of Biology and Food Engineering, Hefei Normal University, Hefei, Anhui, China.

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|November 24, 2024
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Summary

Leafy spurge exhibits codon usage bias (CUB) influenced by natural selection, impacting gene expression. Understanding this bias is key for improving gene expression and developing transgenic leafy spurge applications.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Science

Background:

  • Leafy spurge (Euphorbia esula) is a valuable herb with medicinal and energy potential.
  • Codon usage bias (CUB) is a genomic feature shaped by evolution, crucial for molecular breeding.
  • Understanding CUB in leafy spurge can optimize gene expression for biotechnological applications.

Purpose of the Study:

  • To analyze codon usage bias in the leafy spurge genome.
  • To identify factors influencing CUB and its relationship with gene expression.
  • To lay the groundwork for selecting effective exogenous expression systems in leafy spurge.

Main Methods:

  • Transcriptome data analysis using TransDecoder to identify coding regions.
  • Whole-genome analysis to detect base composition bias and high-frequency codons.
  • Comparative analysis of codon usage frequencies and gene expression levels.

Main Results:

  • Leafy spurge genome displays A/T bias, particularly at terminal positions, with seven high-frequency codons identified.
  • Natural selection and other factors were dominant in shaping CUB, alongside mutation pressure and base composition.
  • A significant positive correlation was observed between CUB and gene expression levels; highly expressed genes showed greater CUB and a tendency for terminal G/C bases.

Conclusions:

  • Codon usage bias in leafy spurge is significantly influenced by evolutionary pressures, primarily natural selection.
  • Highly expressed genes in leafy spurge exhibit distinct CUB patterns, favoring terminal G/C bases.
  • This study provides a foundation for optimizing gene expression and developing transgenic leafy spurge.