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Related Experiment Video

Updated: Jun 8, 2025

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
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Selection on synonymous codon usage in soybean (Glycine max) WRKY genes.

Krishnendu Sinha1, Sourav Jana2, Payel Pramanik2

  • 1Department of Zoology, Jhargram Raj College, Jhargram, 721507, India. dr.krishnendusinha@gmail.com.

Scientific Reports
|November 3, 2024
PubMed
Summary

Soybean WRKY genes show a balance between codon diversity and translation efficiency, shaped by selection forces. This research offers insights for enhancing soybean resilience and stress response in crops.

Keywords:
MutationNatural selectionSoybean (Glycine max)Synonymous codon usage biasTFBSWRKY

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Evolutionary biology

Background:

  • The WRKY transcription factor gene family (GmWRKY) in soybean (Glycine max) is crucial for plant development and stress tolerance.
  • Understanding the evolutionary dynamics and codon usage bias (CUB) of GmWRKY genes is key to optimizing their function.

Purpose of the Study:

  • To investigate the evolutionary patterns of the GmWRKY gene family using synonymous codon usage bias (CUB) analysis.
  • To explore the interplay between codon usage, translational efficiency, and selective pressures.
  • To identify potential adaptive evolution and its implications for soybean improvement.

Main Methods:

  • Analysis of 179 soybean GmWRKY coding sequences.
  • Calculation of various CUB indices, including Codon Adaptation Index (CAI).
  • Neutrality plots, NC plots, selection signature analysis, and phylogenetic analysis.
  • Promoter binding site analysis and ancestral sequence reconstruction.

Main Results:

  • GmWRKY genes exhibit a preference for A/T-ending codons with relatively low CUB, but are optimized for efficient translation (CAI).
  • Selective forces, particularly purifying selection, dominate over mutational forces, with evidence of episodic positive selection in some clades.
  • Codon usage correlates with transcriptional regulation, and modern GmWRKY genes show relaxed codon preferences compared to ancestral forms.
  • Phylogenetic analysis revealed 11 distinct clades, suggesting diversification and adaptation.

Conclusions:

  • The GmWRKY gene family's codon usage reflects a balance between diversity and translational efficiency, driven by selection.
  • Positive selection and relaxed constraints in modern genes may contribute to adaptation and neofunctionalization.
  • Findings provide a basis for improving gene expression and enhancing stress resilience in transgenic soybean crops.