ArticleScientific reports2024
Selection on synonymous codon usage in soybean (Glycine max) WRKY genes.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Integrative genomic and machine learning approaches reveal evolutionary signatures in the winged bean mitochondrial genome.BMC plant biology · 2025Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
- Integrative Approaches to Soybean Resilience, Productivity, and Utility: A Review of Genomics, Computational Modeling, and Economic Viability.Plants (Basel, Switzerland) · 2025Review
- Comprehensive analysis of the codon usage patterns in the polyprotein coding sequences of the honeybee viruses.Frontiers in veterinary science · 2025Article
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4 authors.
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Abstract
The WRKY transcription factor gene family in soybean [Glycine max (L.) Merr.] (GmWRKY) is critical for the plant's development and stress responses. This study examines the evolutionary dynamics of the GmWRKY gene family, focusing on its synonymous codon usage bias (CUB) in a comprehensive set of 179 coding sequences. CUB was analyzed using various indices, revealing a preference for A/T-ending codons and relatively low codon bias. Codon adaptation index (CAI) analysis suggested that these genes are optimized for efficient translation despite relatively low bias, reflecting a balance between codon diversity and translation efficiency. Neutrality and NC plots indicated that selective forces dominate over mutational forces in shaping codon usage, while selection signature analysis showed purifying selection being prevalent across the gene family. However, episodic positive selection was also detected in certain clades, highlighting potential adaptive diversification in response to environmental stress. Additionally, promoter binding site analysis uncovered correlations between codon usage and transcriptional regulation, indicating a context-dependent relationship between CUB and gene expression. Phylogenetic analysis identified 11 well-supported clades in the modern GmWRKY gene family and ancestral sequence reconstruction revealed more relaxed codon preferences and reduced selection constraints in modern GmWRKY genes, potentially linked to neofunctionalization and adaptation to environmental changes. These findings provide a framework for optimizing gene expression in transgenic soybean crops with resilience. Further functional validation of positively selected genes is recommended to elucidate their role in stress responses.
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