Natural Selection Primarily Shaping Codon Usage Bias in Glycine max (soybean) WRKY Genes

Abstract

Background: Codon usage biases in genomes emerge from the interaction of two prominent evolutionary factors: mutational pressure and natural selection. Studying codon usage bias facilitates the understanding of the fundamental evolutionary mechanisms influencing genetic structure. Glycine max (soybean) holds considerable agricultural and industrial significance as a widely cultivated crop. Despite the pivotal role of WRKY transcription factors in plant regulation and stress responses, investigations of these transcription factors in Glycine max are limited, providing an opportunity to probe evolutionary trends within this gene family. Results: Examination of the base composition of the Glycine max WRKY genes revealed an average GC content of 44.85% and an average GC3 content of 42.01%, indicating a preference for A/T(U)-ending codons. Relative synonymous codon usage (RSCU) analysis identified 27 codons with RSCU > 1, predominantly ending with A and U bases. The effective number of codons (NC) ranged from 42.17 to 61, with codon adaptation index (CAI) values ranging from 0.713 to 0.904, suggesting a phenomenon of weak codon bias yet high expression levels in WRKY genes. Neutrality analysis indicated a significantly weak correlation between GC12 and GC3, while NC plot analysis revealed the predominant role of natural selection in shaping the codon usage pattern. Parity rule 2 plot (PR2) analysis highlighted disproportionate usage of AT and GC bases. One optimal codon was identified. Conclusion: Natural selection is the primary driving force of codon usage preferences in Glycine max WRKY genes. These findings provide new insights into the genetic landscape and evolutionary mechanisms of translational efficiency in Glycine max, contributing to the enhancement of genetic resources in soybeans.