Codon Usage Bias Analysis of the WRKY Gene Family in Musa acuminata

Abstract

Codon usage bias (CUB) is a universal phenomenon across all organisms and species, providing valuable insights into codon usage patterns to understand evolutionary mechanisms. The WRKY transcription factor family plays a pivotal role in regulating plant responses to various stresses at both physiological and biochemical levels. Bananas (Musa spp.), widely consumed as a fruit or staple food, are an important horticulture crop in the tropical and subtropical regions around the world. A total of 151 WRKY transcription factors were identified across the genome of the Musa acuminata banana cultivar ‘Guijiao 9’, which has been shown to be resistant to the Tropical Race 4 of the Fusarium wilt of banana. The codons of these transcription factors, selected based on their expression from RNA-Seq data, were analysed to investigate the evolutionary patterns of WRKY genes in Musa acuminata. The average GC content of MaWRKY genes was 55.49%, with a GC3 content of 62.13%, indicating a preference for G/C-ending codons. Among the codons, 27 were identified as high frequency, with 22 ending in G or C. The high effective number of codons (ENC) values (34.53–60.79) and low codon adaptation index (CAI) values (0.143–0.3) suggested weak CUB and that was associated with low gene expression levels. ENC-plot, PR2-plot, and neutrality analysis revealed that both natural selection and mutation pressure contributed to the observed CUB, with natural selection being the dominant factor influencing the codon usage of MaWRKY genes in M. acuminata ‘Guijiao 9’. Fourteen optimal codons, all ending in G or C, were identified. This analysis provides a theoretical foundation for further understanding the evolutionary mechanisms of WRKY genes and identifying key genes involved in resistance to biotic stress in Musa. Analysing the evolution of WRKY family genes can offer valuable genetic insights into banana growth and development, supporting the phenotypic selection of banana hybrids in breeding programs.