Genome‐Wide Identification of WRKY Transcription Factors in Lagerstroemia indica and Their Involvement in Color Formation

ABSTRACT Lagerstroemia indica , a globally cultivated ornamental plant, is celebrated for its diverse flower and leaf coloration. Although WRKY transcription factors are known regulators of plant pigmentation, their roles in L. indica remain underexplored. This study systematically identified and characterized the WRKY gene family in L. indica to investigate its involvement in color formation. A total of 108 LiWRKY genes were identified in the genome, with 106 classified into three phylogenetic groups. Comprehensive bioinformatics analyses—encompassing conserved domains, phylogeny, chromosomal localization, gene duplication, conserved motifs, exon‐intron structures, syntenic gene pairs, cis‐acting elements, and interaction networks—uncovered evolutionary relationships and structural‐functional features of the LiWRKY family. Transcriptome‐based data revealed 37 LiWRKY genes linked to petal coloration. Integration of transcriptomic and metabolomic data with qPCR validation identified six LiWRKY genes as central regulators of leaf color variation. Notably, LiWRKY100 displayed distinct expression profiles across leaf color phenotypes, underscoring its critical regulatory role. These results advance the understanding of LiWRKY gene evolution, structure, and function, while demonstrating their direct contributions to both floral and foliar pigmentation. The study establishes a foundation for leveraging WRKY genes in the genetic enhancement of L. indica 's ornamental traits, offering actionable targets for future breeding programs.