Genome-wide identification and transcriptional expression profiles of the transcription factor WRKY in Gentiana macrophylla

Gentiana macrophylla Pall., a valuable Chinese traditional medicinal herb, exhibits notable anti-inflammatory and analgesic effects. The WRKY transcription factor plays a pivotal role in regulating development and stress responses. Although the WRKY family extensively characterized in diverse plant species, a comprehensive analysis of this gene family in G. macrophylla remains unexplored. In this study, we systematically identified 84 WRKY genes (GmWRKYs) from the G. macrophylla genome and classified them into three primary clades based on phylogenetic analysis. Further characterization of motif architectures, gene structures, chromosomal distributions, and syntenic relationships revealed conserved evolutionary patterns within this gene family. Notably, both phylogenetic evidence and whole-genome duplication (WGD) event analyses suggested that GmWRKYs originated from a common ancestor and underwent expansion through lineage-specific WGDs. RNA-seq and qRT-PCR analysis revealed that GmWRKYs had different expression patterns in different tissues of G. macrophylla. Weighted gene co-expression network analysis (WGCNA) further identified significant co-expression relationships between GmWRKYs and key genes involved in iridoid biosynthesis. Our results provide a potential theoretical basis for future investigation on the role of WRKY genes in the biosynthesis of iridoid in G. macrophylla.