Identification and Transcriptional Expression of the WRKY Transcription Factor Family in Robinia pseudoacacia and Its Association with Heartwood Formation

Background: As a transcription factor superfamily unique to plants, WRKY plays broad roles in both secondary development and secondary metabolic processes. Robinia pseudoacacia is renowned for its durable and naturally durable heartwood, which holds significant commercial value. However, their potential association with heartwood formation remains largely unexplored. Results: Leveraging published genomic data from Robinia pseudoacacia, we conducted a comprehensive bioinformatics analysis that identified 85 WRKY transcription factors. An uneven distribution across 11 chromosomes was observed for the RpWRKY genes, which were systematically named RpWRKY1 to RpWRKY85 according to their genomic locations, as determined by chromosomal localization. By conducting a phylogenetic comparison between RpWRKY and AtWRKY (from Arabidopsis thaliana), the RpWRKY family was categorized into three primary clades (I, II, and III), wherein group II was additionally partitioned into subgroups designated IIa through IIe. Conserved structural features and motif patterns were observed among members of each subgroup. Purifying selection was suggested by collinearity analysis as the primary evolutionary driver of RpWRKY, leading to structural and functional diversification. Finally, four candidate genes (RpWRKY78, RpWRKY45, RpWRKY50, RpWRKY80) potentially involved in heartwood formation regulation were identified through analysis of xylem tissue-specific expression patterns. Conclusions: For this economically important tree species, the present study not only provides the first systematic characterization of RpWRKY but also identifies potential regulators of heartwood development. Thus, the present study lays the groundwork for subsequent research aimed at uncovering the molecular processes that regulate heartwood development.