Genome-wide identification and salt stress response analysis of the WD40 protein family in Populus yunnanensis

Abstract Background The WD40 proteins constitute a large regulatory family involved in a wide range of biological processes and stress responses. Advances in sequencing technologies have facilitated the identification of numerous WD40 proteins with diverse functions in many plant species. However, research on tree species remains limited. Populus yunnanensis is an economically and ecologically important tree species that faces salt stress in certain habitats. Therefore, studying WD40 proteins in P. yunnanensis is of particular significance for understanding its salt tolerance mechanisms. Results A variable number of WD40 proteins were identified across six poplar species, generally correlating with their genome sizes. In P. yunnanensis , 258 PyWD40s were identified, exhibiting considerable variation in amino acid number, and other physicochemical properties, suggesting potential functional diversity. The chromosomal distribution of these genes was uneven, indicative of gene family formation and replication events. High collinearity among members and low Ka/Ks values suggested strong sequence conservation and purifying selection. Notable similarities were also observed between the WD40 proteins of P. yunnanensis and A. thaliana . Structural analysis revealed that representative PyWD40s from the eight subfamilies could be modeled into three-dimensional structures rich in β-sheets. Variations in conserved domains and exon numbers contributed to sequence and functional divergence. Expression profiling under salt stress indicated that most PyWD40s were upregulated under both short-term and prolonged stress conditions, a finding validated by qRT-PCR for 14 selected genes. Protein–protein interaction network analysis demonstrated that PyWD40s interact with proteins involved in process such as signal transduction, and their co-expression under salt stress suggests a coordinated role in facilitating the stress response. Conclusions In summary, this study provides comprehensive insights into the roles of PyWD40 proteins in the salt stress response of P. yunnanensis . These findings contribute significantly to the understanding of stress tolerance mechanisms in this species and offer a valuable resource for future functional studies.