Genome-Wide Characterization of the WOX Gene Family in Polygonatum cyrtonema and Its Applications for Regeneration

Polygonatum cyrtonema is a medicinally and edible perennial herb, yet functional studies in this species are constrained by limited knowledge of regeneration-associated developmental regulators. Here, we performed a genome-wide characterization of the WUSCHEL-related homeobox (WOX) gene family in P. cyrtonema. Eleven PcWOX genes were identified and classified into the ancient, intermediate, and modern/WUS clades. Comparative phylogenetic, syntenic, structural, and chromosomal analyses indicated that the PcWOX family retains a conserved evolutionary framework but also exhibits clear lineage-specific diversification. Tissue- and stage-specific expression profiling, promoter cis-element analysis, and subcellular localization further supported functional differentiation among PcWOX members, particularly between PcWOX5 and PcWUS. Weighted gene co-expression network analysis identified 33 co-expression modules, including six key modules strongly associated with PcWOX abundance patterns, and prioritized 49 candidate transcription factors (TFs) to construct PcWOX-centered regulatory networks. These TFs showed marked tissue- and stage-dependent heterogeneity. Heterologous assays in Nicotiana benthamiana showed that both PcWUS and PcWOX5 enhanced regeneration competence but produced distinct developmental outputs. These findings support PcWUS and PcWOX5 as promising candidate morphogenic regulators and provide a useful framework for future mechanistic studies, homologous validation, and regeneration improvement in P. cyrtonema.