Abstract

Background WUSCHEL -related homeobox ( WOX ) transcription factors play pivotal roles in plant development and evolutionary innovation. However, their functions remain largely unexplored in the basal angiosperm Annona atemoya , an economically significant species. This study aimed to elucidate the role of the WOX gene family in growth and regeneration in atemoya using genome-wide identification and functional characterization. Results In the atemoya genome, 11 WOX genes were identified and phylogenetically classified into three distinct clades: Ancient, Intermediate, and Modern. This classification was confirmed by their conserved gene structures and motif compositions. A comparative genomic analysis revealed conserved synteny and purifying selection (Ka/Ks < 1) among WOX orthologs of atemoya , Amborella , and Arabidopsis , highlighting evolutionary constraints and essential functional roles. Analysis of promoters in cis -elements showed the enrichment of development- and hormone-responsive motifs, indicating that AaWOX genes are integrated in conserved regulatory networks. Tissue-specific expression profiling revealed divergent spatiotemporal patterns. AaWOX1 and AaWOX3 were highly expressed in shoot tissues and during shoot regeneration. AaWOX11/12 and AaWOX5/7 were preferentially expressed in roots, but only AaWOX11/12 was significantly upregulated during root regeneration. Notably, AaWUS was almost undetectable in normal roots but became strongly induced upon callus formation, implying a role in de-differentiation and cellular reprogramming. Conclusions Our study provides a comprehensive genome-wide analysis of the AaWOX family in atemoya , revealing its clade-specific evolutionary conservation and putative functional divergence during organ development and regeneration. These findings highlight the pivotal roles of WOX transcription factors in coordinating regenerative responses in a basal angiosperm and establish a critical fo