Evolutionary Dynamics and Functional Diversification of bZIP Transcription Factors in Cucurbitaceae: A Pan-Genome Approach

The basic leucine zipper (bZIP) transcription factors are central regulators of plant growth and stress responses. This study presents a pan-genome analysis of bZIP genes across nine Cucurbitaceae species: cucumber, watermelon, melon, bitter gourd, bottle gourd, wax gourd, monk fruit, snake gourd, and <i>Herpetospermum pedunculosum</i>. We cataloged 502 bZIPs (350 core, 151 dispensable) in 12 subfamilies. Intron variation was the primary source of intrasubfamily diversity; core-only subfamilies showed lower polymorphism and stronger purifying selection. Core bZIPs mainly originated from whole-genome/segmental duplication, while dispensable bZIPs expanded via small-scale duplication. Integrating 393 transcriptomes revealed that both core and dispensable <i>bZIP</i>s contribute to development and abiotic-stress responses, with dispensable members more specifically hormone-induced and core <i>bZIP</i>s engaging broader gene-interaction networks. This pan-genome survey delineates bZIP genomic architecture, evolutionary dynamics, and functional specialization in Cucurbitaceae, providing a robust resource for downstream mechanistic studies and molecular breeding.