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 Herpetospermum pedunculosum. 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 bZIPs contribute to development and abiotic-stress responses, with dispensable members more specifically hormone-induced and core bZIPs 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.