Evolutionary and pan-genomic analysis of the bZIP gene family in 21 Camellia sinensis

Basic leucine zipper ( bZIP ) transcription factors are important regulators of plant development and stress responses, yet their evolutionary dynamics in tea plant have largely been inferred from a single reference genome. Here, we performed a broad evolutionary and pan-genomic analysis of the bZIP family using 1,015 plant genomes and 21 Camellia sinensis genomes. Across plants, 81,340 bZIP genes were identified, revealing broad conservation of this family across major lineages and a significant copy-number expansion in angiosperms. In tea, 1,635 non-redundant bZIP genes were identified, with 73–88 members per genome, indicating an overall conserved family size among tea germplasms. Phylogenetic analysis classified these genes into 13 subfamilies, among which S, A, D, I and G represented the major expanded groups. Orthogroup analysis resolved 77 bZIP orthogroups, including 22 core orthogroups and 55 dispensable orthogroups, suggesting substantial hidden variation despite stable total gene numbers. WGD/segmental duplication was the dominant expansion mechanism, accounting for 59.20% of tea bZIP genes, followed by dispersed duplication. Copy-number variation was widespread, with 72 of 77 orthogroups showing CNV across genomes. Most homologous gene pairs evolved under purifying selection, whereas dispensable genes exhibited relatively relaxed constraints compared with core genes. Transcriptome analysis in ‘Shuchazao’ revealed tissue-biased expression and divergent drought responses, with A, S, I and M subfamilies showing stronger PEG-induced responsiveness. Together, these results establish a pan-genome-informed bZIP resource and highlight CNV, duplication mode and dispensable gene variation as potential drivers of tea bZIP diversification.