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.

碱性亮氨酸拉链（basic leucine zipper, bZIP）转录因子是植物生长与胁迫响应的核心调控因子。本研究对9种葫芦科（Cucurbitaceae）植物的bZIP基因开展泛基因组分析，涉及物种包括黄瓜、西瓜、甜瓜、苦瓜、瓠瓜、冬瓜、罗汉果、蛇瓜以及棒锤瓜（Herpetospermum pedunculosum）。本研究共鉴定得到502个bZIP基因，其中350个为核心基因、151个为附属基因，可划分为12个亚家族。内含子变异是亚家族内多样性的主要来源；仅含核心基因的亚家族多呈现更低的多态性与更强的纯化选择作用。核心bZIP基因主要起源于全基因组/片段重复事件，而附属bZIP基因则通过小规模复制实现扩张。整合393套转录组数据的分析结果显示，核心与附属bZIP基因均参与植物生长发育与非生物胁迫响应过程，其中附属bZIP基因更特异性地响应激素诱导，而核心bZIP基因则参与更广泛的基因互作网络。本泛基因组研究阐明了葫芦科植物bZIP基因的基因组结构、进化动态与功能特化，为后续相关机制研究与分子育种提供了高质量的研究资源。