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Background <p>GATA transcription factors are ubiquitous in plants, where they regulate target gene expression to modulate plant growth, development, and responses to environmental stresses. The <i>GATA</i> gene family has been identified in numerous plant species, with characterization reported in cucumber and melon among Cucurbitaceae crops. However, the <i>GATA</i> gene family remains unstudied in most other Cucurbitaceae species. Here, we systematically identified <i>GATA</i> genes in 10 Cucurbitaceae species (watermelon, cucumber, melon, pumpkin, wax gourd, sponge gourd, bottle gourd, bitter gourd, chayote, snake gourd) using the latest high-quality genomic datasets.</p> Results <p>A total of 281 <i>GATA</i> genes were identified across these 10 species, and phylogenetic analysis clustered them into four subgroups (Groups A, B, C, D). For watermelon <i>GATA</i> (<i>ClGATA</i>) genes, <i>cis</i>-acting element analysis revealed abundant stress-responsive elements in their promoter regions. Predictions of ClGATA protein secondary and tertiary structures showed random coils as the dominant secondary structural component, with subgroup-specific tertiary characteristics supporting functional synergy within each subgroup. Intraspecific synteny analysis identified 7 segmentally duplicated <i>ClGATA</i> gene pairs, with no tandem duplications detected, indicating segmental duplication drove the expansion of the <i>ClGATA</i> family. Transcriptome reanalysis under 17 types of abiotic and biotic stresses showed <i>ClGATA7</i> exhibited significant differential expression under 5 abiotic and 3 biotic stress types, and <i>ClGATA11</i> showed significant differential expression under 3 abiotic and 5 biotic stress types. Quantitative real-time PCR (qRT-PCR) validation of 6 key <i>ClGATA</i> genes further confirmed the role of <i>ClGATA7</i> in mediating abiotic stress responses, with consistent down-regulation under low temperature in both leaf and root tissues. Protein–protein interaction prediction identified potential interactions among 21 of the 24 ClGATA proteins, including a direct interaction between ClGATA7 and ClGATA17.</p> Conclusions <p>These findings advance our understanding of <i>GATA</i> gene family evolution and function in Cucurbitaceae. Given the broad stress responsiveness of <i>ClGATA7</i> and <i>ClGATA11</i>, they are highlighted as priority candidate genes for functional studies and genetic improvement of stress tolerance in watermelon.</p>

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Genome-wide identification of the GATA transcription factor family in ten Cucurbitaceae species and expression analysis of ClGATA genes in watermelon stress responses

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月2日

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  • Jiong Gao,
  • Li Jia,
  • Rongjing Cui,
  • Zhu Wang,
  • Congsheng Yan,
  • Ming Qian,
  • Yingjie Shu,
  • Kaijing Zhang

摘要

Background

GATA transcription factors are ubiquitous in plants, where they regulate target gene expression to modulate plant growth, development, and responses to environmental stresses. The GATA gene family has been identified in numerous plant species, with characterization reported in cucumber and melon among Cucurbitaceae crops. However, the GATA gene family remains unstudied in most other Cucurbitaceae species. Here, we systematically identified GATA genes in 10 Cucurbitaceae species (watermelon, cucumber, melon, pumpkin, wax gourd, sponge gourd, bottle gourd, bitter gourd, chayote, snake gourd) using the latest high-quality genomic datasets.

Results

A total of 281 GATA genes were identified across these 10 species, and phylogenetic analysis clustered them into four subgroups (Groups A, B, C, D). For watermelon GATA (ClGATA) genes, cis-acting element analysis revealed abundant stress-responsive elements in their promoter regions. Predictions of ClGATA protein secondary and tertiary structures showed random coils as the dominant secondary structural component, with subgroup-specific tertiary characteristics supporting functional synergy within each subgroup. Intraspecific synteny analysis identified 7 segmentally duplicated ClGATA gene pairs, with no tandem duplications detected, indicating segmental duplication drove the expansion of the ClGATA family. Transcriptome reanalysis under 17 types of abiotic and biotic stresses showed ClGATA7 exhibited significant differential expression under 5 abiotic and 3 biotic stress types, and ClGATA11 showed significant differential expression under 3 abiotic and 5 biotic stress types. Quantitative real-time PCR (qRT-PCR) validation of 6 key ClGATA genes further confirmed the role of ClGATA7 in mediating abiotic stress responses, with consistent down-regulation under low temperature in both leaf and root tissues. Protein–protein interaction prediction identified potential interactions among 21 of the 24 ClGATA proteins, including a direct interaction between ClGATA7 and ClGATA17.

Conclusions

These findings advance our understanding of GATA gene family evolution and function in Cucurbitaceae. Given the broad stress responsiveness of ClGATA7 and ClGATA11, they are highlighted as priority candidate genes for functional studies and genetic improvement of stress tolerance in watermelon.