Background Plant defensins (PDF) represent a crucial superfamily of innate immune proteins that exhibit antifungal and antibacterial activities, significantly contributing to biotic stress. Despite being significant horticultural and economic crops, a comprehensive genome-wide analysis of Cucurbitaceae plant defensin genes (CuPDF) remains unreported. Results In this study, 19 CuPDF family members homologous to Arabidopsis PDF were predicted in four Cucurbitaceae and validated based on the presence of conserved PDF-related domains. The 19 CuPDF are unevenly distributed across the chromosomes, and phylogenetic analysis reveals their classification into two distinct subgroups, consistent with those identified in Arabidopsis thaliana. The similarity in 3D protein structures, together with the conserved intron-exon organization and core motif distribution, collectively indicates strong evolutionary conservation. Synteny analysis suggests that the expansion of the CuPDF family in cucurbits is predominantly driven by tandem duplication events. Promoter analysis revealed that the upstream regions of CuPDF are enriched with numerous cis-acting elements associated with plant hormone signaling, defense responses, stress responses, and developmental regulation, including MYB (59 elements), MYC (58), ARE (37), ABRE (40), ERE (40), and AAGAA-motif (36). RNA-seq analysis showed that the expression levels of CmPDF9, ClPDF1.1/1.2/2, and CmoPDF20 were differentially upregulated or downregulated in response to various biotic stresses, including Phytophthora capsici, Fusarium oxysporum, Pseudoperonospora cubensis, Podosphaera xanthii, cucumber green mottle mosaic virus (CGMMV), and Meloidogyne incognita. These findings suggest that these genes may play regulatory roles in biotic stress responses, as further confirmed by RT-qPCR. Conclusions In this study, the structure, chromosomal distribution, and evolutionary relationship of PDF family members in four Cucurbitaceae were analyzed. We identified the CuPDF genes involved in biotic stress by combining promoter element analysis, transcriptome data, and RT-qPCR analysis. These findings enrich the knowledge of the molecular characteristics of the CuPDF family and provide crucial insights into their potential roles in responses to biotic stress.

PDF gene family in four Cucurbitaceae species: genome-wide identification, classification and expression in response to biotic stress

期刊论文
出版模式：

开放获取
发表日期：

2025年8月30日

查看全文

Ba Dun,
Sun Chengzhen,
Ding Zhuo,
Cui Haonan

摘要

Background

Plant defensins (PDF) represent a crucial superfamily of innate immune proteins that exhibit antifungal and antibacterial activities, significantly contributing to biotic stress. Despite being significant horticultural and economic crops, a comprehensive genome-wide analysis of Cucurbitaceae plant defensin genes (CuPDF) remains unreported.

Results

In this study, 19 CuPDF family members homologous to Arabidopsis PDF were predicted in four Cucurbitaceae and validated based on the presence of conserved PDF-related domains. The 19 CuPDF are unevenly distributed across the chromosomes, and phylogenetic analysis reveals their classification into two distinct subgroups, consistent with those identified in Arabidopsis thaliana. The similarity in 3D protein structures, together with the conserved intron-exon organization and core motif distribution, collectively indicates strong evolutionary conservation. Synteny analysis suggests that the expansion of the CuPDF family in cucurbits is predominantly driven by tandem duplication events. Promoter analysis revealed that the upstream regions of CuPDF are enriched with numerous cis-acting elements associated with plant hormone signaling, defense responses, stress responses, and developmental regulation, including MYB (59 elements), MYC (58), ARE (37), ABRE (40), ERE (40), and AAGAA-motif (36). RNA-seq analysis showed that the expression levels of CmPDF9, ClPDF1.1/1.2/2, and CmoPDF20 were differentially upregulated or downregulated in response to various biotic stresses, including Phytophthora capsici, Fusarium oxysporum, Pseudoperonospora cubensis, Podosphaera xanthii, cucumber green mottle mosaic virus (CGMMV), and Meloidogyne incognita. These findings suggest that these genes may play regulatory roles in biotic stress responses, as further confirmed by RT-qPCR.

Conclusions

In this study, the structure, chromosomal distribution, and evolutionary relationship of PDF family members in four Cucurbitaceae were analyzed. We identified the CuPDF genes involved in biotic stress by combining promoter element analysis, transcriptome data, and RT-qPCR analysis. These findings enrich the knowledge of the molecular characteristics of the CuPDF family and provide crucial insights into their potential roles in responses to biotic stress.