Genome-wide identification and expression analysis of trihelix transcription factor family in cucumber (Cucumis sativus L.) and their roles in biotic stress responses.

backgroundThe Trihelix transcription factor family, characterized by a unique triple-helix structure, plays important roles in plant growth, development, and responses to biotic stresses. Cucumber (Cucumis sativus L.), a globally important horticultural crop, suffers significant growth and yield losses under biotic stresses (e.g., pathogens, insects, nematodes). Although Trihelix transcription factors have been well characterized in model plants like Arabidopsis thaliana, systematic analyses in cucumber are still limited. This study aims to comprehensively identify the Trihelix transcription factor gene family in cucumber using bioinformatics methods and analyze their expression patterns under biotic stresses, thereby providing insights into their potential roles in cucumber growth, development, and stress responses.

resultsUsing Arabidopsis Trihelix sequences as queries, we identified 29 CsaTri genes in Cucumis sativus L. cv. Chinese Long v4.0 genome (all containing the canonical Trihelix domain, named CsaTri1-CsaTri29 by chromosomal position). Phylogenetic analysis classified these genes into 5 subfamilies (GT-1, GT-2, SH4, GT-γ, and SIP1), and they are unevenly distributed across 7 chromosomes. Gene structure and functional motif analyses revealed highly conserved motifs and domain architectures within the same subfamily. Cis-regulatory element analysis indicated that these genes may be involved in hormone responses, stress responses, and growth and development processes. Tissue expression analysis showed that CsaTri12/CsaTri27/CsaTri28/CsaTri29 are highly expressed in stems, while CsaTri8/CsaTri21 are highly expressed in roots. Transcriptome data and qRT-PCR results indicated that CsaTri genes actively respond to pathogen stress. Co-expression analysis linked CsaTri genes to immune pathways (PAMP recognition via LRR-RLK, post-transcriptional regulation via RNA metabolism/ubiquitin-proteasome system).

conclusionsOur study provides the first systematic characterization of the Cucumis sativus L. Trihelix transcription factor family, encompassing genomic, structural, evolutionary, and expression features. The identification of stress-responsive genes (e.g., CsaTri18, SIP1 subfamily) and their associated regulatory networks provides valuable insights into the potential biotic stress defense mechanisms of Cucumis sativus L. These findings lay a foundation for future functional validation of key CsaTri genes and offer potential candidate targets for breeding stress-resistant cucumber varieties.