Genome-wide phylogenetic analysis and expression profiling of F-box gene family in Verbena bonariensis under cold stress

BACKGROUND: The F-box gene family is extensively present in plants and plays key functions in plant growth and development. Verbena bonariensis (V. bonariensis) is a valuable horticultural plant, for which a low-temperature environment is the main factor affecting it ornamental value and yield. RESULTS: This study identifies 232 F-box genes (VbF-boxs) in the genome of V. bonariensis. Phylogenetic analysis divides these genes into four sub-groups, with the first subgroup showing high homology between V. bonariensis, Arabidopsis thaliana, and Sesamum indicum. Promoter sequence analysis confirms that the F-box promoter exhibits not only cis-acting elements associated with hormonal regulation but also contains elements involved in light-responsive and low-temperature mechanisms. Results of chromosomal localization show that the VbF-box genes are distributed across 7 chromosomes of V. bonariensis, with 51 pairs of tandem repeat genes detected. Collinearity analysis reveals 22 pairs of significant homologous genes in the VbF-box gene family. A total of 232 VbF-box genes are identified with differential expression across tissue-specific developmental stages, as confirmed by qRT-PCR and transcriptome analyses. A subset of these genes showed consistent upregulation under cold stress, indicating their probable involvement in stress tolerance mechanisms. These findings delineate a stage-specific transcriptional framework of F-box family genes in V. bonariensis. CONCLUSION: According to RNA-seq data, this study performs qRT-PCR analysis of six highly expressed genes, demonstrating that VbF-box071, VbF-box162, VbF-box025, VbF-box042, VbF-box224, and VbF-box115 display a sustained rise throughout 24 h of low-temperature treatment. Notably, VbF-box071 is up-regulated 348-fold at the 24-hour low-temperature stage. Observations of phenotype and cell morphology indicate that overexpression of VbF-box071 can inhibit the enlargement of tobacco leaves. Cold stress experiments demonstrate that this gene significantly enhances the cold tolerance of tobacco plants during seed germination and mature plant stages. This research not only establishes a theoretical basis for studies on the growth, development, and low-temperature tolerance of V. bonariensis, but also highlights the potential of using these identified cold stress-responsive genes in breeding programs or biotechnology to improve plant cold resistance.