Genome-Wide Identification of the CIF Gene Family and Protein Interaction with GSO1s Under the p-HBA-Induced Continuous Cropping Obstacle in Pogostemon cablin

Casparian strip integrity factors (CIFs), which are tyrosine-sulfated small peptides, are crucial genes involved in the formation and regulation of the Casparian strip and play an important role in the regulation of plant stress response. In order to explore the evolution, characteristics, role, and function of <i>CIFs</i> in response to continuous cropping obstacles (CCOs), the bioinformatics and gene expression analysis of <i>CIF</i> genes in <i>Pogostemon cablin</i> was carried out by determining the phylogenetic relationship, chromosome location, gene structure, and RT-qPCR results. Results showed that a total of 12 <i>PatCIF</i> family genes were identified on 12 different chromosomes. Promoter prediction analysis revealed 16 different <i>cis</i>-regulatory elements. A systematic evolutionary study of 33 species indicates <i>CIF</i> family genes originated from Spermatophyta. Collinearity analysis revealed <i>P. cablin</i> shared 19 syntenic genes with <i>Solanum lycopersicum</i> and only 8 with <i>Oryza sativa</i>. Transcriptome analysis indicated that the expression of <i>PatCIF1-4</i> and <i>PatGSO1b/1c/1f</i> genes decreased under p-hydroxybenzoic acid treatment, and further RT-qPCR validation of four <i>PatCIF</i> genes was consistent with the results. AlphaFold prediction showed a protein interaction region between PatCIF1-4 mature peptide and PatGSO1b/1c/1f via the LRR domain, which provides a key binding surface for mature PatCIFs. This study offers a theoretical basis to investigate the roles of <i>PatCIFs</i> and <i>PatGSO1s</i> in CCOs and their protein interactions in <i>P. cablin</i>.