A Genome-Wide Analysis of Pathogenesis-Related Protein-1 () Genes from Reveals Its Critical Role during Infection.

Black pepper ( L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. , the causative agent of footrot disease, causes a drastic constraint in cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related () proteins. Through a genome-wide survey, eleven genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from . Despite the critical functional domains, homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of proteins were identified using MEME. Most of the proteins were basic in nature. Secondary and 3D structure analyses of the proteins were also predicted, which may be linked to a functional role in . The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed genes mapped to the interaction pathway. An altered expression pattern was detected for transcripts among which a significant upregulation was noted for basic -1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of genes. This is the first genome-wide study that identified the role of genes during interactions. The detailed in silico experimental analysis revealed the vital role of genes in regulating the first layer of defense towards a infection in Panniyur-1 plants.