Genome-wide identification, evolution and expression analysis of the Calcineurin B-like (CBL) and CBL-interacting protein kinase (CIPK) gene families under viral stress in Nicotiana benthamiana

Nicotiana benthamiana is a crucial model organism, widely used in gene study and molecular farming industry. Calcineurin B-like proteins (CBLs), which function as plant-specific calcium sensors, play critical roles in mediating plant growth and their response to diverse stress through their interactions with CBL-interacting protein kinases (CIPKs). Although CBLs and CIPKs have been identified in various species, their special characteristics in N. benthamiana remain limited. We identified 17 CBLs and 48 CIPKs in N. benthamiana , which were classified into 4 and 7 distinct clades, respectively, each exhibiting conserved motif and gene structures, based on their phylogenetic analyses. Segmental duplications were identified as a major driver for duplication patterns, both NbCBLs and NbCIPKs were unevenly distributed across 19 chromosomes and exhibited a relatively weak codon usage bias, shaped by both mutational and selective pressures. The expression levels of NbCBLs and NbCIPKs varied across distinct tissues, and influenced by viral infection. Furthermore, silencing of NbCBL10 increased viral susceptibility. Collectively, these findings not only provided novel insights into the functional exploration of the CBL - CIPK molecule, but also offered a valuable resource for antiviral genetic enhancement. • Genome-wide characterization 17 CBL and 48 CIPK members in tobacco ( Nicotiana benthamiana ). • Evolutionary relationships of CBLs and CIPKs in monocots and dicots were comprehensively analyzed. • A set of NbCBLs and NbCIPKs , including NbCBL10 , were importantly induced in response to viral infection. • Silencing of NbCBL10 promoted tomato yellow leaf curl virus (harboring single-stranded, ssDNA) and bamboo mosaic virus (harboring single-stranded RNA, ssRNA) accumulation.