Genome-wide profiling of CBL interacting protein kinases (CIPKs) in banana unveils their role in abiotic stress signaling and stress tolerance enhancement

• Published in: Plant stress (Amsterdam) 2024-03, Vol.11, p.100417, Article 100417
• Main Authors: Narwal, Parul, Singh, Ravi Kumar, Pathak, Ashish Kumar, Kumar, Deepak, Negi, Neelam Prabha
• Format: Article
• Language: English
• Subjects: Banana; Calcium; CBL; CIPK; Cold stress; Drought stress
• ISSN: 2667-064X; 2667-064X
• DOI: 10.1016/j.stress.2024.100417

•Gene Identification and Characterization: The study identifies and characterizes 34 CIPK genes in banana, previously lacking information on this gene family.•Evolutionary and Structural Analysis: Analysis reveals distinct clades based on intron richness, with intron-less homologs showing higher conservation. Ten conserved motifs are identified, indicating functional diversity.•Localization and Expansion: Most CIPK proteins are predicted to localize in the cytoplasm and nucleus. Uneven distribution on chromosomes suggests expansion through duplications, with strong purifying selection post-duplications.•Functional Insights and Network Analysis: Promoter analysis reveals growth, developmental, and stress-related cis-acting elements. Interaction prediction between MaCIPKs and MaCBLs highlights specific functional associations. Predicted 3D structures show variations, suggesting functional diversity.•Expression Patterns and Stress Response: qRT-PCR analysis demonstrates specific and overlapping expressions of several MaCIPK genes in response to drought and cold stress, indicating their crucial role in plant development and stress adaptation. Calcineurin B-like (CBL)-interacting protein kinases (CIPKs) play a crucial role in the complex molecular systems of plants, acting as coordinators in different plant development processes, manage hormone signaling, and respond to environmental stress. Despite their well-established importance in various physiological process, the CIPK gene family in banana has remained an unexplored, creating a knowledge gap that this research aims to address. Through comprehensive analysis, we identified and characterized 34 CIPK genes in the banana genome. Structural diversity analysis revealed distinct clades characterized by homologs with varying intron-rich and intron-poor members. Particularly, evolutionary conservation was observed in intron-less members. Exploring conserved motifs and physicochemical properties provided insights into the detailed structure of specific homologs. Subcellular localization predictions indicated that most CIPK proteins primarily reside in the cytoplasm and nucleus, indicating their involvement in essential cellular activities. The predicted chromosomal distribution pattern suggests that the CIPK gene family largely expanded through segmental duplications in the banana genome. The phylogenetic analysis has uncovered two monophyletic clades for intron-less and intron-containing homologs, providing insig