Key message This research is the first comprehensive, genome-wide study of the calcium-dependent protein kinase (CDPK) gene family in the Aquilaria agallocha tree. A total of 24 CDPK genes were identified in the study. Protein–protein interaction, gene ontology, promoter composition, RNA sequencing, and RT-qPCR are studied in detail. The results suggest that AaCDPK proteins act as signaling molecules that are involved in defense responses of A. agallocha. Abstract Calcium (Ca2+) ions function as a ubiquitous secondary messenger in plant signal transduction. Calcium-Dependent Protein Kinases (CDPKs) are key sensors that translate fluctuations of calcium ion concentration into biochemical responses by phosphorylating downstream proteins. These phosphorylating events influence physiological processes, including phytohormone signaling and secondary metabolite biosynthesis. Aquilaria agallocha is the tree known for its commercially valuable agarwood in Northeast India. The tree produces this valuable resin as a defense response to abiotic and biotic stresses, particularly those caused by fungal infections. However, molecular pathways underlying the biosynthesis of agarwood resin, particularly the role of CDPK genes, remain unexplored. In this study, 24 AaCDPK genes were identified through a genome-wide analysis, and they were classified into four distinct phylogenetic groups. Promoter analysis revealed the presence of stress and hormone-responsive cis-regulatory elements. Evolutionary analysis revealed that dispersed duplication—rather than whole-genome or segmental events drove the expansion of the AaCDPK family, highlighting a unique evolutionary pattern in this resin-producing tree species. RT-qPCR analysis confirmed their upregulation of key candidates’ genes such as AaCDPK10, 32, 1.1,17.2, 21 and 20 in response to MeJA, H2O2, and CaCl2 treatments. Integration of PPI, GO, RNA-seq, and qRT-PCR analyses links AaCDPKs to ROS-mediated resin initiation, providing new insight into agarwood formation biology. These findings highlight the association of AaCDPK in calcium-mediated signal-transduction mechanisms associated with A. agallocha defense responses and secondary metabolism. This study offers foundational insights into the regulatory landscape of AaCDPKs, opening avenues for future research as candidate regulators in the initiation of agarwood formation.

Calcium-dependent protein kinase (CDPK) gene family in Aquilaria agallocha tree: genome-wide identification and expression analysis under stress conditions

期刊论文
发表日期：

2026年7月21日

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Khaleda Begum,
Ankur Das,
Raja Ahmed,
Suraiya Akhtar,
Sofia Banu

摘要

Key message

This research is the first comprehensive, genome-wide study of the calcium-dependent protein kinase (CDPK) gene family in the Aquilaria agallocha tree. A total of 24 CDPK genes were identified in the study. Protein–protein interaction, gene ontology, promoter composition, RNA sequencing, and RT-qPCR are studied in detail. The results suggest that AaCDPK proteins act as signaling molecules that are involved in defense responses of A. agallocha.

Abstract

Calcium (Ca²⁺) ions function as a ubiquitous secondary messenger in plant signal transduction. Calcium-Dependent Protein Kinases (CDPKs) are key sensors that translate fluctuations of calcium ion concentration into biochemical responses by phosphorylating downstream proteins. These phosphorylating events influence physiological processes, including phytohormone signaling and secondary metabolite biosynthesis. Aquilaria agallocha is the tree known for its commercially valuable agarwood in Northeast India. The tree produces this valuable resin as a defense response to abiotic and biotic stresses, particularly those caused by fungal infections. However, molecular pathways underlying the biosynthesis of agarwood resin, particularly the role of CDPK genes, remain unexplored. In this study, 24 AaCDPK genes were identified through a genome-wide analysis, and they were classified into four distinct phylogenetic groups. Promoter analysis revealed the presence of stress and hormone-responsive cis-regulatory elements. Evolutionary analysis revealed that dispersed duplication—rather than whole-genome or segmental events drove the expansion of the AaCDPK family, highlighting a unique evolutionary pattern in this resin-producing tree species. RT-qPCR analysis confirmed their upregulation of key candidates’ genes such as AaCDPK10, 32, 1.1,17.2, 21 and 20 in response to MeJA, H₂O₂, and CaCl₂ treatments. Integration of PPI, GO, RNA-seq, and qRT-PCR analyses links AaCDPKs to ROS-mediated resin initiation, providing new insight into agarwood formation biology. These findings highlight the association of AaCDPK in calcium-mediated signal-transduction mechanisms associated with A. agallocha defense responses and secondary metabolism. This study offers foundational insights into the regulatory landscape of AaCDPKs, opening avenues for future research as candidate regulators in the initiation of agarwood formation.