Shi Fu, Li Li, Chen Mingjie, Chang Junli, Tu Min, He Guangyuan, Li Yin, Yang Guangxiao
The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
Hubei Province Key Laboratory of Agricultural Waste Resource Utilization, Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
Plants (Basel). 2025 May 20;14(10):1542. doi: 10.3390/plants14101542.
The genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development and stress responses. Four kinase families, namely CPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PPCK-related kinases (PEPRKs), and calcium- and calmodulin-dependent kinases (CCaMKs), are frequently called CPK-related kinases. This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of and their related kinases in 34 genomes by leveraging the rich genomics resources of the genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding and their related kinases in wild rice. We depicted the protein domain architectures of CPKs and their related kinases, highlighting the complexity of EF-hand motifs in CPKs and CCaMKs. Transcriptome analysis determined that alternative splicing was a mechanism contributing to the diversity in the domain architectures of CPKs and CCaMKs. We also generated the expression atlas of and their related kinases in multiple species of genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our -wide analysis of and their related kinases revealed their evolutionary trajectories and highlighted their diversified domain architectures and expression dynamics, providing gene resources of wild relatives for rice improvement.
该属不仅是水稻改良的基因库，也是植物进化研究的模型系统。钙依赖蛋白激酶（CPK）在钙信号传导中既作为效应器又作为传感器，在植物发育和胁迫反应中发挥多种作用。四个激酶家族，即CPK相关激酶（CRK）、磷酸烯醇式丙酮酸羧化酶激酶（PPCK）、PPCK相关激酶（PEPRK）和钙调蛋白依赖激酶（CCaMK），常被称为CPK相关激酶。本研究利用进化基因组学方法，借助该属丰富的基因组资源，提供了34个该属基因组中CPK及其相关激酶的泛基因组信息。基因重复分析表明，不同的重复类型有助于野生稻中CPK及其相关激酶的扩增。我们描绘了CPK及其相关激酶的蛋白质结构域架构，突出了CPK和CCaMK中EF手基序的复杂性。转录组分析确定，可变剪接是导致CPK和CCaMK结构域架构多样性的一种机制。我们还生成了该属多个物种中CPK及其相关激酶的表达图谱，强调了异源四倍体野生稻中不同组织和物种间同源基因的表达模式差异。总体而言，我们对该属CPK及其相关激酶的全基因组分析揭示了它们的进化轨迹，突出了它们多样化的结构域架构和表达动态，为水稻改良提供了野生近缘种的基因资源。
