Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics
The <i>Oryza</i> 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 st...
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2025-05-01
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| author | Fu Shi Li Li Mingjie Chen Junli Chang Min Tu Guangyuan He Yin Li Guangxiao Yang |
| author_facet | Fu Shi Li Li Mingjie Chen Junli Chang Min Tu Guangyuan He Yin Li Guangxiao Yang |
| author_sort | Fu Shi |
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| description | The <i>Oryza</i> 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 <i>CPKs</i> and their related kinases in 34 <i>Oryza</i> genomes by leveraging the rich genomics resources of the <i>Orzya</i> genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding <i>CPKs</i> 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 <i>CPKs</i> and their related kinases in multiple species of <i>Oryza</i> genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our <i>Oryza</i>-wide analysis of <i>CPKs</i> 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. |
| format | Article |
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| language | English |
| publishDate | 2025-05-01 |
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| series | Plants |
| spelling | doaj-art-0a06bf90a2074b4cbffdb04bddcd2cef2025-08-20T01:56:45ZengMDPI AGPlants2223-77472025-05-011410154210.3390/plants14101542Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression DynamicsFu Shi0Li Li1Mingjie Chen2Junli Chang3Min Tu4Guangyuan He5Yin Li6Guangxiao Yang7The 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, ChinaThe 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, ChinaThe 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, ChinaThe 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, ChinaHubei 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, ChinaThe 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, ChinaThe 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, ChinaThe 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, ChinaThe <i>Oryza</i> 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 <i>CPKs</i> and their related kinases in 34 <i>Oryza</i> genomes by leveraging the rich genomics resources of the <i>Orzya</i> genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding <i>CPKs</i> 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 <i>CPKs</i> and their related kinases in multiple species of <i>Oryza</i> genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our <i>Oryza</i>-wide analysis of <i>CPKs</i> 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.https://www.mdpi.com/2223-7747/14/10/1542calcium-dependent protein kinasesCPKs and their related kinases<i>Oryza</i>duplicated geneEF-hand motifstranscriptome analysis |
| spellingShingle | Fu Shi Li Li Mingjie Chen Junli Chang Min Tu Guangyuan He Yin Li Guangxiao Yang Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics Plants calcium-dependent protein kinases CPKs and their related kinases <i>Oryza</i> duplicated gene EF-hand motifs transcriptome analysis |
| title | Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics |
| title_full | Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics |
| title_fullStr | Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics |
| title_full_unstemmed | Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics |
| title_short | Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics |
| title_sort | genus wide pan genome analysis of i oryza i calcium dependent protein kinase genes and their related kinases highlights the complexity of protein domain architectures and expression dynamics |
| topic | calcium-dependent protein kinases CPKs and their related kinases <i>Oryza</i> duplicated gene EF-hand motifs transcriptome analysis |
| url | https://www.mdpi.com/2223-7747/14/10/1542 |
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