Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for <i>Prunus mume</i> and <i>Prunus mume</i> var. Tortuosa

Calcium-dependent protein kinases (CDPK) are known to mediate plant growth and development and respond to various environmental changes. Here, we performed whole-genome identification of CDPK families in cultivated and wild mei (<i>Prunus mume</i>). We identified 14 and 17 CDPK genes in...

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Main Authors: Runtian Miao, Mingyu Li, Zhenying Wen, Juan Meng, Xu Liu, Dongqing Fan, Wenjuan Lv, Tangren Cheng, Qixiang Zhang, Lidan Sun
Format: Article
Language:English
Published: MDPI AG 2023-07-01
Series:Plants
Subjects:
Online Access:https://www.mdpi.com/2223-7747/12/13/2548
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author Runtian Miao
Mingyu Li
Zhenying Wen
Juan Meng
Xu Liu
Dongqing Fan
Wenjuan Lv
Tangren Cheng
Qixiang Zhang
Lidan Sun
author_facet Runtian Miao
Mingyu Li
Zhenying Wen
Juan Meng
Xu Liu
Dongqing Fan
Wenjuan Lv
Tangren Cheng
Qixiang Zhang
Lidan Sun
author_sort Runtian Miao
collection DOAJ
description Calcium-dependent protein kinases (CDPK) are known to mediate plant growth and development and respond to various environmental changes. Here, we performed whole-genome identification of CDPK families in cultivated and wild mei (<i>Prunus mume</i>). We identified 14 and 17 CDPK genes in <i>P. mume</i> and <i>P. mume</i> var. Tortuosa genomes, respectively. All 270 CPDK proteins were classified into four clade, displaying frequent homologies between these two genomes and those of other Rosaceae species. Exon/intron structure, motif and synteny blocks were conserved between <i>P. mume</i> and <i>P. mume</i> var. Tortuosa. The interaction network revealed all PmCDPK and PmvCDPK proteins is interacted with respiratory burst oxidase homologs (RBOHs) and mitogen-activated protein kinase (MAPK). RNA-seq data analysis of cold experiments show that cis-acting elements in the <i>PmCDPK</i> genes, especially <i>PmCDPK14</i>, are associated with cold hardiness. Our results provide and broad insights into CDPK gene families in mei and their role in modulating cold stress response in plants.
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spelling doaj.art-9830ecb91a604f3290cef74aa7abc96f2023-11-18T17:19:04ZengMDPI AGPlants2223-77472023-07-011213254810.3390/plants12132548Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for <i>Prunus mume</i> and <i>Prunus mume</i> var. TortuosaRuntian Miao0Mingyu Li1Zhenying Wen2Juan Meng3Xu Liu4Dongqing Fan5Wenjuan Lv6Tangren Cheng7Qixiang Zhang8Lidan Sun9Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, ChinaCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaBeijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, ChinaCalcium-dependent protein kinases (CDPK) are known to mediate plant growth and development and respond to various environmental changes. Here, we performed whole-genome identification of CDPK families in cultivated and wild mei (<i>Prunus mume</i>). We identified 14 and 17 CDPK genes in <i>P. mume</i> and <i>P. mume</i> var. Tortuosa genomes, respectively. All 270 CPDK proteins were classified into four clade, displaying frequent homologies between these two genomes and those of other Rosaceae species. Exon/intron structure, motif and synteny blocks were conserved between <i>P. mume</i> and <i>P. mume</i> var. Tortuosa. The interaction network revealed all PmCDPK and PmvCDPK proteins is interacted with respiratory burst oxidase homologs (RBOHs) and mitogen-activated protein kinase (MAPK). RNA-seq data analysis of cold experiments show that cis-acting elements in the <i>PmCDPK</i> genes, especially <i>PmCDPK14</i>, are associated with cold hardiness. Our results provide and broad insights into CDPK gene families in mei and their role in modulating cold stress response in plants.https://www.mdpi.com/2223-7747/12/13/2548cold stressreplication eventstranscriptional expression profilesprotein-protein interaction networkgene expression
spellingShingle Runtian Miao
Mingyu Li
Zhenying Wen
Juan Meng
Xu Liu
Dongqing Fan
Wenjuan Lv
Tangren Cheng
Qixiang Zhang
Lidan Sun
Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for <i>Prunus mume</i> and <i>Prunus mume</i> var. Tortuosa
Plants
cold stress
replication events
transcriptional expression profiles
protein-protein interaction network
gene expression
title Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for <i>Prunus mume</i> and <i>Prunus mume</i> var. Tortuosa
title_full Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for <i>Prunus mume</i> and <i>Prunus mume</i> var. Tortuosa
title_fullStr Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for <i>Prunus mume</i> and <i>Prunus mume</i> var. Tortuosa
title_full_unstemmed Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for <i>Prunus mume</i> and <i>Prunus mume</i> var. Tortuosa
title_short Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for <i>Prunus mume</i> and <i>Prunus mume</i> var. Tortuosa
title_sort whole genome identification of regulatory function of cdpk gene families in cold stress response for i prunus mume i and i prunus mume i var tortuosa
topic cold stress
replication events
transcriptional expression profiles
protein-protein interaction network
gene expression
url https://www.mdpi.com/2223-7747/12/13/2548
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