Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for Prunus mume and Prunus mume var. Tortuosa.
Runtian MiaoMingyu LiZhenying WenJuan MengXu LiuDongqing FanWenjuan LvTangren ChengQixiang ZhangLidan SunPublished in: Plants (Basel, Switzerland) (2023)
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 ( Prunus mume ). We identified 14 and 17 CDPK genes in P. mume and P. mume 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 P. mume and P. mume 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 PmCDPK genes, especially PmCDPK14 , 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.
Keyphrases
- rna seq
- genome wide
- single cell
- bioinformatics analysis
- genome wide identification
- transcription factor
- signaling pathway
- copy number
- plant growth
- oxidative stress
- dna methylation
- genome wide analysis
- machine learning
- high frequency
- gene expression
- climate change
- cell proliferation
- protein protein
- small molecule
- deep learning