Genome-Wide Identification and Characterization of the CDPK Family of Genes and Their Response to High-Calcium Stress in Yinshania henryi.

Abstract

Background/Objectives: Calcium-dependent protein kinases (CDPKs) are a crucial class of calcium-signal-sensing and -response proteins that significantly regulate abiotic stress. Yinshania henryi is a member of the Brassicaceae family that primarily grows in the karst regions of southwestern China, with a notable tolerance to high-calcium soils. Currently, the function of the CDPK family of genes in Y. henryi has yet to be explored. Methods: This study employed a comprehensive approach starting with bioinformatic methods to analyze the whole-genome sequencing data of Y. henryi and identified YhCDPK genes by combining phylogenetic characteristics and protein domain analysis. Results: It then delved into the physicochemical properties, gene structure, chromosomal localization, phylogenetic tree, and promoter cis-acting elements of these YhCDPK genes. Subsequently, RNA-seq data and qRT-PCR analysis were utilized to understand the expression patterns of YhCDPK genes. Twenty-eight YhCDPK genes were found to be unevenly distributed across six chromosomes; these can be classified into four subfamilies, with many cis-acting elements in their promoter regions involved in plant growth and stress responses. Furthermore, the differential expression patterns of YhCDPK genes under different concentrations of calcium treatments were investigated using RNA-seq data and qRT-PCR analysis. Conclusions: These results are a critical first step in understanding the functions of YhCDPK genes, and they lay a foundation for further elucidating the adaptability and response mechanism of YhCDPK genes in Y. henryi to the karst environment.