Genome-Wide Identification and Expression Analysis of ACA/ECAs in Capsicum annuum L

Pepper (Capsicum annuum L.) is a popular vegetable in people's daily lives. During pepper growth, calcium (Ca) is an essential macronutrient, and calcium-transporting ATPase (ACA/ECA) is a vital protein for calcium transport. However, reports on the ACA/ECA gene family in the pepper genome are lacking. Hence, we used various bioinformatics methods to identify the ACA/ECA gene family in pepper. We identified eleven CaACA/ECA-family genes in pepper. The chromosomal distribution, phylogenetic evolution, characteristics, gene collinearity, gene and protein structures, cis-acting elements, and specific expression patterns of CaACA/ECAs were analyzed, revealing evolutionary relationships and correlations between CaACA/ECAs and other species (Arabidopsis, rice, and tomato). The experimental results indicate that CaACA/ECAs are stable and hydrophobic proteins, with each of the eleven CaACA/ECA proteins containing all ten motifs. Eleven CaACA/ECA genes are unevenly distributed on the eight chromosomes, and they substantially differ in the number of exons. We found a close correlation between the ACA/ECAs of pepper, Arabidopsis, and tomato. The CaACA/ECA genes contain various plant-hormone-, growth-, and stress-related cis-acting elements. The qRT-PCR results indicate that the expression levels of the eleven CaACA/ECAs exhibit differential temporal expression patterns under various exogenous Ca²⁺ concentrations. These results provide a theoretical basis for further studying the function of the pepper ACA/ECA gene family and valuable information for identifying and screening genes for pepper stress tolerance breeding.