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

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