Insights into the PYR/PYL/RCAR Gene Family in Pomegranates (Punica granatum L.): A Genome-Wide Study on Identification, Evolution, and Expression Analysis

Abstract

The response of plants to abiotic stress is intricately mediated by PYR/PYL/RCARs, key components within the ABA signal transduction pathway. Despite the widespread identification of PYL genes across diverse plant species, the evolutionary history and structural characteristics of these genes within the pomegranate (Punica granatum L.) remained unexplored. In this study, we uncovered, for the first time, 12 PgPYLs from the whole genome dataset of ‘Tunisia’, mapping them onto five chromosomes and categorizing them into three distinct subgroups (Group I, Group II, and Group III) through phylogenetic analysis. Detailed examination of the composition of these genes revealed similar conserved motifs and exon–intron structures among genes within the same subgroup. Fragment duplication emerged as the primary mechanism driving the amplification of the PYL gene family, as evidenced by intra-species collinearity analysis. Furthermore, inter-species collinearity analysis provided insights into potential evolutionary relationships among the identified PgPYL genes. Cis-acting element analysis revealed a rich repertoire of stress and hormone response elements within the promoter region of PgPYLs, emphasizing their putative roles in diverse signaling pathways. Upon treatment with 100 μmol/L ABA, we investigated the expression patterns of the PgPYL gene family, and the qRT-PCR data indicated a significant up-regulation in the majority of PYL genes. This suggested an active involvement of PgPYL genes in the plant’s response to exogenous ABA. Among them, PgPYL1 was chosen as a candidate gene to explore the function of the gene family, and the CDS sequence of PgPYL1 was cloned from pomegranate leaves with a full length of 657 bp, encoding 218 amino acids. Tobacco transient expression analysis demonstrated a consistent trend in the expression levels of pBI121-PgPYL1 and the related genes of the ABA signaling pathway, both of which increased initially before declining. This study not only contributes to the elucidation of the genomic and structural attributes of PgPYL genes but also provides a foundation for understanding their potential functions in stress responses. The identified conserved motifs, evolutionary relationships, and expression patterns under ABA treatment pave the way for further research into the PgPYL gene family’s role in pomegranate biology, offering valuable insights for future studies on genetic improvement and stress resilience in pomegranate cultivation.