Pan-Genome-Based Characterization of the PYL Transcription Factor Family in Populus

Abscisic acid (ABA) is a key phytohormone involved in regulating plant growth and responses to environmental stress. As receptors of ABA, pyrabactin resistance 1 (PYR)/PYR1-like (PYL) proteins play a central role in initiating ABA signal transduction. In this study, a total of 30 PopPYL genes were identified and classified into three sub-families (PYL I–III) in the pan-genome of 17 Populus species, through phylogenetic analysis. Among these subfamilies, the PYL I subfamily was the largest, comprising 21 members, whereas PYL III was the smallest, with only four members. To elucidate the evolutionary dynamics of these genes, we conducted synteny and Ka/Ks analyses. Results indicated that most PopPYL genes had undergone purifying selection (Ka/Ks < 1), while a few were subject to positive selection (Ka/Ks > 1). Promoter analysis revealed 258 cis-regulatory elements in the PYL genes of Populus euphratica (EUP) and Populus pruinosa (PRU), including 127 elements responsive to abiotic stress and 33 ABA-related elements. Furthermore, six structural variations (SVs) were detected in PYL_EUP genes and significantly influenced gene expression levels (p < 0.05). To further explore the functional roles of PYL genes, we analyzed tissue-specific expression profiles of 17 PYL_EUP genes under drought stress conditions. PYL6_EUP was predominantly expressed in roots, PYL17_EUP exhibited leaf-specific expression, and PYL1_EUP showed elevated expression in stems. These findings suggest that the drought response of PYL_EUP genes is tissue-specific. Overall, this study highlights the utility of pan-genomics in elucidating gene family evolution and suggests that PYL_EUP genes contribute to the regulation of drought stress responses in EUP, offering valuable genetic resources for functional characterization of PYL genes.