Genome-wide identification of the papaya-like cysteine protease family in poplar and determination of the functional role of PeRD19A in conferring salt tolerance

Papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes involved in plant growth and development as well as plant responses to biological and abiotic stresses. However, there is no detailed characterization of PLCPs genes in poplar. In this study, a genome-wide analysis of the poplar PtrPLCPs family revealed 47 PtrPLCPs, which were classified into nine subfamilies according to their phylogeny: RD21, CEP, XCP, XBCP3, SAG12, RD19 (5), ALP, CTB, and the lost THI subgroups. SAG12 was the largest subfamily, with 22 members, and had the largest number of tandem repeats and homologous gene pairs. The PtrPLCPs family seems to have undergone whole-genome duplication (WGD), with the SAG12 subfamily as the main driving force in evolutionary amplification. An analysis of the abiotic stress expression profile showed that the 47 PtrPLCPs genes were induced by stresses such as cold, drought, and, especially, salt. Overexpression of the PeRD19A gene enhanced the scavenging ability of reactive oxygen species (ROS) in poplar, regulated several major metabolic pathways such as glyoxylate and dicarboxylate metabolic pathways, and provided energy for the synthesis of flavonoids and lignin compounds, thereby improving the antioxidant capacity of cells and increasing the mechanical strength of cell wall to prevent cell damage, and further helping poplar to cope with stress and improve the salt tolerance of poplar. Our study provides valuable insights that can be applied in future functional genome studies of poplar, and specifically studies of the PtrPLCPs gene family.