PATHOGENESIS-RELATED (PR) PROTEINS: identification, evolution and functional analysis in pear (Pyrus bretschneideri)

Pathogenesis-related (PR) proteins play a crucial role in plant defense against diverse threats, including biotic and abiotic factors. These versatile proteins exhibit a wide range of functions such as chitinases, peroxidases, antimicrobial agents, hydrolases, and protease inhibitors. However, the knowledge concerning PRs in pears is constrained. In this study, a total of 637 PR proteins categorized into 17 PR families were discerned in Pyrus bretschneideri. Through phylogenetic, sequence similarity, and secondary structure analyses, several PR proteins with similar sequences were successfully classified, including PR-11, PR-8, PR-15, and PR-16. By analyzing their corresponding genomic data, it was discovered that the expansion of most PR families can be attributed to recent whole-genome duplication (WGD) events that occurred approximately 30-45 million years ago (Mya). Various types of gene duplication events have collectively contributed to the expansion of PR families, and the dominance of purifying selection is evident from the small Ka/Ks ratios. By analyzing the composition of the apoplast fluid, it was found that only a small number of members from each PR protein family were present in the apoplast. Transcriptomic data from pear infected with Erwinia amylovora and Colletotrichum fructicola revealed that certain PR genes are significantly upregulated following infection. These differentially expressed genes (DEGs) served as reliable indicators of disease resistance response in pears and also represented potential resources for future disease-resistant breeding. Notably, several clusters of significantly downregulated PR genes also underscored the complexity of PR gene regulation. The findings of this study enhanced our understanding of the intricate nature of PR genes and will facilitate future investigations into their functional characterization.