Pangenome-wide identification of chloroplast RNA splicing and ribosome maturation (CRM) genes in eight Pyrus genomes indicated their involvement in multiple stresses.

Chloroplast RNA splicing and ribosome maturation (CRM) domain proteins are central to chloroplast intron splicing, rRNA processing, and plant stress responses. While extensively studied in model plants such as Arabidopsis, rice, and maize, the CRM gene family has not been characterized in Pyrus, a major fruit crop of global commercial agricultural productivity . This study presents the first pangenome-wide analysis of CRM genes across 8 Pyrus genomes, aiming to unravel their evolutionary patterns, structural diversity, and potential functional roles in stress adaptation. In this study, we identified 25 PyCRM pan-genes, comprising 9 core, 15 variable, and 1 species-specific members, reflecting gene presence-absence variation within the family. Phylogenetic analysis grouped these proteins into four conserved subfamilies, with the CRS1 subfamily being the largest. Gene structure and motif profiling revealed subfamily-specific conservation alongside distinct motif variations, suggesting functional divergence. Ka/Ks calculation revealed that most of the PyCRM genes evolved under purifying selection, while a few members experienced positive selection, highlighting functional diversification within the CRM gene family. Promoter analysis identified multiple cis-regulatory elements linked to the light response, hormone signaling, stress responses, and developmental processes. Functional enrichment highlighted roles in RNA binding and mRNA processing. Members of the same family share similar motifs and conserved protein 3D structures. Furthermore, expression profiling under cold, drought, and disease revealed that most PyCRM genes were downregulated under stress conditions, while a few members exhibited stress-specific upregulation, suggesting functional diversification within the gene family. These findings lay the foundation for future investigations into CRM-mediated stress tolerance and crop improvement.