Orthology-Based Reconstruction of Parental Gene Inheritance in the Chromosome-Scale PR25 Perennial Rice Genome

Abstract

Perennial rice integrates a cultivated rice background with genetic elements from wild species; however, the role of parental gene repertoires in hybrid genomes is not fully understood. This study examined the gene repertoires linked to parents and their functional characteristics within the chromosome-scale PR25 perennial rice genome, which originated from Oryza sativa ssp. indica cv. RD23 and Oryza longistaminata. Structural annotations were transferred using Liftoff, followed by phylogenetic orthology analysis using OrthoFinder, and functional annotation using eggNOG-mapper v2 and InterProScan. Of the 37,581 structurally annotated PR25 loci, 33,305 were aligned using the parental orthology framework. Most of these genes (20,204; 60.7%) had identifiable orthologs in both parents (BOTH), whereas 12,808 (38.5%) were categorized as RD23_only and 293 (0.9%) as OL_only. Among the 25,828 genes with consistent functional annotations, RD23_only genes exhibited a higher presence of secretory and membrane-associated features, such as SignalP-TM (4.42%), whereas OL_only genes had a higher presence of defense-related features, including NB-ARC (6.22%) and Ser/Thr kinase domains (2.90%). Functional annotation was unresolved for 5,746 RD23_only genes (44.9%). These results provide a detailed catalog of parent-associated gene repertoires and functions in PR25. The small proportion of OL_only should be interpreted with caution because of the fragmented nature of the O. longistaminata assembly. This catalog serves as a foundation for functional validation and molecular breeding research.