Genome-wide analysis of pentatricopeptide repeat genes in castor and their potential functions in seed development

Pentatricopeptide repeat (PPR) proteins, defined by tandem 35 amino acids helical motifs, are pivotal regulators of RNA recognition and processing in plant organelles, especially plastids and mitochondria, thereby shaping plant development. However, their structural diversity and functional roles remain poorly understood, particularly in non-model oilseed crops. Castor ( Ricinus communis L.), a non-edible yet industrially important oilseed species, provides an ideal system to explore PPR gene family characteristics. In this study, we identified 434 RcPPR genes and comprehensively analyzed their motif composition, RNA-binding site preferences, and subcellular localization. Although conserved amino acid patterns were observed across different PPR subclasses, the canonical residues at positions 5 (N) and 35 (D/N), previously considered critical for nucleotide recognition, showed notable variation, implying flexibility in RNA-binding specificity. Chromosomal mapping revealed that RcPPR were frequedtly clustered in transposon-rich regions, suggesting transposable element-mediated gene family expansion. Phylogenetic and evolutionary analyses indicated that RcPPR are conserved across angiosperms but have experienced rapid evolution, as evidenced by elevated Ks values, likely driven by functional diversification. Subcellular localization predictions and experimental validation in castor leaf protoplasts confirmed predominant targeting of RcPPR proteins to mitochondria and plastids. Expression profiling revealed strong tissue specificity, with 116 RcPPRs exhibiting seed-specific expression and co-expression with genes involved in seed development and oil biosynthesis. Collectively, this study provides new insights into the structure, evolution, and functional relevance of PPR proteins in castor, enriching our understanding of organelle RNA regulation in developing oilseed crops. Identified 434 PPR genes in Ricinus communis and analyzed their conserved motifs and organelle-targeted RNA-binding features. RcPPR genes are often clustered with transposons, suggesting transposon-mediated gene family expansion. Phylogenetic and evolutionary analyses indicate conservation across angiosperms alongside signs of rapid diversification. Subcellular localization assays confirmed RcPPRs are primarily targeted to mitochondria and plastids. Expression profiling revealed 116 RcPPRs with seed-specific expression, linked to seed development and oil biosynthesis.