Genome-wide characterization of the PPR gene family and its potential roles in stress responses and chloroplast RNA editing in Brassica rapa.

Pentatricopeptide repeat proteins are a large family of RNA-binding proteins that play essential roles in post-transcriptional regulation within plant organelles. However, a systematic understanding of their evolutionary expansion and functional relevance in Brassica rapa remains limited. This study identified and characterized the PPR gene family in B. rapa and investigated their potential roles in stress responses and chloroplast RNA editing. Using the B. rapa Chiifu v4.0 genome assembly, we performed a genome-wide identification and characterization of PPR genes. Phylogenetic relationships, gene structures, duplication patterns, chromosomal distribution, subcellular localization, and cis-regulatory elements were analyzed. Tissue-specific expression patterns were investigated using publicly available RNA-seq datasets and qRT-PCR validation, while stress-associated transcriptional responses and organellar RNA editing profiles were analyzed using public RNA-seq datasets. A genome-wide analysis identified 493 PPR genes, classified into P and PLS subfamilies, with uneven chromosomal distribution and expansion mainly driven by dispersed and whole-genome duplication events. Furthermore, subcellular localization prediction indicated that most PPR proteins are targeted to mitochondria and chloroplasts, consistent with their roles in organellar gene regulation. In addition, Gene Ontology enrichment analysis suggested potential associations of PPR proteins with RNA processing and RNA editing pathways. Moreover, promoter analysis identified numerous stress-responsive cis-acting elements, indicating that PPR genes may participate in transcriptional responses under environmental stress conditions. Meanwhile, expression profiling based on publicly available RNA-seq datasets revealed tissue-preferential expression patterns and stress-associated transcriptional changes under drought, heat, and immune elicitor treatments, with some PPR genes showing altered expression across multiple stress conditions. Chloroplast RNA editing analysis based on heat-stress RNA-seq datasets revealed dynamic and site-specific changes in editing efficiency. Several editing sites, including cemA, psbZ, and ndhD, showed relatively higher editing levels in the heat-tolerant line than in the heat-sensitive line. In contrast, prolonged heat stress was associated with reduced editing efficiency at multiple sites such as atpF, rpoB, rps14, and clpP. Collectively, this study provides a comprehensive overview of PPR genes in B. rapa and identifies candidate PPR genes and stress-associated RNA editing events that may be relevant to stress-responsive regulation.