Transcriptome Profiling of RNA Editing in Mitochondrial nad Genes of Catharanthusroseus: Organ-Specific Patterns and Functional Implications

Abstract

Abstract RNA editing is a major post-transcriptional process in plant organelles that frequently alters coding sequences and can influence mitochondrial gene function. However, organ-resolved RNA editing in mitochondrial nad transcripts remains poorly characterized in Catharanthus roseus (L.) G.Don, despite the biological importance of these Complex I genes and prior evidence for organ-dependent organellar editing in this species. This study analyzed RNA editing in mitochondrial nad transcripts across six C. roseus organs: flower, stem, leaf, hairy root, root, and seedling. Editing-site distribution, novel editing events, organ-shared and organ-differentiated sites, amino acid conversions, silent sites, and qRT-PCR validation of selected nad9 editing sites were assessed. A total of 442 organ-specific editing events were identified across all organs, with the highest number in hairy root (97; 21.95%) and the lowest in seedling (52; 11.76%). These events corresponded to 108 unique editing sites distributed among the nad genes. Whereas nad5 (24 sites), nad1 (20), and nad2 (19) contributing most of the novel events. Figure-based analysis showed 24 sites shared across all organs and 88 organ-differentiated sites, indicating that variable editing predominated over constitutive editing. Editing-induced amino acid changes totaled 108 events, whereas only four sites were silent; the most frequent substitutions were Ser → Phe and Pro → Leu, each accounting for 22.22% of all amino acid conversions. qRT-PCR validation confirmed marked site-specific variation in nad9 editing, with C92 showing consistently high editing and C167, C298, and C368 showing stronger organ dependence. Mitochondrial nad RNA editing in C. roseus is extensive, organ specific, and predominantly protein altering, with nad5 representing the principal editing hotspot. These findings identify RNA editing as a major layer of post-transcriptional regulation in the mitochondrial Complex I transcript set of C. roseus.