Comparative chloroplast RNA editing analysis in wild and genetically diverse niger (Guizotia abyssinica L.F. Cass) genotypes reveal domestication-driven divergence and wild-specific resilience

Abstract

RNA editing is a key post-transcriptional mechanism that alters RNA sequences, thereby influencing gene expression, protein function, and stress adaptability in plants. Despite extensive characterization in model species, its prevalence and functional significance in underutilized crops remains limited. Here, we present the first comprehensive analysis of chloroplast RNA editing in Guizotia abyssinica (niger), an underutilized but economically important oilseed crop, and its wild relative G. scabra (GS), along with three geographically diverse domesticated genotypes, JNS-28 (India), ETH-19 (Ethiopia), and USDA-15 (USA). Using high-throughput Illumina RNA-sequencing and REDItools, 404 RNA editing sites were identified in GS, followed by 304 in USDA-15, 220 in ETH-19, and 166 in JNS-28, with C-to-U conversions being most prevalent. Homology-based analyses revealed putative PPR, MORF, and OZ1 family members, whose expression patterns, analyzed by DESeq2, showed significant divergence between wild and cultivated genotypes, reflecting domestication and environment-driven selection. Phylogenetic analyses further suggested diversification of RNA editing factors in G. abyssinica compared to other oilseed and model species. Notably, domestication has reduced RNA editing diversity in cultivated genotypes, while the wild G. scabra retained extensive editing patterns with potential adaptive significance These findings illuminate organellar transcriptomic plasticity in niger, establish a molecular link between RNA editing and stress resilience, and highlight novel targets for breeding and biotechnological improvement of this underutilized oilseed crop.