Mapping of plastid RNA editing sites of Helianthus and identification of differential editing in fungal infected plants

Abstract

RNA editing is a post transcriptional modification which occurs at specific sites of RNA molecules in the chloroplasts of higher plants. Although, systematic studies have been carried out in several plants, very scant information is available with regard to the oilseed crop, sunflower. Here, we systematically investigated and compared chloroplast RNA editing status of four Helianthus species viz., H. annuus (including its three genotypes 2023B, TX16R, ID25), H. debilis, H. praecox and H. niveus and their respective fungal (powdery mildew) infected plants using bioinformatics approach from RNA-Seq data. We discovered 244 RNA editing sites (RES), including 106 (43.62%) in protein coding regions with an average number of 67 edit sites and 32 common RES distributed among six controls and their respective pathogen infected plants. A comparison of these Helianthus species transcriptomes to the genomes of A. thaliana, O. sativa and Z. mays led to discovery of 54 novel RES in 21 genes which were C to U conversions in all species. These studies provide a comprehensive picture of plastid RNA editing events in Helianthus species. We identified complete RNA editing events in four species of Helianthus and pathogen specific differential RNA editing for the first time, which would be a basis for future understanding of disease specific phenomena.