RNA editing in chloroplast NADH dehydrogenase (ndhA) of salt stressed wild barley revealed novel type G to A

Abstract

The ndhA gene of NAD(P)H dehydrogenase in chloroplast DNA is vital for the electron transport chain and needs to be studied, especially in the context of RNA editing and its effects. Wild barley (Hordeum vulgare subsp. spontaneum) plants were studied in 4 groups, with exposure to 500 mM NaCl for 0 h – control (accession no. OM262848), and three treatment groups: 2 h (accession no. OM262849), 12 h (accession no. OM262850) and 24 h (accession no. OM262851) and their RNA was sent for RNA-seq sequencing. The sequences were submitted to NCBI SRA archives and analyzed together after filtering for high quality. This was done to show the RNA editing position and percentages at 10 sites across the ndhA gene. The RNA edits were validated using quantitative-PCR and homology models for the ndhA protein after exposure to salt stress were also generated. The four treatments showed five C to U changes (C50, C303, C563, C1042, C1047), three U to C changes (U550, U592, U1066), and two G to A changes (G111, G1046). We investigated the extent and effect of RNA editing in ndhA transcripts from chloroplasts of barley. We observed high RNA editing percentages after the second hour of salt stress.We have also observed for the first time about ‘U to C’ RNA edits in ndhA gene of wild barley.