Identification and analysis of RNA editing sites of chloroplast genes in foxtail millet [<italic>Setaria italica</italic> (L.) P. Beauv.

Abstract

<p id="C3">RNA editing is one of the post-transcriptional regulation mechanisms of gene expression in the chloroplast genomes of higher plants, which affects the chloroplast development and leads to albino phenotype or yellow phenotype of plant leaves. In this study, chlorophyll content was measured with a UV spectrophotometer at seeding stage among Changnong 35, E752, and E1005, and chloroplast structure of leaves was observed with a transmission electron microscopy; the online tool Prep-CP was used to predict the RNA editing sites of chloroplast genes; RNA editing site was verified by PCR, RT-PCR, and sequencing method, and the editing sites were compared and analyzed between foxtail millet and other monocotyledon. Furthermore, the relative expression patterns of <italic>rpoB</italic> and PEP-transcription-dependent photosynthetic pathway related genes (<italic>ndhG</italic>,<italic> psaA</italic>,<italic> psbA</italic>, and<italic> rbcL</italic>) were analyzed by qRT-PCR at different developmental stages, and the secondary structure of rpoB protein before and after editing was analyzed by bioinformatics. The results showed that chlorophyll content of E752 and E1005 were significantly lower and their chloroplasts were abnormal compared with Changnong 35. A total of 20 RNA editing sites of 10 chloroplast genes were identified, among which all were C to U conversion; the number of editing sites among chloroplast genes was varied, and <italic>ndhB</italic> had the most editing sites with the number of 6. Among the 20 editing sites, 19 editing sites were highly conserved in the evolution of species, however <italic>rpoC1-2753</italic> was a unique editing site in foxtail millet. The editing efficiency of<italic> rpoB-467</italic>, <italic>rpoB-545</italic>, and<italic> rpoB-</italic>560 was distinctly different from those of the other editing sites among Changnong 35, E752, and E1005, leading to the expression level change of <italic>ropB</italic>, which might further affect the expression levels changes of <italic>ndhG</italic>,<italic> psaA</italic>,<italic> psbA</italic>, and<italic> rbcL</italic>. Bioinformatics analysis revealed that secondary structure of rpoB protein was changed due to the RNA editing of <italic>rpoB-467</italic> and <italic>rpoB-560</italic>. Our results laid a foundation for the molecular mechanism analysis of chloroplast RNA editing in chloroplast development of foxtail millet.