Deep sequencing analysis of chloroplast transcription and splicing in Euglena gracilis

The transcription and splicing of the Euglena gracilis (E. gracilis) chloroplast have been studied only on the scale of individual genes, and a comprehensive genome-scale analysis is lacking. We addressed this question in this study using transcriptomic RNA sequencing (RNA-seq) technology. Upon mapping tens of millions of RNA-seq reads onto the E. gracilis chloroplast genome, the transcription of protein-coding genes, including monocistronic genes and genes in operons, was visualized, and the expression levels of these genes were quantified. The splicing of intron-containing genes in the E. gracilis chloroplast genome was also visualized and quantified, with introns, including some twintrons, and exons being clearly discerned. The correct coding sequences of psbD, rpl23 and rpl16 were deduced based on read coverage of the corresponding genes and confirmed experimentally. Additionally, a new group III intron was identified from the 5’ UTR of petB. This study updates our knowledge on the transcription and splicing of the E. gracilis chloroplast, and will be instrumental in the mechanistic exploration of gene transcription and intron splicing in the E. gracilis chloroplast.