A study of RNA-editing in Populus trichocarpa nuclei revealed acquisition of RNA-editing on the endosymbiont-derived genes,and a preference for intracellular remodeling genes in adaptation to endosymbiosis

摘要

RNA-editing is a post-transcriptional modification that can diversify genome-encoded information by modifying individual RNA bases.In contrast to the well-studied RNA-editing in organelles,little is known about nuclear RNA-editing in higher plants.We performed a genome-wide study of RNA-editing in Populus trichocarpa nuclei using the RNA-seq data generated from the sequenced poplar genotype,‘Nisqually-1’.A total of 24,653 nuclear RNA-editing sites present in 8,603 transcripts were identified.Notably,RNA-editing in P.trichocarpa nuclei tended to occur on endosymbiont-derived genes.We then scrutinized RNA-editing in a cyanobacterial strain closely related to chloroplast.No RNA-editing sites were identified therein,implying that RNA-editing of these endosymbiont-derived genes was acquired after endosymbiosis.Gene ontology enrichment analysis of all the edited genes in P.trichocarpa nuclei demonstrated that nuclear RNA-editing was primarily focused on genes involved in intracellular remodeling processes,which suggests that RNA-editing plays contributing roles in organellar establishment during endosymbiosis.We built a coexpression network using all C-to-U edited genes and then decomposed it to obtain 18 clusters,six of which contained a conserved core motif,A/G-C-A/G.Such a short core motif not only attracted the RNA-editing machinery but also enabled large numbers of sites to be targeted though further study is necessary to verify this finding.