title: RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species.
abstract: RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor.
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America.
authors.forename: Wenqin
authors.initials: W
authors.lastname: Wang
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America.
authors.forename: Yongrui
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America.
authors.forename: Pal
authors.initials: P
authors.lastname: Maliga
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America.
authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
mesh_terms: D059001:Aquatic Organisms / Q000235:genetics / Q000502:physiology; D029064:Araceae / Q000235:genetics* / Q000502:physiology; D002736:Chloroplasts / Q000235:genetics* / Q000502:physiology; D002874:Chromosome Mapping; D015870:Gene Expression / Q000502:physiology; D054628:Genome, Chloroplast / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017393:RNA Editing / Q000502:physiology*; D016415:Sequence Alignment