title: Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes.
abstract: Sequence analysis of organelle genomes and comprehensive analysis of C-to-U editing sites from flowering and non-flowering plants have provided extensive sequence information from diverse taxa. This study includes the first comprehensive analysis of RNA editing sites from a gymnosperm mitochondrial genome, and utilizes informatics analyses to determine conserved features in the RNA sequence context around editing sites. We have identified 565 editing sites in 21 full-length and 4 partial cDNAs of the 39 protein-coding genes identified from the mitochondrial genome of Cycas taitungensis. The information profiles and RNA sequence context of C-to-U editing sites in the Cycas genome exhibit similarity in the immediate flanking nucleotides. Relative entropy analyses indicate that similar regions in the 5' flanking 20 nucleotides have information content compared to angiosperm mitochondrial genomes. These results suggest that evolutionary constraints exist on the nucleotide sequences immediately adjacent to C-to-U editing sites, and similar regions are utilized in editing site recognition.
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, 92697-2300, USA.
authors.forename: Michael Lee
authors.initials: ML
authors.lastname: Salmans
authors.forename: Shu-Miaw
authors.initials: SM
authors.lastname: Chaw
authors.forename: Ching-Ping
authors.initials: CP
authors.lastname: Lin
authors.forename: Arthur Chun-Chieh
authors.initials: AC
authors.lastname: Shih
authors.forename: Yu-Wei
authors.initials: YW
authors.lastname: Wu
authors.forename: R Michael
authors.initials: RM
authors.lastname: Mulligan
mesh_terms: D001483:Base Sequence; D032462:Cycadopsida / Q000235:genetics*; D029784:Cycas / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D050259:Genes, Mitochondrial; D017343:Genes, Plant; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics*; D008928:Mitochondria; D015388:Organelles; D017393:RNA Editing; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D004272:DNA, Mitochondrial; D018749:RNA, Plant