title: Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions.
abstract: BACKGROUND
  Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. We used a genomic tiling array to draw a transcriptomic atlas of Oryza sativa japonica (rice) mitochondria, which was predicted to be approximately 490-kb long.
  
  
  RESULTS
  Whereas statistical analysis verified the transcription of all previously known functional genes such as the ones related to oxidative phosphorylation, a similar extent of RNA expression was frequently observed in the inter-genic regions where none of the previously annotated genes are located. The newly identified open reading frames (ORFs) predicted in these transcribed inter-genic regions were generally not conserved among flowering plant species, suggesting that these ORFs did not play a role in mitochondrial principal functions. We also identified two partial fragments of retrotransposon sequences as being transcribed in rice mitochondria.
  
  
  CONCLUSIONS
  The present study indicated the previously unexpected complexity of plant mitochondrial RNA metabolism. Our transcriptomic data (Oryza sativa Mitochondrial rna Expression Server: OsMES) is publicly accessible at [http://bioinf.mind.meiji.ac.jp/cgi-bin/gbrowse/OsMes/#search].
authors.affiliation: Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan.
authors.forename: Sota
authors.initials: S
authors.lastname: Fujii
authors.forename: Takushi
authors.initials: T
authors.lastname: Toda
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Kikuchi
authors.forename: Ryutaro
authors.initials: R
authors.lastname: Suzuki
authors.forename: Koji
authors.initials: K
authors.lastname: Yokoyama
authors.forename: Hiroko
authors.initials: H
authors.lastname: Tsuchida
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
authors.forename: Kinya
authors.initials: K
authors.lastname: Toriyama
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics; D020869:Gene Expression Profiling; D050259:Genes, Mitochondrial / Q000235:genetics; D023281:Genomics; D008928:Mitochondria / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000166:cytology* / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D004251:DNA Transposable Elements