Open Access Highly Accessed Research article

Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions

Sota Fujii12, Takushi Toda1, Shunsuke Kikuchi3, Ryutaro Suzuki3, Koji Yokoyama3, Hiroko Tsuchida3, Kentaro Yano3 and Kinya Toriyama1*

Author Affiliations

1 Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan

2 Graduate School of Science, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan

3 School of Agriculture, Meiji University, Kawasaki 214-8571, Japan

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BMC Genomics 2011, 12:279  doi:10.1186/1471-2164-12-279

Published: 1 June 2011



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.


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.


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 [ webcite].