Abstract
BackgroundPlant 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.ResultsWhereas 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.ConclusionThe 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].
Highlights
Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans
By setting the transcriptional borders by defining transcriptional units, we showed that 36.9% of open reading frames (ORFs) present in inter-genic regions were being transcribed without association with known mitochondrial housekeeping genes
Identification of transcribed region To restrict the transcribed region, we used the relative transcription levels of orf490 and orf181 as background controls. Transcripts of these two ORFs were not detected in our preliminary transcription analysis by northern blotting (Additional file 2). These genes are partly transposable elements (TEs) fragments, making them highly unlikely to have any function in mitochondria, and we concluded that these genes were not transcribed
Summary
Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. The obvious expansion of its genomic size indicates that higher plant mitochondria experienced a dramatic evolution. The common size of mitochondria genetic information is limited to approximately 16 kb in metazoans [1], whereas in higher plants the sequence length can be 2002400 kb (Additional file 1) [2]. The principal role of mitochondria (i.e. oxidative phosphorylation) is undoubtedly shared between metazoans and higher plants. Usually a higher plant mitochondrion encodes about 40 genes with known functions, whereas in most cases there are 13 tightly conserved genes encoded by metazoan mitochondria. A greater number of mitochondrial genes would explain only a small proportion of the genome size increase of plant mitochondria
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