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Open Access Research article

Deep sequencing of the tobacco mitochondrial transcriptome reveals expressed ORFs and numerous editing sites outside coding regions

Benjamin T Grimes1, Awa K Sisay2, Hyrum D Carroll2 and A Bruce Cahoon1*

Author Affiliations

1 Department of Biology, Box 60, Middle Tennessee State University, Murfreesboro, TN 37132, USA

2 Computational Science Program, Middle Tennessee State University, Box 48, Murfreesboro, TN 37132, USA

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BMC Genomics 2014, 15:31  doi:10.1186/1471-2164-15-31

Published: 17 January 2014

Abstract

Background

The purpose of this study was to sequence and assemble the tobacco mitochondrial transcriptome and obtain a genomic-level view of steady-state RNA abundance. Plant mitochondrial genomes have a small number of protein coding genes with large and variably sized intergenic spaces. In the tobacco mitogenome these intergenic spaces contain numerous open reading frames (ORFs) with no clear function.

Results

The assembled transcriptome revealed distinct monocistronic and polycistronic transcripts along with large intergenic spaces with little to no detectable RNA. Eighteen of the 117 ORFs were found to have steady-state RNA amounts above background in both deep-sequencing and qRT-PCR experiments and ten of those were found to be polysome associated. In addition, the assembled transcriptome enabled a full mitogenome screen of RNA C→U editing sites. Six hundred and thirty five potential edits were found with 557 occurring within protein-coding genes, five in tRNA genes, and 73 in non-coding regions. These sites were found in every protein-coding transcript in the tobacco mitogenome.

Conclusion

These results suggest that a small number of the ORFs within the tobacco mitogenome may produce functional proteins and that RNA editing occurs in coding and non-coding regions of mitochondrial transcripts.

Keywords:
Mitochondrial transcriptome; Plant mitogenome; Tobacco; Nicotiana tabacum; RNA editing