High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora

Wu Z.Q., Stone J.D., Štorchová H., Sloan D.B.
BMC GENOMICS 16: 938, 2015

Keywords: antisense RNA; junk DNA; mtDNA; ORFs; plant mitochondrial genome; regulatory RNA; spurious transcription
Abstract: Background: Species within the angiosperm genus Silene contain the largest mitochondrial genomes ever identified. The enormity of these genomes, which can be up to 11 Mb in size, appears to be the result of increased non-coding DNA that represents >99% of the genome content rather than a larger gene content. These genomes are also fragmented into dozens of circular-mapping chromosomes, some of which contain no identifiable genes, raising questions about if and how these ‘empty’ chromosomes are maintained by selection. One possibility is that they contain novel and unannotated functional elements. To assess this possibility, we have performed RNA-seq to analyze the mitochondrial transcriptome of Silene noctiflora. Results: We identified regions of high transcript abundance in almost every chromosome in the mitochondrial genome including those that lack any identifiable genes. In some cases, these transcribed regions exhibited higher expression levels than some core mitochondrial protein-coding genes. We also identified RNA editing sites throughout the genome, including 105 sites that were outside of protein-coding gene sequences and found in pseudogenes, introns, UTRs, and transcribed intergenic regions. Finally, analysis of mitochondrial small RNAs indicated that most were likely degradation products from longer transcripts, but we did identify candidates for functional small RNAs that mapped to intergenic regions and were not associated with longer RNA transcripts. Conclusions: Our findings clearly demonstrate transcriptional activity in many localized regions within the massive amounts of intergenic content in the S. noctiflora mitochondrial genome, supporting the possibility that the genome contains previously unidentified functional elements. However, transcription by itself is not proof of functional importance, and there are indications that some of the observed transcription and post-transcriptional modifications are non-adaptive. For example, unlike in protein-coding sequences, most of the identified RNA editing sites in intergenic transcripts were only edited at intermediate frequencies. Therefore, further investigations are required to determine whether any of the identified transcribed regions are functionally important and have played a role in the proliferation and maintenance of the enormous non-coding regions in Silene mitochondrial genomes.
IEB authors: Helena Štorchová