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

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dc.contributor.authorWu, Zhiqiang, author
dc.contributor.authorStone, James D., author
dc.contributor.authorŠtorchovaá, Helena, author
dc.contributor.authorSloan, Daniel B., author
dc.contributor.authorBMC Genomics, publisher
dc.date.accessioned2015-12-02T21:17:17Z
dc.date.available2015-12-02T21:17:17Z
dc.date.issued2015
dc.description.abstractBackground: Species within the angiosperm genus Silene contain the largest mitochondrial genomes ever identified. The enormity of these genomes (up to 11 Mb in size) appears to be the result of increased non-coding DNA, which represents >99 % of the genome 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. To assess the possibility that they contain novel and unannotated functional elements, 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 annotated 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 97 sites that were outside of protein-coding gene sequences and found in pseudogenes, introns, UTRs, and transcribed intergenic regions. Unlike in protein-coding sequences, however, most of these RNA editing sites were only edited at intermediate frequencies. 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 demonstrate transcriptional activity in many localized regions within the extensive intergenic sequence 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 we discuss evidence that some of the observed transcription and post-transcriptional modifications are non-adaptive. Therefore, further investigations are required to determine whether any of the identified transcribed regions have played a functional role in the proliferation and maintenance of the enormous non-coding regions in Silene mitochondrial genomes.
dc.description.sponsorshipPublished with support from the Colorado State University Libraries Open Access Research and Scholarship Fund.
dc.format.mediumborn digital
dc.format.mediumarticles
dc.identifier.bibliographicCitationWu, Zhiqiang, Stone, James D., Helena Štorchová, and Daniel B. Sloan. High Transcript Abundance, RNA Editing, and Small RNAs in Intergenic Regions Within the Massive Mitochondrial Genome of the Angiosperm Silene noctiflora. BMC Genomics 16, no. 1 (2015): 938. http://dx.doi.org/10.1186/s12864-015-2155-3
dc.identifier.doihttps://dx.doi.org/10.1186/s12864-015-2155-3
dc.identifier.urihttp://hdl.handle.net/10217/170060
dc.languageEnglish
dc.language.isoeng
dc.publisherColorado State University. Libraries
dc.relation.ispartofOpen Access Research and Scholarship Fund (OARS)
dc.rights.licenseThis article is open access and distributed under the terms and conditions of the Creative Commons Attribution 4.0 International (CC BY 4.0).
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectJunk DNA
dc.subjectORFs
dc.subjectPlant mitochondrial genome
dc.subjectRegulatory RNA
dc.subjectSpurious transcription
dc.subject.lcshAntisense RNA
dc.subject.lcshmtDNA
dc.titleHigh transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora
dc.typeText

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