Cytoplasmic male sterility (CMS), encoded by the interacting mitochondrial and nuclear genes, causes pollen abortion or non-viability. CMS is widely used in agriculture and extensively studied in crops. Much less is known about CMS in wild species. We performed a comparative transcriptomic analysis of male sterile and fertile individuals of Silene vulgaris, a model plant for the study of gynodioecy, to reveal the genes responsible for pollen abortion in this species. We used RNA-seq datasets previously employed for the analysis of mitochondrial and plastid transcriptomes of female and hermaphrodite flower buds, making it possible to compare the transcriptomes derived from three genomes in the same RNA specimen. We assembled de novo transcriptomes for two haplotypes of S. vulgaris and identified differentially expressed genes between the females and hermaphrodites, associated with stress response or pollen development. The gene for alternative oxidase was downregulated in females. The genetic pathways controlling CMS in S. vulgaris are similar to those in crops. The high number of the differentially expressed nuclear genes contrasts with the uniformity of organellar transcriptomes across genders, which suggests these pathways are evolutionarily conserved and that selective mechanisms may shield organellar transcription against changes in the cytoplasmic transcriptome.

• Keywords
• Silene vulgaris, cytoplasmic male sterility, differential gene expression,
• MeSH
• Molecular Sequence Annotation MeSH
• Cell Nucleus genetics   MeSH
• Down-Regulation genetics   MeSH
• Gene Ontology MeSH
• Haplotypes genetics   MeSH
• RNA, Messenger genetics   metabolism   MeSH
• Mitochondrial Proteins genetics   metabolism   MeSH
• Plant Infertility genetics   MeSH
• Oxidative Stress genetics   MeSH
• Oxidoreductases genetics   metabolism   MeSH
• Pollen genetics   MeSH
• Gene Expression Regulation, Plant * MeSH
• Plant Proteins genetics   metabolism   MeSH
• Silene genetics   physiology   MeSH
• Gene Expression Profiling * MeSH
• Transcriptome genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• alternative oxidase MeSH Browser
• RNA, Messenger MeSH
• Mitochondrial Proteins MeSH
• Oxidoreductases MeSH
• Plant Proteins MeSH

The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis. We summarize current knowledge of the role of nucleus encoded regulatory non-coding RNAs (long non-coding RNA, microRNA as well as small interfering RNA) in CMS. We also focus on the emerging data of non-coding RNAs encoded by mitochondrial genome and their possible involvement in mitochondrial-nuclear interactions and CMS development.

• Keywords
• cytoplasmic male sterility, gene expression, global transcriptome, non-coding RNA, pollen development,
• MeSH
• Self-Incompatibility in Flowering Plants genetics   MeSH
• Magnoliopsida physiology   MeSH
• Genes, Mitochondrial MeSH
• RNA, Untranslated genetics   metabolism   MeSH
• Plant Infertility genetics   MeSH
• Pollen genetics   physiology   MeSH
• Genes, Plant MeSH
• Publication type
• Journal Article MeSH
• Review MeSH
• Names of Substances
• RNA, Untranslated MeSH

Cytoplasmic male sterility (CMS) is a widespread phenomenon in flowering plants caused by mitochondrial (mt) genes. CMS genes typically encode novel proteins that interfere with mt functions and can be silenced by nuclear fertility-restorer genes. Although the molecular basis of CMS is well established in a number of crop systems, our understanding of it in natural populations is far more limited. To identify CMS genes in a gynodioecious plant, Silene vulgaris, we constructed mt transcriptomes and compared transcript levels and RNA editing patterns in floral bud tissue from female and hermaphrodite full siblings. The transcriptomes from female and hermaphrodite individuals were very similar overall with respect to variation in levels of transcript abundance across the genome, the extent of RNA editing, and the order in which RNA editing and intron splicing events occurred. We found only a single genomic region that was highly overexpressed and differentially edited in females relative to hermaphrodites. This region is not located near any other transcribed elements and lacks an open-reading frame (ORF) of even moderate size. To our knowledge, this transcript would represent the first non-coding mt RNA associated with CMS in plants and is, therefore, an important target for future functional validation studies.

• Keywords
• Cytoplasmic male sterility, Silene vulgaris, editing, mitochondrion, non-coding RNA, splicing, transcriptome.,
• MeSH
• RNA Editing MeSH
• Flowers genetics   growth & development   MeSH
• Genes, Mitochondrial * MeSH
• RNA, Untranslated * MeSH
• Plant Infertility * MeSH
• Plant Proteins genetics   metabolism   MeSH
• Silene genetics   physiology   MeSH
• Transcriptome * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Names of Substances
• RNA, Untranslated * MeSH
• Plant Proteins MeSH

BACKGROUND: 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.

• MeSH
• RNA Editing MeSH
• Genome, Mitochondrial * MeSH
• Genome, Plant * MeSH
• DNA, Intergenic MeSH
• RNA, Messenger MeSH
• Open Reading Frames MeSH
• Pseudogenes MeSH
• RNA, Mitochondrial MeSH
• RNA MeSH
• Genes, Plant MeSH
• Sequence Analysis, RNA MeSH
• Silene genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Names of Substances
• DNA, Intergenic MeSH
• RNA, Messenger MeSH
• RNA, Mitochondrial MeSH
• RNA MeSH