ArticleProceedings of the National Academy of Sciences of the United States of America2022
Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 40 citations in OpenAlex.
- Transfer of chloroplastSynthetic and systems biotechnology · 2027Article
- A poly(A)-independent PacBio strategy for organellar transcriptome profiling.Plant physiology · 2026Article
- Causes and consequences of cytonuclear incompatibility in hybrids of flowering plants.Journal of experimental botany · 2026Review
- Correlated Evolutionary Rates Reveal Novel Components and Cross-Compartment Connectivity in Plant Proteostasis Systems.Genome biology and evolution · 2026Article
- The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids.Nucleic acids research · 2026Article
- Practical RNA-Seq with Spike-Ins: A Bench-to-Bioinformatics Guide.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- Plant MutS2 proteins function in plastid ribosome quality control.bioRxiv : the preprint server for biology · 2025Article
- Restoring cytonuclear harmony: Distinct strategies in Arabidopsis auto- and allopolyploids.The Plant journal : for cell and molecular biology · 2025Article
- Monkeyflower (Mimulus) uncovers the evolutionary basis of the eukaryote telomere sequence variation.PLoS genetics · 2025Article
- An improved nuclei isolation protocol from leaf tissue for single-cell transcriptomics.PloS one · 2025Article
- Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids.The New phytologist · 2025Article
- Photosynthetic demands on translational machinery drive retention of redundant tRNA metabolism in plant organelles.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Widespread adaptive evolution in angiosperm photosystems provides insight into the evolution of photosystem II repair.The Plant cell · 2024Article
- Integrating the Study of Polyploidy Across Organisms, Tissues, and Disease.Annual review of genetics · 2024Review
- Polyploid plants take cytonuclear perturbations in stride.The Plant cell · 2024Article
- Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Plant phase extraction: A method for enhanced discovery of the RNA-binding proteome and its dynamics in plants.The Plant cell · 2023Article
- The Evolutionary Constraints on Angiosperm Chloroplast Adaptation.Genome biology and evolution · 2023Article
- No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas.Genome biology and evolution · 2023Article
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11 authors at 5 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9 to 82.3%) of messenger RNA (mRNA) transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3 to 3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than 10-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.
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