ArticleNucleic acids research2011
Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Massive RNA Editing in Ascetosporean Mitochondria.Microbes and environments · 2025Article
- Genetic Diversity in the mtDNA ofGenes · 2023Review
- Complete chloroplast genome of the desert date (Balanites aegyptiaca (L.) Del. comparative analysis, and phylogenetic relationships among the members of Zygophyllaceae.BMC genomics · 2022Article
- Gene Losses and Plastome Degradation in the Hemiparasitic SpeciesPlants (Basel, Switzerland) · 2022Article
- Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution.Plants (Basel, Switzerland) · 2021Article
- Complete chloroplast genome sequences ofSaudi journal of biological sciences · 2021Article
- Complete Chloroplast Genome ofPlants (Basel, Switzerland) · 2021Article
- Comparative Plastomics of Ashwagandha (Plants (Basel, Switzerland) · 2020Article
- Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids.Nucleic acids research · 2020Article
- Comparison of Four Complete Chloroplast Genomes of Medicinal and Ornamental Meconopsis Species: Genome Organization and Species Discrimination.Scientific reports · 2019Article
- In vivo cleavage specificity of Trypanosoma brucei editosome endonucleases.Nucleic acids research · 2017Article
- Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids.Genome biology and evolution · 2017Article
- Review
- Article
- The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.Genome biology and evolution · 2015Article
- Comprehensive high-resolution analysis of the role of an Arabidopsis gene family in RNA editing.PLoS genetics · 2013Article
- A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes.RNA biology · 2013Article
- PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation.Bioinformatics and biology insights · 2013Article
- A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level.Gene regulation and systems biology · 2012Article
- Comparison of insertional RNA editing in Myxomycetes.PLoS computational biology · 2012Article
Corrections and comments
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5 authors.
Funding
Abstract
RNAs transcribed from the mitochondrial genome of Physarum polycephalum are heavily edited. The most prevalent editing event is the insertion of single Cs, with Us and dinucleotides also added at specific sites. The existence of insertional editing makes gene identification difficult and localization of editing sites has relied upon characterization of individual cDNAs. We have now determined the complete mitochondrial transcriptome of Physarum using Illumina deep sequencing of purified mitochondrial RNA. We report the first instances of A and G insertions and sites of partial and extragenic editing in Physarum mitochondrial RNAs, as well as an additional 772 C, U and dinucleotide insertions. The notable lack of antisense RNAs in our non-size selected, directional library argues strongly against an RNA-guided editing mechanism. Also of interest are our findings that sites of C to U changes are unedited at a significantly higher frequency than insertional editing sites and that substitutional editing of neighboring sites appears to be coupled. Finally, in addition to the characterization of RNAs from 17 predicted genes, our data identified nine new mitochondrial genes, four of which encode proteins that do not resemble other proteins in the database. Curiously, one of the latter mRNAs contains no editing sites.
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