ArticleNucleic acids research2009
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 222 papers.
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222 citing papers in PubMed.
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- The mitochondrial genome of the soil pH-indicator plant Hydrangea macrophylla provides insights into mitogenome variation and evolution in superasterids.BMC plant biology · 2026Article
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- De novo assembly of the first mitochondrial genome in Benincasa reveals structural dynamics and evolutionary insights in Cucurbitaceae.BMC plant biology · 2026Article
- Organellar genome evolution in Camellia tianeensis (Theaceae): comparative insights into RNA editing, codon usage, and DNA transfer between chloroplast and mitochondrion.BMC genomics · 2026Article
- Ongoing structural changes highlight the dynamic nature of chloroplast genomes.Nucleic acids research · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genome of Tetrastigma Hemsleyanum Diels & Gilg: an invaluable traditional Chinese medicine.BMC plant biology · 2026Article
- Comparative chloroplast genomics of sixFrontiers in plant science · 2026Article
- Structural divergence and molecular adaptation ofFrontiers in plant science · 2026Article
- The complete chloroplast genome of Secale strictum ssp. strictum provides insights into Triticeae evolution and breeding.Scientific reports · 2025Article
- Integrated Mitochondrial Genome and Transcriptomic Analyses Reveal Long Non-Coding RNAs Associated with Drought Tolerance inBiology · 2025Article
- Chloroplast Genome Diversity and Marker Potentials of DiverseInternational journal of molecular sciences · 2025Article
- Characterization of the Mitochondrial Genome ofPlants (Basel, Switzerland) · 2025Article
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- Complete mitochondrial genome assembly and comparative analysis of Fagopyrum dibotrys (Golden Buckwheat).BMC plant biology · 2025Article
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- Plastome and transcriptome analysis reveals a degenerated photosynthesis-related pathway in the mycoheterotrophic vanilloid orchid Cyrtosia lindleyana.BMC plant biology · 2025Article
- Evolution of mitochondrial RNA editing sites and stop codon-lacking transcripts in angiosperms.Communications biology · 2025Article
162 more citing papers are in PubMed but not listed here.
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Abstract
RNA editing alters plant mitochondrial and chloroplast transcripts by converting specific cytidines to uridines, which usually results in a change in the amino acid sequence of the translated protein. Systematic studies have experimentally identified sites of RNA editing in organellar transcriptomes from several species, but these analyses have not kept pace with rate of genome sequencing. The PREP (predictive RNA editors for plants) suite was developed to computationally predict sites of RNA editing based on the well-known principle that editing in plant organelles increases the conservation of proteins across species. The PREP suite provides predictive RNA editors for plant mitochondrial genes (PREP-Mt), for chloroplast genes (PREP-Cp), and for alignments submitted by the user (PREP-Aln). These servers require minimal input, are very fast, and are highly accurate on all seed plants examined to date. PREP-Mt has proved useful in several research studies and the newly developed PREP-Cp and PREP-Aln servers should be of further assistance for analyses that require knowledge of the location of sites of RNA editing. The PREP suite is freely available at http://prep.unl.edu/.
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