Help - Plant Editosome Database - BIG Data Center

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  1. Introduction
    1. What is Plant Editosome Database?
  2. Datasets and Curation Model
    1. Datasets
    2. Curation model
  3. Database Usage
    1. What information is provided for RNA editing factors?
    2. How can I get detailed RNA editing events for any organelle gene of interest?
    3. How can I get RNA editing events for any given species?
  4. Terminology
    1. Plant RNA Editing
    2. Editosome
    3. Editing Type
  5. Support
    1. Comments & Collaborations
    2. Contact us

  1. Introduction

    1. What is Plant Editosome Database?

      Plant Editosome Database (PED) is a curated database of RNA editosome in plants, dedicating to the curation, integration and standardization of plant RNA editing factors (editosome) as well as other related data that are vital for plant growth and development. Based on manual curation of related literatures and extraction of organelle genome annotations, PED integrates RNA editing factors, RNA editing events of targeted organelle genes, interactions between editing factors and events in multiple species, biological functional effects of editing factors in regulating plant phenotypes and the corresponding experimental detailed information.

  2. Datasets and Curation Model

    1. Datasets

      RNA editing events were obtained based entirely on plant organelle genome annotation files derived from NCBI Reference Sequence Database (RefSeq: https://www.ncbi.nlm.nih.gov/nuccore/). Totally, 2651 organelle complete genome annotation files (including mitochondrion, chloroplast, plastid) were downloaded, from which RNA editing events were extracted. For each editing site, the related information including species, organelle, gene name, RNA editing loci, RNA editing type, strand, codon/aa change were collected. As a result, 20,836 RNA editing events in 203 organelle genes were integrated in PED, involving 1,673 organelle genomes and covering 1,621 species.

    2. Curation model

      Molecular interactions between RNA editing factors and RNA editing sites were collected based on manual curation of literatures. We curated detailed description in association with RNA editing factors and RNA editing events across different experimental conditions.

      The curation model we used is detailed below.

      Data type Description Value
      RNA Editing Factor Gene identifier Gene name or systematic name
      Protein Family Controlled vocabulary PPR, MORF/RIP, ORRM, Zinc Finger Protein, Adenosine Deaminases, etc
      Subclass Controlled vocabulary P, PLS, E, E+, DYW
      Treatment Controlled vocabulary Conclusion term
      Mutant Type Controlled vocabulary Homozygous, Heterozygous, Knockout, Knockdown
      Trait Controlled vocabulary Conclusion term
      Tissue Controlled vocabulary Conclusion term
      Organelle Controlled vocabulary Mitochondrion, Chloroplast, Plastid
      Edited Gene Gene identifier Gene name or systematic name
      Function Category Controlled vocabulary Conclusion term
      Region Controlled vocabulary CDS, 3'UTR, 5'UTR, Intronic, Intergenic
      RNA Editing Type Controlled vocabulary C-to-U, A-to-I, etc
      CDS Position RNA editing position cDNA position (Position in other region is annotated specially)
      Codon From Controlled vocabulary Codon before editing
      Codon To Controlled vocabulary Codon after editing
      AA From Controlled vocabulary Amino acid before editing
      AA To Controlled vocabulary Amino acid after editing
      Molecular Effect Controlled vocabulary Recoding, Synonymous
      Editing Extent Controlled vocabulary Unedited 0%, Poor (0%-20%), Low [20%-40%), Medium [40%-60%), High [60%-100%), Complete 100%
      Mutant Effect Controlled vocabulary (The effect is compared to individual wild type) None, Absent, Decreased, Increased, Restored, Similar
      Detection Method Type of experiment used to detect editing frequency Conclusion term
      Reference Publication in which the interaction is described PubMed ID
  3. Database Usage

    1. What information is provided for RNA editing factors?

      PED offers a list of all collected editing factors and provides detailed relevant information, including factor name, protein family, subclass, structure, species, associated plant phenotype(s), edited gene(s), organelle and PMID(s). For each editing factor, you can find more details covering treatment, trait, phenotype, editing frequency, etc..

    2. How can I get detailed RNA editing events for any organelle gene of interest?

      Please visit the page of Edited Genes and you can find the gene name, function category, organelle, species, associated editing factors, statistics of editing events and editing types. For each edited gene, PED lists detailed editing events identified in different species.

    3. How can I get RNA editing events for any given species?

      If you are interested in the RNA editing events for a species of interest, please visit the page of Species, which includes editing position, region, editing type, codons and amino acids before and after editing,etc.

  4. Terminology

    1. Plant RNA Editing

      RNA editing is a process that modifies the genetic information on RNA molecules, which includes nucleotide insertion/deletion/conversion. In plants, the majority of editing events to date are identified to occur in organelle transcripts. Studies have shown that RNA editing plays important roles in various plant developmental processes, including organelle biogenesis, adaptation to environmental changes, and signal transduction.

    2. Editosome

      A number of factors are involved in plant RNA editing, such as pentatricopeptide repeat (PPR) proteins, multiple organelle RNA editing factors (MORF, also known as RIP), organelle RNA recognition motif (ORRM) containing proteins, protoporphyrinogen IX oxidase 1 (PPO1) and organelle zinc finger 1 (OZ1). Numerous studies have demonstrated that these proteins form different multiple-component complex, termed RNA editosome, to be responsible for RNA editing. A striking feature of the plant RNA editosome is its diversity and complexity in composition without consistency between individual RNA targets.

    3. Editing Type

      Different types of RNA editing have been reported in divergent species. In plants, RNA Editing types includes C-to-U, U-to-C and A-to-I. The most frequent editing type is C-to-U, found in all lineages of terrestrial plants except in one subclass of early land plants, the marchantiids.

  5. Support

    1. Comments & Collaborations

      We look forward to worldwide comments, suggestions and guidance from colleagues and peers with common research interests. We also invite the scientific community to submit their analysis results of RNA editing factors and RNA editing events to PED and to build collaborations in improving the functionalities of PED.

    2. Contact us

      We would love to hear from you for any questions or comments. Please find our contact information here [contact us].

Last update: Oct 2018 (version 1.0)