Information

A database for tRNA genes of photosynthetic organisms

The PlantRNA 2.0 database is hosted and maintained by the IBMP (Institut de biologie mol├ęculaire des plantes, Strasbourg, France). It compiles tRNA gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. Currently, the PlantRNA database contains genome wide information concerning 47 Archeplastida (covering the whole phylogenetic tree from glaucophytes to angiosperms), 2 heterokontophytes, 1 cryptophyte and 1 haptophyte.
The existence of tRNAs was first predicted by using trnascan-SE version 2 with default parameters and using different sources (Mixed/Eukaryotic). tRNA genes from alga obtained from SPLITSdb were also included. Importantly, to minimize the number of false positives, we also manually curated the lists of tRNA genes extracted from each genome. By means of the manual curation :
  • we correctly annotated a few genes or pseudogenes that were misannotated
  • we correctly annotated numerous non-expressed mitochondrial or plastidial tRNA gene sequences inserted into nuclear genomes and recognized by tRNAscan-SE
  • we re-annotated some tRNAs in terms of amino acid and codon recognition due to the presence of post-transcriptional anticodon modifications
In addition to tRNA gene sequences with their (linear) secondary structure, the database provides other important biological information on:
  • 5'- and 3'- flanking sequences
  • tRNA intron sequences
  • tRNA isoacceptors
  • sites of transcription initiation and poly(T) stretches thought to act as transcription terminators
  • sequences of A and B boxes involved in TFIIIC (Transcription factor for Polymerase III) binding
  • aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation (RNase P, RNase Z, tRNA-nucleotidyl transferase and other tRNA modification enzymes). Organellar targeting predictions were determined with Predotar, TargetP or PredAlgo
  • tRNA import into mitochondria
  • references to published articles.
When using the PlantRNA database (http://plantrna.ibmp.cnrs.fr/), please cite the following references:
PlantRNA, a database for tRNAs of photosynthetic eukaryotes. Cognat V et al. Nucleic Acids Res, 41 : 273-279 (2013) and
PlantRNA 2.0 : an updated database dedicated to tRNAs of photosynthetic eukaryotes. Cognat et al. BioRxiv , doi: https://doi.org/10.1101/2021.12.21.473619
Last update: 17/03/2023

Contact

For biological questions, please contact Laurence Drouard - laurence.drouard@ibmp-cnrs.unistra.fr
For bioinformatic questions, please contact Valérie Cognat - valerie.cognat@ibmp-cnrs.unistra.fr
For technical questions (standards, data structure, source request, ...), please contact Gael Pawlak - gael.pawlak@ibmp-cnrs.unistra.fr
SQL dump of the database is available upon request ( laurence.drouard@ibmp-cnrs.unistra.fr )

Funding

Libraries and technical environment