PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes

Abstract

SUMMARY PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 51 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. tRNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, about 37 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, non‐canonical splicing sites in the D‐ or T‐regions of tRNA molecules were identified and experimentally validated. As for PlantRNA 1.0, comprehensive biological information including 5′‐ and 3′‐flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.

Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias

“…Plastid tRNAs were predicted for all amino acids except valine (V) and histidine (H). These tRNA numbers are similar to the tRNA repertoire reported for the related green alga Ostreococcus tauri , which encodes 45 nuclear, 28 mitochondrial, and 27 plastidial tRNAs ( Cognat et al 2022 ).…”

Distinct localization of chiral proofreaders resolves organellar translation conflict in plants

“…To probe the discriminator base status in plant organelles, we analyzed all the available tRNA sequences (from http://gtrnadb.ucsc.edu/ , http://plantrna.ibmp.cnrs.fr/plantrna/ ) ( 16 – 18 ). We increased the organellar tRNA dataset by predicting tRNAs for about 16595 organelle (11927 mitochondria and 4668 chloroplasts) genomes available in NCBI by using tRNAscan-SE ( 19 ) and analyzed the discriminator base ( Fig.…”

Transcriptional reactivation of the tRNASer/tRNATyrgene cluster inArabidopsis thalianaroot tip (V2)

“…Out of the 20 tDNA families encountered in the Col-0 nuclear genome, tDNA Tyr one is the most abundant, and counts 70 genes (Cognat et al, 2022). For the sake of description, and to explore their genetic diversity and organization, we sought to hierarchize tDNAs Tyr based on three factors: the layout (dispersed/clustered), nucleotide polymorphisms (NPs), and gene copy numbers ( Supplemental Fig.…”

“…tRNA sequences and intron informations were retrieved from the PlantRNA 2.0 database (Cognat et al, 2022). tRNA structures were predicted using R2DT (Sweeney et al, 2021).…”

“…The nuclear genome of the plant Arabidopsis thaliana Col-0 consists of five chromosomes carrying 586 tDNAs (Cognat et al, 2022). While most are dispersed along arms, a subset of proline, serine and tyrosine tDNAs organize in clusters (Green and Weil, 1989; Beier et al, 1991; Theologis et al, 2000; Michaud et al, 2011; Hummel et al, 2020; Hummel and Liu, 2022).…”