PltRNAdb: Plant transfer RNA database

PLoS One. 2022 May 23;17(5):e0268904. doi: 10.1371/journal.pone.0268904. eCollection 2022.

Abstract

Transfer RNAs (tRNAs) are intermediate-sized non-coding RNAs found in all organisms that help translate messenger RNA into protein. Recently, the number of sequenced plant genomes has increased dramatically. The availability of this extensive data greatly accelerates the study of tRNAs on a large scale. Here, 8,768,261 scaffolds/chromosomes containing 229,093 giga-base pairs representing whole-genome sequences of 256 plant species were analyzed to identify tRNA genes. As a result, 331,242 nuclear, 3,216 chloroplast, and 1,467 mitochondrial tRNA genes were identified. The nuclear tRNA genes include 275,134 tRNAs decoding 20 standard amino acids, 1,325 suppressor tRNAs, 6,273 tRNAs with unknown isotypes, 48,475 predicted pseudogenes, and 37,873 tRNAs with introns. Efforts also extended to the creation of PltRNAdb (https://bioinformatics.um6p.ma/PltRNAdb/index.php), a data source for tRNA genes from 256 plant species. PltRNAdb website allows researchers to search, browse, visualize, BLAST, and download predicted tRNA genes. PltRNAdb will help improve our understanding of plant tRNAs and open the door to discovering the unknown regulatory roles of tRNAs in plant genomes.

MeSH terms

  • Databases, Nucleic Acid*
  • Genes, Mitochondrial
  • Genome, Plant
  • Plants / genetics
  • RNA
  • RNA, Plant / genetics
  • RNA, Transfer* / genetics

Substances

  • RNA, Plant
  • RNA
  • RNA, Transfer

Grants and funding

The author(s) received no specific funding for this work.