PltRNAdb

PltRNAdb catalogs transfer RNA (tRNA) genes identified from whole-genome sequences of 256 plant species (8,768,261 scaffolds/chromosomes totaling 229,093 gigabase pairs), providing a curated inventory of nuclear, chloroplast, and mitochondrial tRNAs to support genomic and evolutionary analyses.

Key Features:

• Genome-scale dataset: Contains analyses of 8,768,261 scaffolds/chromosomes comprising 229,093 gigabase pairs from 256 plant species.
• tRNA inventory: Reports 331,242 nuclear tRNA genes, 3,216 chloroplast tRNA genes, and 1,467 mitochondrial tRNA genes.
• Nuclear tRNA classification: Details 275,134 tRNAs decoding the 20 standard amino acids, 1,325 suppressor tRNAs, 6,273 tRNAs with unknown isotypes, 48,475 predicted pseudogenes, and 37,873 intron-containing tRNAs.
• Search and retrieval: Provides search, browse, and data download capabilities for retrieved tRNA entries.
• BLAST searches: Includes BLAST search functionality for sequence similarity queries against the tRNA dataset.
• Visualization: Offers visualization of predicted tRNA gene entries and annotations.

Scientific Applications:

• Molecular biology of tRNAs: Enables analysis of tRNA complement and features within plant genomes for studies of tRNA structure and function.
• Evolutionary genomics: Supports comparative and evolutionary analyses of nuclear and organellar tRNA gene repertoires across 256 plant species.
• Regulatory role investigations: Facilitates exploration of potential regulatory functions of tRNAs and their contributions to protein synthesis in plants.

Methodology:

Analysis and identification of tRNA genes from whole-genome assemblies comprising 8,768,261 scaffolds/chromosomes (229,093 gigabase pairs) from 256 plant species and cataloging of predicted nuclear, chloroplast, and mitochondrial tRNA entries.