plantRNA

plantRNA provides a curated database of transfer RNA (tRNA) gene sequences and detailed annotations from fully annotated nuclear, plastidial, and mitochondrial genomes of photosynthetic organisms for use in comparative and functional tRNA research.

Key Features:

• Database scope: Contains tRNA genes derived from nuclear, plastidial, and mitochondrial genomes of photosynthetic organisms.
• Species coverage: Expanded in version 2 to include 51 photosynthetic species, up from 11 species in PlantRNA 1.0, spanning basal groups such as the glaucophyte Cyanophora paradoxa to diverse land plants.
• Gene count and curation: Includes approximately 37,000 tRNA genes with manual curation to ensure annotation quality.
• Sequence-level annotations: Annotates 5'- and 3'-flanking sequences, A and B box sequences, regions of transcription initiation, and poly(T) transcription termination stretches.
• Intron and splicing annotations: Records tRNA intron sequences and documents non-canonical splicing sites within D- or T-regions with experimental evidence in Chondrus crispus.
• Mitochondrial import data: Provides information on mitochondrial import for nuclear-encoded tRNAs.
• Enzymatic annotations: Includes data on aminoacyl-tRNA synthetases and enzymes involved in tRNA maturation and modification.
• Phylogenetic breadth: Covers a broad phylogenetic spectrum of photosynthetic organisms for comparative analyses.
• Versioning and updates: Maintained with successive releases and incorporation of new genome annotations.

Scientific Applications:

• Comparative tRNA genomics: Enables cross-species comparison of tRNA gene content, sequence conservation, and phylogenetic distribution across photosynthetic lineages.
• tRNA transcription and processing studies: Supports analysis of transcription initiation signals, poly(T) termination stretches, intron positions, and non-canonical splicing events.
• tRNA maturation and modification research: Facilitates investigation of aminoacyl-tRNA synthetases and enzymes involved in tRNA maturation and modification pathways.
• Mitochondrial import and organelle tRNA biology: Provides data for studying mitochondrial import of nuclear-encoded tRNAs and organelle-specific tRNA repertoires.

Methodology:

tRNA genes and annotations were extracted from fully annotated nuclear, plastidial, and mitochondrial genomes and subjected to manual curation.