tRNADB-CE

tRNADB-CE curates a comprehensive database of transfer RNA (tRNA) gene sequences from prokaryotes, eukaryotes, viruses, chloroplasts and metagenomic samples to support analysis of tRNA sequence variation and the use of identical or phylotype-specific tRNA sequences as phylogenetic markers for microbial community studies.

Key Features:

• Taxonomic scope: Contains tRNA sequences from prokaryotes, eukaryotes, viruses and chloroplasts and includes metagenomic-derived sequences from environmental samples.
• Dataset expansion: Built from examination of 939 complete and 1310 draft genomes, 171 complete viral genomes, 121 complete chloroplast genomes, and ~230 million metagenomic sequences from 210 environmental samples.
• Total entries: Contains 287,102 tRNA genes, approximately double the previous compilation.
• Sequence data: Provides detailed tRNA nucleotide sequences and inferred cloverleaf secondary-structure information.
• Similarity searches: Includes results from sequence similarity searches and oligonucleotide-pattern searches for tRNA identification and comparison.
• Expert curation: Incorporates expert-curated annotations and an expert comment field attached to individual tRNA gene entries.
• Phylogenetic signal: Highlights high phylogenetic preservation of tRNA sequences at the phylum level and supports identification of identical tRNA sequences as phylogenetic markers.
• Phylotype-specific markers: Enables identification of phylotype-specific markers such as genus-specific tRNA sequences for ecosystem microbial community analysis.

Scientific Applications:

• Phylogenetic marker discovery: Identification and use of identical or phylotype-specific tRNA sequences as markers for taxonomic inference.
• Microbial community analysis: Elucidation of microbial community structure in ecosystems using tRNA-based markers.
• Evolutionary research: Comparative analysis of tRNA sequence conservation and divergence across taxa.
• Molecular biology studies: Reference resource for tRNA sequence and structural analyses in diverse organisms.
• Environmental microbiology: Use of metagenomic tRNA data to investigate environmental microbial diversity and distribution.

Methodology:

Compilation from examination of 939 complete and 1310 draft genomes, 171 complete viral genomes, 121 complete chloroplast genomes and ~230 million metagenomic sequences from 210 environmental samples, followed by sequence similarity searches, oligonucleotide-pattern searches and expert curation/comments.