Genomic organization of tRNA genes and distribution of tRNA charging and modification enzymes across Bacteria, Archaea and major eukaryotic lineages
Year: 2026
Type: dataset
Abstract: This dataset contains the data tables, analysis scripts, figures and supplementary tables for the manuscript “Genomic organization of tRNA genes and distribution of tRNA charging and modification enzymes across Bacteria, Archaea and major eukaryotic lineages” (D.W. Cheng, version 12). The study compares tRNA gene repertoires with the distributions of tRNA charging and modification enzyme families across Bacteria, Archaea, fungi, non-flowering green plants, flowering plants and animals, with the human genome and proteome as references. Contents: High-confidence tRNA gene predictions parsed from GtRNAdb Release 22: 439,964 genes from 4,852 genomes. A one-assembly-per-species selection of 2,125 species was used. Per-genome tRNA metrics: gene number, anticodon richness, copies per anticodon, introns, adjacent-gene proximity, A34 anticodons, and Ile2-CAU and Ile-UAU genes. Presence or absence of 31 InterPro protein-family markers (aminoacyl-tRNA synthetases, amidotransferase subunits, wobble-modification enzymes and AIMP2) in 22,134 UniProt reference proteomes (release 2026_03). The 18,612-proteome analysis set has a BUSCO completeness of at least 90% and one proteome per species. Co-detection counts for alternative charging-enzyme families, eukaryotic lineage assignments and figure source data. NCBI Taxonomy lineages for the 2,125 genomes, rebuilt on 5 November 2026. Python scripts for parsing, analysis and figures. Figures 1–5 and Supplementary Tables S1–S8. All comparisons are descriptive. A protein-family marker hit shows that the family is present; it does not show pathway activity or cellular location. All input data are public. When reusing them, please also cite GtRNAdb (Chan and Lowe 2016), tRNAscan-SE 2.0 (Chan et al. 2021), UniProt (UniProt Consortium 2025) and InterPro (Blum et al. 2025). See README.md inside the archive for the file list, the analysis pipeline and notes on the lineage table.
Author: Cheng, Davis W.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7225314449