Nuclear genome tRNA allelic variation in 3 Caenorhabditis species (2025 CaeNDR data)

This dataset contains the breakdown of nuclear-encoded tRNA genes and alleles at these genes in three Caenorhabditis species (C. elegans, C. briggsae, and C. tropicalis); wild strains used here are as detailed at CaeNDR (202506 data releases used here). This repository comprises supplemental data for the linked preprint/publication. Specifically, these files contain all the tRNA annotations and alleles generated in the study. Details: tRNAscan-SE output files The following files contain raw tRNAscan-SE outputs for all alleles (each allelic sequence was provided as an input sequence). One set of files per species. <species>_strainspec_trnas_isospecific.out: isotype-specific scores <species>_strainspec_trnas.out: overarching output file <species>_strainspec_trnas.SS: secondary structure prediction output file Strain x tRNA gene data matrix <species>_strainsxtrnas_alleles_wmissing.txt.gz files contain a strains x tRNA genes matrix specifying the predicted allele for each strain at each tRNA. Allele details can be found in other files. One file per species. Overarching tRNA gene and tRNA allele information and count summaries Each of these files has an accompanying 'About' file that describes each column's contents in detail. All species' tRNAs are combined in these files. threespecies_202506caendr_tRNA_alleleinfo.txt.gz: allele-level information (see file about_threespecies_202506caendr_tRNA_alleleinfo.xlsx) threespecies_202506caendr_tRNA_geneinfo.txt.gz: gene-level information (see file about_threespecies_202506caendr_tRNA_geneinfo.xlsx) Preprint fully describing this dataset Nuclear-encoded tRNA genes harbor substantial allelic diversity in three nematode species. Avery Davis Bell, Corinne Simonti, Hector Baños, Ling Wang, Christine Heitsch, Joseph Lachance, Annalise B Paaby. bioRxiv 2025.10.14.682033; doi: https://doi.org/10.1101/2025.10.14.682033