Nuclear-encoded tRNA genes harbor substantial allelic diversity in three nematode species

Cytosolic transfer RNAs, which are encoded as hundreds of genes in eukaryotic nuclear genomes, experience exceptionally high rates of mutation and have been hypothesized to carry significant mutational load in natural populations. Comparisons across species show pervasive losses, gains, and functional remolding at tRNA loci, indicating rapid evolution over intermediate timescales, but the underlying molecular changes happening over short timescales remain poorly understood. A central gap in our understanding is the nature of deleterious tRNA mutations, how they affect fitness, and the extent to which tRNA pools vary functionally across genomes. Furthermore, new technologies for capturing tRNA expression and modification emphasize the importance of tRNA activity to organismal fitness, as tRNA dysregulation is associated with disease burden in humans, but this research area has not yet included possible consequences of mutational variation. To infer the dynamics of tRNA evolution over short timescales, and to integrate our understanding of fitness consequences of tRNA regulation with mutation load, we first require a comprehensive view of standing variation in cytosolic tRNAs within populations. In this study, we resolve within-species allelic variation in nuclear-encoded tRNAs in three nematode species: Caenorhabditis elegans , C. briggsae , and C. tropicalis . We show that these tRNA repertoires have been shaped by transcription-associated mutagenesis and selection and exhibit extensive allelic variation, including isotype switching between tRNA backbones and anticodons, and genomic organization and patterns of variation that differ markedly from those of protein-coding regions. Individual genomes harbor remarkably different pools of tRNA genes predicting a wide range tRNA functional complements within a species.