Data and code from: Sex-biased duplicates are rapidly generated during metazoan tRNA repertoire evolution

Abstract: Eukaryotic species encode hundreds of transfer RNA genes ostensibly to ensure efficient translation. How these seemingly redundant tRNA copies arise and are maintained in metazoan genomes and populations remains largely unexplored. Here, we leverage long-read genome assemblies of 24 Drosophilid species to infer origination times of the Drosophila melanogaster tRNA gene repertoire. We find that continuous gain and loss of tRNA duplicates throughout 60 million years of divergence has resulted in rapid taxonomic restriction of isodecoding and isoaccepting copies. We show that recently duplicated, lineage-specific tRNA copies particularly have sexually dimorphic patterns of expression, fragmentation, and nucleoside modification in D. melanogaster. Our results uncover that nearly neutral processes, sexual selection, and directional selection together affect the evolutionary dynamics and extra-translational functions of the tRNA gene family in metazoan species.