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

Abstract: Eukaryotic genomes encode hundreds of transfer RNA (tRNA) genes ostensibly to ensure efficient translation. How these seemingly redundant tRNA copies arise and are naturally selected in eukaryotic genomes and populations remains largely unexplored. We dated tRNA gene origination events between 24 Drosophilid species to investigate how tRNA repertoires expand in metazoans. This revealed that Drosophila tRNA genes have been continuously lost and gained throughout 60 million years of divergence resulting in rapid taxonomic restriction of specific isodecoding and isoaccepting copies, even producing one specific to D. melanogaster. Moreover, we identified patterns of global codon usage, especially in new genes, incongruous with translational selection. However, through tRNA sequencing we observed that recently duplicated, lineage-specific tRNA copies had sexually dimorphic patterns of expression, fragmentation, and nucleoside modification. Our findings show that the expansion and contraction of tRNA repertoires in metazoans is a continuous process influenced by sexual selection and implicate the emergence of taxonomically restricted tRNA genes as sources of phenotypic and extra-translational functional diversity.