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, owing to challenges in accurate estimation and analysis of tRNA abundance. We dated tRNA gene origination events between 24 Drosophilid species to investigate the evolutionary dynamics of tRNA repertoires in metazoans. We report that Drosophila tRNA genes have been continuously gained and lost throughout 60 million years of divergence resulting in rapid taxonomic restriction of specific isodecoding and isoaccepting copies, even producing one D. melanogaster-specific copy. Moreover, we identified patterns of global codon usage, especially in new genes, incongruous with translational selection which we define as translational conflict. Through generation of tRNA sequencing in D. melanogaster we observed that recently duplicated, lineage-specific tRNA copies had sexually dimorphic patterns of expression, fragmentation, and nucleoside modification. Our findings implicate the emergence of taxonomically restricted tRNA genes as sources of phenotypic and regulatory diversity and reveal that the expansion and contraction of the tRNA gene family in metazoans is influenced by sexual selection and non-adaptive processes.