Evolution Of Micrornas In Drosophila

Abstract

The molecular evolutionary signatures of miRNAs inform our understanding of their emergence, biogenesis, and function. In this work, we use methods and principles from comparative and population genomics, molecular biology, and genetics to assess these signatures in Drosophila. First, we examine the impact of age, biogenesis pathway, and genomic arrangement on Drosophila miRNA evolution. We observe that recently-emerged miRNAs exhibit evolutionary signatures similar to well-conserved miRNAs, which suggest even young miRNAs may be selected for regulatory activities. Moreover, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs. These findings affirm that miRNAs do not evolve as a unitary class. Second, we show that the Drosophila testis specifically expresses substantial numbers of recently-evolved miRNAs with "seed" region divergences. Since miRNAs preferentially target transcripts via sites that pair with miRNA positions ~2-8 (the "seed"), changes within this region could have detrimental regulatory effect. We unexpectedly found that testis-restricted miRNAs have evolved under positive selection, are higher expressed than miRNAs of a similar age, and have greater regulatory capacity than other young miRNAs in transgenic assays. Third, we examined the birth and expansion of conserved Drosophila miRNA clusters. Beyond duplication and de novo birth, we highlight a diversity of modes that contribute to miRNA evolution, including neofunctionalization of miRNA copies, fissioning of locally duplicated miRNA clusters, miRNA deletion, and miRNA cluster expansion via the acquisition and/or neofunctionalization of miRNA copies from elsewhere in the genome. We proposed that miRNA clustering by acquisition represents an expedient strategy to bring cohorts of target genes under coordinate control of pre-existing miRNAs. Finally, we investigate the diversity in abundance, processing, and evolutionary turnover of miRNAs within 12 Drosophila genomes. Using ~3 billion small RNA reads we find over 668 novel miRNAs, show heterogeneity in 5' cleavage precision among conserved miRNAs, and expand the collection of testes-restricted miRNAs. The annotation of many recently-evolved miRNAs motivated a reassessment of miRNA birth and death rates. Using a novel phylogenetic model that addresses uncertainty in miRNA annotation, we observed striking differences in birth and death rates across miRNA classes and identify variation heterogeneity among Drosophila clades.