ArticleGenome biology and evolution2010
The evolution of tRNA genes in Drosophila.
Article in Genome biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 45 citations in OpenAlex.
- Comparative analysis of tRNAs across mouse strains reveals gene-specific conservation, divergence, and copy number variation.BMC genomics · 2026Article
- Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.Genome biology and evolution · 2026Article
- Sex-biased duplicates are rapidly generated duringbioRxiv : the preprint server for biology · 2025Article
- Evolution of genome structure in theGenome research · 2021Article
- Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map.Journal of molecular evolution · 2021Article
- Predicting transfer RNA gene activity from sequence and genome context.Genome research · 2020Article
- SMORE: Synteny Modulator of Repetitive Elements.Life (Basel, Switzerland) · 2017Article
- Novel Genomic and Evolutionary Perspective of Cyanobacterial tRNAs.Frontiers in genetics · 2017Article
- Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.BMC genomics · 2016Article
- The Roles of Compensatory Evolution and Constraint in Aminoacyl tRNA Synthetase Evolution.Molecular biology and evolution · 2016Article
- Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes.Nucleic acids research · 2015Article
- Evidence that natural selection on codon usage in Drosophila pseudoobscura varies across codons.G3 (Bethesda, Md.) · 2014Article
- tRNA anticodon shifts in eukaryotic genomes.RNA (New York, N.Y.) · 2014Article
- Article
- The duplication-loss small phylogeny problem: from cherries to trees.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Widespread purifying selection on RNA structure in mammals.Nucleic acids research · 2013Article
- Regulatory RNAs in the light of Drosophila genomics.Briefings in functional genomics · 2012Review
- tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote.RNA (New York, N.Y.) · 2012Article
- The dynamics and evolutionary potential of domain loss and emergence.Molecular biology and evolution · 2012Article
- Population genomic analysis of base composition evolution in Drosophila melanogaster.Genome biology and evolution · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The structure and function of transfer RNA (tRNA) genes have been extensively studied for several decades, yet the general mechanisms controlling tRNA gene family evolution remain unclear, primarily because previous phylogenetics-based methods fail to distinguish between paralogs and orthologs that are highly similar in sequence. We have developed a system for identifying orthologs of tRNAs using flanking sequences to identify regions of conserved synteny and used it to annotate sets of orthologous tRNA genes across the 12 sequenced species of Drosophila. These data have allowed us to place the gains and losses of individual tRNA genes on each branch of the Drosophila tree and estimate rates of tRNA gene turnover. Our results show extensive rearrangement of the Drosophila tRNA gene complement over the last 60 My. We estimate a combined average rate of 2.18 +/- 0.10 tRNA gene gains and losses per million years across the Drosophila lineage. We have identified 192 tRNAs that are ancestral to the genus, of which 157 are "core" tRNAs conserved in at least 11 of 12 extant species. We provide evidence that the core set of tRNA genes encode a nearly complete set of anticodons and have different properties from other "peripheral" tRNA genes, such as preferential location outside large tRNA clusters and higher sequence conservation. We also demonstrate that tRNA isoacceptor and alloacceptor changes by anticodon shifts have occurred several times in Drosophila, annotating 16 such events in functional tRNAs during the evolution of the genus.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.