Journal Article

The Evolution of tRNA Genes in <i>Drosophila</i>

Hubert H. Rogers, Casey M. Bergman and Sam Griffiths-Jones

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 2, issue , pages 467-477
Published in print January 2010 |
Published online June 2010 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evq034

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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.

Keywords: transfer RNA; genome evolution; noncoding RNA; tRNA identity; synteny map; gene duplication

Journal Article.  6575 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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