The evolution of tRNA genes in Drosophila.

Genome Biology and Evolution
Hubert H RogersSam Griffiths-Jones

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 ...Continue Reading

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Citations

Apr 9, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Patrick HollowayNadia El-Mabrouk
Sep 5, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sandro AndreottiStefan Canzar
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Mar 14, 2012·PloS One·Hubert H Rogers, Sam Griffiths-Jones
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Software Mentioned

RepeatMasker
UCSC Genome Browser
BlastN
SE
tRNAscan
ClustalW
WU

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