Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
- 1 Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95691, USA;
- 2 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA;
- 3 UC Davis Genome Center and Department of Statistics, University of California, Davis, California 95691, USA
Abstract
Recent genomic sequencing of 10 additional Drosophila genomes provides a rich resource for comparative genomics analyses aimed at understanding the similarities and differences between species and between Drosophila and mammals. Using a phylogenetic approach, we identified 64 genomic elements that have been highly conserved over most of the Drosophila tree, but that have experienced a recent burst of evolution along the Drosophila melanogaster lineage. Compared to similarly defined elements in humans, these regions of rapid lineage-specific evolution in Drosophila differ dramatically in location, mechanism of evolution, and functional properties of associated genes. Notably, the majority reside in protein-coding regions and primarily result from rapid adaptive synonymous site evolution. In fact, adaptive evolution appears to be driving substitutions to unpreferred codons. Our analysis also highlights interesting noncoding genomic regions, such as regulatory regions in the gene gooseberry-neuro and a putative novel miRNA.
Footnotes
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↵4 Corresponding author.
↵4 E-mail akholloway{at}ucdavis.edu; fax (530) 752-1449.
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[Supplemental material is available online at www.genome.org. Sequence data have been submitted to GenBank under accession nos. EU588685–EU588714.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.077131.108
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- Received February 6, 2008.
- Accepted June 19, 2008.
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Freely available online through the Genome Research Open Access option.
- Copyright © 2008, Cold Spring Harbor Laboratory Press
