Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster

Holloway, A. K., Begun, D. J., Siepel, A., Pollard, K. S. (2008) Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Research, 18 (10). pp. 1592-601. ISSN 1088-9051

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URL: http://www.ncbi.nlm.nih.gov/pubmed/18583644
DOI: 10.1101/gr.077131.108

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.

Item Type: Paper
Uncontrolled Keywords: Animals Codon Conserved Sequence Drosophila melanogaster/*genetics Evolution, Molecular *Genome, Insect MicroRNAs/genetics/metabolism Models, Genetic Molecular Sequence Data Phylogeny Regulatory Sequences, Nucleic Acid
Subjects: organism description > animal > insect > Drosophila
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
evolution
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 14 Jan 2015 20:00
Last Modified: 14 Jan 2015 20:00
PMCID: PMC2556263
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31070

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