MBE Advance Access first published online on June 29, 2007
This version published online on December 7, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm129
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Research Article |
Evolutionary Analysis of Amino Acid Repeats Across the Genomes of 12 Drosophila Species
Department of Molecular Biology and Genetics, Cornell University
Corresponding author. Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, E-mail: mah223{at}cornell.edu, Tel: 607-255-1707, Fax: 607-255-6249
Received for publication April 2, 2007. Revision received June 8, 2007. Accepted for publication June 18, 2007.
Repeated motifs of amino acids within proteins are an abundant feature of eukaryotic sequences and may catalyze the rapid production of genetic and even phenotypic variation among organisms. The completion of the genome sequencing projects of 12 distinct Drosophila species provides a unique dataset to study these intriguing sequence features on a phylogeny with a variety of timescales. We show that there is a higher percentage of proteins containing repeats within the Drosophila genus than most other eukaryotes, including non-Drosophila insects, which makes this collection of species particularly useful for the study of protein repeats. We also find that proteins containing repeats are overrepresented in functional categories involving developmental processes, signaling and gene regulation. Using the set of 1-to-1 ortholog alignments for the 12 Drosophila species we test the ability of repeats to act as reliable phylogenetic signals and find that they resolve the generally accepted phylogeny despite the noise caused by their accelerated rate of evolution. We also determine that in general the position of repeats within a protein sequence is non-random, with repeats more often being absent from the middle regions of sequences. Finally we find evidence to suggest that the presence of repeats is associated with an increase in evolutionary rate upon the entire sequence in which they are embedded. With additional evidence to suggest a corresponding elevation in positive selection we propose that some repeats may be inducing compensatory substitutions in their surrounding sequence
Key Words: protein repeats • simple sequence • homopeptides
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