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MBE Advance Access published online on December 4, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn277
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Comparative and Functional Characterization of Intragenic Tandem Repeats in Ten Aspergillus Genomes

John G. Gibbons and Antonis Rokas*

Department of Biological Sciences, Vanderbilt University, Box 351634 Station B, Nashville, TN 37235-1634, USA. Email: john.g.gibbons{at}vanderbilt.edu; antonis.rokas{at}vanderbilt.edu

* Author for correspondence: Antonis Rokas (email: antonis.rokas{at}vanderbilt.edu, tel: +1-615-936-3892, fax: +1-615-443-6707)

Received for publication August 15, 2008. Revision received November 25, 2008. Accepted for publication November 30, 2008.

Intragenic tandem repeats (ITRs) are consecutive repeats of three or more nucleotides found in coding regions. ITRs are the underlying cause of several human genetic diseases, and have been associated with phenotypic variation, including pathogenesis, in several clades of the tree of life. We have examined the evolution and functional role of ITRs in ten genomes spanning the fungal genus Aspergillus, a clade of relevance to medicine, agriculture, and industry. We identified several hundred ITRs in each of the species examined. ITR content varied extensively between species, with an average 79% of ITRs unique to a given species. For the fraction of conserved ITR regions, sequence comparisons within species and between close relatives revealed that they were highly variable. ITR-containing proteins were evolutionarily less conserved, compositionally distinct, and overrepresented for domains associated with cell-surface localization and function relative to the rest of the proteome. Furthermore, ITRs were preferentially found in proteins involved in transcription, cellular communication and cell-type differentiation but were underrepresented in proteins involved in metabolism and energy. Importantly, although ITRs are evolutionarily labile, their functional associations appear to be remarkably conserved across eukaryotes. Fungal ITRs likely participate in a variety of developmental processes and cell-surface associated functions, suggesting that their contribution to fungal lifestyle and evolution may be more general than previously assumed.

Key Words: fungi • Aspergillus • intragenic tandem repeats • polymorphism • comparative functional genomics


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