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Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers

Jerilyn A Walker1†, Miriam K Konkel1†, Brygg Ullmer2, Christopher P Monceaux1,3,4, Oliver A Ryder5, Robert Hubley6, Arian FA Smit6 and Mark A Batzer1*

  • * Corresponding author: Mark A Batzer mbatzer@lsu.edu

  • † Equal contributors

Author Affiliations

1 Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA

2 Department of Computer Science, Center for Computation and Technology (CCT), Louisiana State University, 316 Johnston Hall, Baton Rouge, LA 70803, USA

3 Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA

4 School of Biological Sciences, Louisiana Tech University, Ruston, LA 71272, USA

5 Conservation and Research for Endangered Species (CRES), Zoological Society of San Diego, San Diego, CA 92112, USA

6 Institute for Systems Biology, Seattle, WA 98103, USA

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Mobile DNA 2012, 3:8 doi:10.1186/1759-8753-3-8

Published: 30 April 2012

Abstract

Background

Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition.

Results

Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes), but absent from Hylobatidae (gibbon and siamang). We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion.

Conclusions

This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion.