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MBE Advance Access published online on December 22, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi071
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Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved.
Accepted December 20, 2004

Research Article

A Novel Abundant Family of Transposable Elements (DAS-SINEs) in The Nine-Banded Armadillo (Dasypus novemcinctus)

Gennady Churakov 1, Arian F.A. Smit 2, Jürgen Brosius 1, and Jürgen Schmitz 1*

1 Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
2 Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904

* To whom correspondence should be addressed.
Jürgen Schmitz, E-mail: jueschm{at}uni-muenster.de


  Abstract

About half of the mammalian genome is composed of retroposons. Long INterspersed Elements (LINEs) and Short INterspersed Elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages except for the South American order Xenarthra, also termed Edentata (armadillos, anteaters, and sloths). Investigating this order, we discovered a novel high copy number family of tRNA derived SINEs in the nine-banded armadillo Dasypus novemcinctus, a species that successfully crossed the Central American land bridge to North America in the Pliocene. A specific computer algorithm was developed and we detected and extracted 687 specific SINEs from databases. Termed DAS-SINEs, we further divided these into six distinct subfamilies. We extracted tRNAAla derived monomers, two types of dimers and three subfamilies of chimeric fusion products of a tRNAAla domain and a ~180 nt sequence of thus far unidentified origin. Comparisons of secondary structures of the DAS-SINEs' tRNA domains suggest selective pressure to maintain a tRNA like D-arm structure in the respective founder RNAs as shown by compensatory mutations. By analysis of subfamily specific genetic variability, comparison of the proportion of direct repeats (DR), and analysis of self-integrations as well as key events of dimerization and deletions 3 or insertions we were able to delineate the evolutionary history of the DASSINE subfamilies.

Keywords: tRNA; SINE; armadillo; retroposition; SINE evolution.
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