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MBE Advance Access originally published online on December 22, 2004
Molecular Biology and Evolution 2005 22(4):886-893; doi:10.1093/molbev/msi071
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Molecular Biology and Evolution vol. 22 no. 4 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

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

Gennady Churakov*, Arian F.A. Smit{dagger}, Jürgen Brosius* and Jürgen Schmitz*

* Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany; and {dagger} Institute for Systems Biology, Seattle

E-mail: jueschm{at}uni-muenster.de.

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 them 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 an approximately 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, and analysis of self-integrations as well as key events of dimerization and deletions or insertions, we were able to delineate the evolutionary history of the DAS-SINE subfamilies.

Key Words: tRNA • SINE • armadillo • retroposition • SINE evolution


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