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Systematic Biology 2006 55(6):875-885; doi:10.1080/10635150601077683
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© 2006 Society of Systematic Biologists

Distribution and Phylogeny of Penelope-Like Elements in Eukaryotes

Irina R. Arkhipova

1 Department of Molecular and Cellular Biology, Harvard University Cambridge, Massachusetts 02138, USA and Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory Woods Hole, Massachusetts 02543, USA E-mail: arkhipov{at}fas.harvard.edu

Edited by Andrew Shedlock: Associate Editor


  Abstract

Penelope-like elements (PLEs) are a relatively little studied class of eukaryotic retroelements, distinguished by the presence of the GIY-YIG endonuclease domain, the ability of some representatives to retain introns, and the similarity of PLE-encoded reverse transcriptases to telomerases. Although these retrotransposons are abundant in many animal genomes, the reverse transcriptase moiety can also be found in several protists, fungi, and plants, indicating its ancient origin. A comprehensive phylogenetic analysis of PLEs was conducted, based on extended sequence alignments and a considerably expanded data set. PLEs exhibit the pattern of evolution similar to that of non-LTR retrotransposons, which form deep-branching clades dating back to the Precambrian era. However, PLEs seem to have experienced a much higher degree of lineage losses than non-LTR retrotransposons. It is suggested that PLEs and non-LTR retrotransposons are included into a larger eTPRT (eukaryotic target-primed) group of retroelements, characterized by 5' truncation, variable target-site duplication, and the potential of the 3' end to participate in formation of non-autonomous derivatives.

Keywords: Penelope-like elements; retrotransposons; reverse transcriptase; GIY-YIG endonuclease

Received August 31, 2006; Revised September 28, 2006; Accepted October 17, 2006
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