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MBE Advance Access published online on July 14, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh207
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted June 2, 2004

Original Articles

Retroelement Dynamics and a Novel Type of Chordate Retrovirus-Like Elements in the Miniature Genome of the Tunicate Oikopleura dioica

Jean-Nicolas Volff 1*, Hans Lehrach 2, Richard Reinhardt 2, Daniel Chourrout 3

1 Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, am Hubland, 97074 Würzburg, Germany
2 Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany
3 Sars Centre for Marine Molecular Biology, Bergen High Technology Centre, Thormoehlensgt. 55, 5020 Bergen, Norway

* To whom correspondence should be addressed. E-mail: volff{at}biozentrum.uniwuerzburg.de.


  Abstract

Retrotransposable elements have played an important role in shaping eukaryotic DNA, and their activity and turnover rate directly influenced the size of genomes. With approximately 15,000 genes within 65-75 megabases, the marine tunicate Oikopleura dioica, a non-vertebrate chordate, has the smallest and most compact genome ever found in animals. Consistent with a massive elimination of retroelements, only one, apparently novel clade of non-long-terminal-repeat (non-LTR) retrotransposons was detected within 41 megabases of non-redundant genomic sequences. In contrast, at least six clades of non-LTR elements were identified in the less compact genome of the tunicate Ciona intestinalis. Unexpectedly, Ty3/gypsy-related Tor LTR retrotransposons presented an astonishing level of diversity in O. dioica. They were generally poorly or apparently not corrupted, indicating recent activity. Both Tor3 and Tor4b families bore an envelope-like open reading frame, suggesting possible horizontal acquisition through infection. The Tor4b envelope-like gene might have been obtained from a paramyxovirus (RNA virus). Tor3 and Tor4b are phylogenetically clearly distinct from vertebrate retroviruses (Retroviridae) and are more reminiscent of certain insect and plant sequences. Tor elements potentially represent a so far unknown, ancient type of infectious retroelements in chordates. Their distribution and transmission dynamics in tunicates and other chordates deserve further studies.

Keywords: Oikopleura; retroelement; retrovirus; compact genome; reverse transcriptase; envelope.
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