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MBE Advance Access published online on February 12, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh072
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted December 2, 2003
© 2004 Society for Molecular Biology and Evolution

Original Articles

A New Group of Tyrosine Recombinase-Encoding Retrotransposons

Timothy J. D. Goodwin 1* and Russell T. M. Poulter 1

1 Department of Biochemistry, University of Otago, Cumberland Street, Dunedin, New Zealand

* To whom correspondence should be addressed. E-mail: timg{at}sanger.otago.ac.nz.


  Abstract

A wide variety of novel tyrosine recombinase (YR)-encoding retrotransposons were identified using the data emerging from the various eukaryotic genome sequencing projects. While many of these elements are clearly members of the previously described DIRS group of YR retrotransposons, a substantial number, including elements from a variety of fungi and animals, belong to a distinct and previously unrecognised group. We refer to these latter elements as the Ngaro group after a representative from zebrafish. Like the members of the DIRS group, Ngaro elements encode proteins bearing reverse transcriptase (RT) and ribonuclease H (RH) domains similar to those of LTR retrotransposons. Phylogenetic analyses based on alignments of RT/RH and YR domains, however, indicate that Ngaro and DIRS are anciently diverged groups. Differences in coding capacity also support the distinction between the two groups. For instance, we found that DIRS elements all encode a protein domain which is similar in sequence to the DNA methyltransferases of certain bacteriophages, whereas this domain is absent from all Ngaro elements. Together, the Ngaro and DIRS groups of YR retrotransposons contain elements with an astonishing diversity in structures, with variations in the nature of the associated repeat sequences and in the arrangement and complement of coding regions. In addition they contain elements with some surprising features, such as spliceosomal introns, and long overlapping open reading frames.

Key Words: DIRS, Ngaro, retrotransposon, tyrosine recombinase


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