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International Journal of Plant Genomics
Volume 2012 (2012), Article ID 874743, 17 pages
Research Article

Evolutionary History of LTR Retrotransposon Chromodomains in Plants

1Laboratory of Molecular Genetic Systems, Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
2Department of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
3Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
4Department of Biological Sciences, University at Albany, Life Sciences Building 2061, 1400 Washington Avenue, Albany, NY 12222, USA

Received 15 September 2011; Revised 27 January 2012; Accepted 12 February 2012

Academic Editor: Jim Leebens-Mack

Copyright © 2012 Anton Novikov et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization.