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International Journal of Plant Genomics
Volume 2012 (2012), Article ID 874743, 17 pages
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.
Supplementary material Table S1 contains list of Plant species used in this study, their taxonomy (according to NCBI Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy) and results of in silico mining of chromodomains by LTR retrotransposons clades.
Supplementary material Table S2 contains list of species genomes of which were analyzed in silico in present study and the sources of the ESTs and/or genomic sequences.
Supplementary material Figure 1S represents the detailed Maximum likelihood (ML) phylogenetic tree (showed in Figure 2) based on LTR retrotransposon chromodomain (CHD) aminoacid sequences, including CHDs from newly identified chromodomain-containing LTR retrotransposons from Selaginella moellendorffii. Statistical support was evaluated by using aLTR; nodes with aLRT statistics over 50% are shown. The plant-specific clades, Chlamyvir, Reina, CRM, Galadriel, and Tekay, as well as the Tcn1 clade, are indicated. The name of the host species and the accession number is indicated for some of the LTR elements taken from GenBank. The taxonomic range of host species is indicated by colored boxes and includes angiosperms, gymnosperms, green algae, and non-seed plants (Selaginella and Physcomitrella).
Supplementary material Protocol S1 provides detailed positive selection test results.