Figure 1

Neighbor-joining (NJ) phylogenetic trees based on RT and partial Int amino acid sequences of Gypsy LTR belonging to Ylt1 and SN_1006 clades. Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The Gypsy LTR retrotransposons clades are shown on the right and include Chromovirus, Osvaldo, mag, Gypsy, mdg3, SN_1006 and Ylt1. Sequences of human immunodeficiency viruses (Retroviridae) were used as outgroup. The name of the host species and accession number are indicated for all elements taken from GenBank. Newly identified retrotransposons are highlighted by bold; localization in genomic sequence is indicated for each of them. Genomic sequences of Laccaria bicolor S238N and Nectria haematococca MPVI have been taken from The DOE Joint Genome Institute [55]; the following species are available at Broad Institute [54]: Botrytis cinerea B05.10; Pyrenophora tritici-repentis Pt-1C-BFP; Coprinus cinereus okayama7#130; Puccinia graminis f. sp. tritici. For more details: Additional files 1, 5 and 6.