Neighbor-joining (NJ) phylogenetic trees based on RT and partial Int amino acid sequences of Gypsy LTR retrotransposons including newly described fungal chromodomain-containing LTR retrotransposons. Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The clades are shown on the right. The name of the host species and accession number are indicated for all elements taken from GenBank. Newly identified retrotransposons are highlighted in bold; localization in genomic sequence is indicated for each of them. Genomic sequences of Trichoderma reesei QM6a, Trichoderma virens Gv29-8, Nectria haematococca MPVI, Aspergillus niger ATCC1015, Alternaria brassicicola ATCC 96866, Stagonospora nodorum SN15, Laccaria bicolor S238N, Postia placenta MAD-698, and Sporobolomyces roseus have been taken from The DOE Joint Genome Institute ; the following species are available at Broad Institute : Chaetomium globosum CBS 148.51; Fusarium oxysporum 4286 FGSC;Fusarium verticillioides 7600; Aspergillus clavatus NRRL 1; Aspergillus terreus NIH2624; Coccidioides immitis RS; Histoplasma capsulatum NAm1; Uncinocarpus reesii 1704; Sclerotinia sclerotiorum 1980; Botrytis cinerea B05.10; Pyrenophora tritici-repentis Pt-1C-BFP; Coprinus cinereus okayama7#130; Puccinia graminis f. sp. tritici; Batrachochytrium dendrobatidis JEL423. The possible horizontal transmission (HT) is marked. For more details: Additional files 1, 5 and 6.