RT phylogenetic tree of 74 LTR families. A Bel-Pao type RT (BEL-1-I_NVp from Repbase) is used as outgroup. The 74 families are grouped into Copia or Gypsy superfamily. In the tree, each family is described by its name and a superfamily label. The superfamily label is given according to the order of domains in the POL. RT similarity and domain organization give consistent categorization. Mtr3, Mtr5 and Mtr62 lack other domains except RT, so they are categorized directly though RT similarity and are marked by the lowercase initials of the superfamilies. The 14 clades, to which the 74 families belong, are shown in the figure. The placement of Mtr3 and Mtr39 is unresolved and they are marked by grey dots [see Additional file 4].