Neighbour-joining (NJ) phylogenies of Copia and Gypsy families. NJ phylogeny of Gypsy families based on reverse transcriptase, with schematic representations of sugarcane elements. Sequences from the Gypsy database  are denoted with a plus symbol, those from Du et al.  with a star. Robustness of the nodes was estimated by 500 bootstrap replications. Bootstrap values below 50% are not shown. Lineages are indicated by names and colored blocks. A star indicates the sequences used as probes for fluorescent in situ hybridization (Figure 3). Schematic representations were created using domain draw . A scale and a key for the domains represented in the schematic representations are shown in the bottom right hand corner. Abbreviations and color coding of domains: LTR = long terminal repeat (orange); gag = Gag (dark green); protease = Protease (light green); rt = Reverse Transcriptase (pink); rnaseh = Ribonuclease H (purple); integrase = Integrase (yellow); chromo = Chromodomain (brown); env = Envelope (brown); pol = Polyprotein (grey).