Figure 1

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 [8] are denoted with a plus symbol, those from Du et al. [7] 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 [17]. 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).