Figure 3

Unrooted N-J tree computed from multiple sequence alignments of Arabidopsis (red) and rice (blue) prolyl oligopeptidase domains. Prolyl oligopeptidase-like domains were aligned using ClustalW [95] program and the alignments were exported to Phylip package [96] for representing the Neighbor-Joining tree (see methods). The colors and circles represent the two evolutionary clades identified in the analysis (see text for details). Clade I is represented in Orange, Clade II is shaded green. For clarity, bootstrap values were replaced with symbols representing bootstrap percentages >50%. Bootstrap values between 50–60% are represented by an asterix, circles represent bootstrap values from 60%–80% while bootstrap values >80% are represented by rectangles. Gene names correspond to those in Additional files 1 and 2. For brevity, rice gene names have been shortened to OsXXg##### instead of LOC_OsXXg#####, XX referring to chromosome 1–12 and a 5 digit number assigned to each gene. Subfamily assignments where possible are indicated in parentheses below the gene name (see Figure SF3 and text for details).