Phylogenetic tree and sequence analysis of tomato and Arabidopsis CLE gene families. (A) Maximum likelihood bootstrap tree phylogeny based on the CLE motif sequences of SlCLE genes in tomato. The unrooted tree was constructed using MEGA 5.05. Numbers at nodes indicate the percentage bootstrap scores and only bootstrap values higher than 40% from 1,000 replicates are shown. Sl, S. lycopersicum; At, A. thaliana; Zm, Z. Maize. (B) Predicted protein sequences of SlCLEs were aligned with AtCLEs with flanking sequences using ClustalX and the output was displayed with Box Shade. (C) Sequence logos for the CLE motifs of tomato and Arabidopsis CLE gene family members. The height of the bars indicates the number of identical residues per position.