Analysis of sequence similarity in the CLE domain. CLANS clustering of 174 sequences based on their sequence similarity in the CLE domain. Sequences are represented by dots and the various groups are highlighted by ovals. Sequences of the same group are assigned the same color. Lines connecting the dots correspond to BLASTP values better than 1.2E-7. Characterized CLE members HgCLE (CLE47), TDIF (CLE49) and ZmESR (CLE143–CLE147), as well as the known orthologs CLV3/FON4 and CLE19/BnCLE19 (CLE162) are highlighted with red stars. The single CLE member found from Physcomitrella patens (moss, CLE170), which clusters into group 11, is highlighted with a grey star. A putative CLE sequence from Chlamydomonas reinhardtii (alga, CLE177) is also marked with a grey star but does not cluster close to any group. The grouping established upon cluster analysis is analogous to previous classifications [8, 12, 24]. Group 2 contains CLE1–CLE7, which were previously shown to have no effect on RAM growth or on vascular cell differentiation in peptide assays and which led to wus-like dwarf growth only at 21 days after germination when ectopically overexpressed. CLE9–CLE13 can be found in group 7. These CLE members had an effect on the RAM but not on vascular cell differentiation in peptide assyas and wus-like dwarf growth could be observed at 14 and 21 days after germination in overexpression studies. The CLE family members CLE41, CLE42, CLE44, which had no effect on RAM but on vascular cell differentiation in peptide assays, and had a shrub-like overexpression phenotype are located in group 5.