Supplementary Figure 4: The tomato CLV3/EMBRYO-SURROUNDING REGION (CLE) peptide family.

(a) Alignment of the dodecapeptide motifs from 15 tomato SlCLE proteins¹⁸. Residues are colored on the basis of their physiochemical properties, and consensus symbols are shown at the top of the sequences indicating positions with strongly similar properties (:) and weakly similar properties (.) with the Arabidopsis thaliana CLV3 dodecapeptide sequence shown for reference. Ten SlCLE peptides start with arginine (R), characteristic of the CLV3 peptide class, and five others start with histidine (H), characteristic of the TDIF peptide class⁶⁴. (b) Neighbor-joining phylogenetic tree of the tomato and Arabidopsis CLE peptide family. CLE dodecapeptides from tomato and Arabidopsis were aligned using ClustalW, and a tree was constructed using the FigTree v1.3 program. The tree is shown with 100 replicate bootstrap values indicated at each node. Red color highlights tomato CLEs; black arrows point to SlCLV3, SlCLE3 and SlCLE9, also in bold. CLE family genes were retrieved from AGRIS (http://arabidopsis.med.ohio-state.edu/) and from the Solanaceae Genomics Network (SGN; http://solgenomics.net). (c–e) Normalized RNA-seq read counts (RPKM) from our tomato gene expression atlas (http://tomatolab/~lippmanlab2/allexp_query.html)⁵² showing that SlCLV3 (c) and SlCLE9 (e) are expressed primarily in meristems, unlike SlCLE3 (d), which is expressed broadly. Data from the EVM and floral meristem (FM) stages are shown⁵².