Sequence retrieval and domain predictions
We retrieved genes containing leucine-rich repeats (LRRs) and a kinase domain (KD) by running the hmmsearch program (HMMER 2.3.2) to search for the kinase Hidden Markov Model (HMM) profile (PF00069.16) within the proteomic sequences of completely sequenced genomes. Within this set of kinase proteins, we then searched for LRR-domain HMM profiles (PF00560.24) (E value cut-off < 1) [19, 20]. Signal peptides (SPs) and transmembrane domains (TMs) were predicted using the SignalP http://www.cbs.dtu.dk/services/SignalP/ and TMHMM http://www.cbs.dtu.dk/services/TMHMM/ websites, respectively, hosted at the Center for Biological Sequence Analysis, Technical University of Denmark . Proteins containing LRRs, a TM and a KD were then considered to be putative LRR-RKs. We used the SMART web site http://smart.embl-heidelberg.de/ to check whether domains other than LRRs were predicted in the extracellular domain (ECD) of each protein . If other domains were detected, the protein was rejected. Proteins containing only LRRs in their extracellular domain (ECD), a TM domain and a KD were classified as LRR-RKs. For the phylogenetic analysis presented in Figure 2, we first retrieved all of the peptide sequences of eukaryotic protein kinases used in  to establish the phylogenetic relationship between plant and animal protein kinases. We next retrieved one LRR-RLK protein per subgroup from the Arabidopsis genome. Finally, we included all of the newly identified LRR-RK proteins from the oomycete, Monosiga, Ectocarpus and Chlorella genomes. In oomycetes, Ectocarpus, Monosiga and Chlorella, we also retrieved proteins sequences of closely related kinases found using a Blastp search. This search was performed using the KD of the LRR-RKs, and we selected the non-LRR-RK best hit. Accessions numbers of all of these sequences are listed in the 'Accession number' section below.
The accession numbers for Arabidopsis thaliana are as follows: AtCKI1 [GenBank, CAA55395]; AtCDC2a [GenBank, AAB23643]; AtCPK7 [GenBank, AAB03247]; AtCKA1 [GenBank, BAA01090]; AtCTR1_Raf [GenBank, AAA32779]; AtAME2 [GenBank, BAA08215]; AtMKK3 [GenBank, BAA28829]; AtMEKK1 [GenBank, BAA09057]; AtNAK [GenBank, AAA18853]; AtNPH1 [GenBank, AAC01753]; AtPVPKlikePK5 [GenBank, BAA01715]; AtGSK3b [GenBank, CAA64408]; AtGSK3i [GenBank, CAA68027]; AtSnRK2 [GenBank, AAA32845]; AtMPK1 [TAIR, AT1G10210]; AtS6KlikePK1 [GenBank, AAA21142] and AtTousled [GenBank, AAA32874]. The accession numbers for Homo sapiens are as follows: hAXL [GenBank, NP_001690]; hRYK [GenBank, P34925]; hTRKalpha [GenBank, BAA34355]; hMuSK [GenBank, AAB63044]; hKLGlikePTK7 [GenBank, AAC50484]; hIR [GenBank, NP_000199]; hLTK [GenBank, P29376.3]; hRET [GenBank, AAH04257]; hTIE1 [GenBank, P35590]; hPDGFRbeta [GenBank, NM_002600.1]; hVGFR1 [GenBank, P17948.2]; hTousledLK1 [GenBank, NP_036422]; hMAPKKK1 [GenBank, Q13233]; hCLK1 [GenBank, P49759]; hMAPK1 [GenBank, NP_002736.3]; hCDK3 [GenBank, NP_001249]; hCKIalpha2 [GenBank, NP_001883]; hCaMK1 [GenBank, BAG70221]; hCK2a [GenBank, CAB65624]; hGRK6 [GenBank, P43250]; hEGFR [GenBank, P00533]; hFGFR2 [GenBank, P21802]; hHGFR [GenBank, P08581]; hEPH [GenBank, P21709]; hDDR [GenBank, Q08345]; hRaf1 [GenBank, AAA60247]; TGF beta receptors, hTGFbRI [GenBank, P36897] and hTGFbRII [GenBank, P37173]; hIRAK1 [GenBank, AAH54000] and hMAPKK1 [GenBank, Q02750]. Additional accession numbers are as follows: mCKIalpha [GenBank, NP_666199] for Mus musculus; xtPELLE [GenBank, NP_001006713] for Xenopus tropicalis; drIRAK1 [GenBank, CAP19555] for Danio rerio and dmPELLE [GenBank, NP_476971] for Drosophila melanogaster. The accessions of representative Arabidopsis thaliana LRR-RLK genes in each subfamily are as follows: [TAIR: AT4G29180] for LRRI, AtNIK1 for LRRII [TAIR: AT5G16000], AtIMK3 for LRRIII [TAIR: AT3G56100], [TAIR: AT2G45340] for LRRIV, AtSCM_SUB for LRRV [TAIR: AT1G11130], [TAIR: AT1G14390] for LRRVI-1, [TAIR: AT5G41180] for LRRVI-2, [TAIR: AT2G24230] for LRRVII, [TAIR: AT1G06840] for LRRVIII-1, [TAIR: AT3G14840] for LRRVIII-2, AtTMK1 for LRRIX [TAIR: AT1G66150], [TAIR: AT3G28450] for LRRXa, AtBRI1 for LRRXb [TAIR: AT4G39400), AtCLV1 for LRRXI [TAIR: AT1G75820], AtFLS2 for LRRXII [TAIR: AT5G46330], AtFEI1 for LRRXIIIa [TAIR: AT1G31420], AtER for LRRXIIIb [TAIR: AT2G26330], [TAIR: AT3G14840] for LRRXIV and AtRPK1 for LRRXV [TAIR: AT1G69270]. We followed the subfamily nomenclature of a previous report .