Résumé
Phylogenetic tree of the Arabidopsis WAK and EGF-containing OsWAK genes from rice. The proteomes of Arabidopsis thaliana (TAIR release 9: 33,200 sequences) and Oryza sativa (TIGR Release 6.0: 67,393 sequences) were downloaded from the GreenPhyl database ( http://www.greenphyl.org/cgi-bin/index.cgi ) (Conte et al., 2008). We retrieved OsWAK genes proceeding into three steps. First, we ran the hmmsearch program (Eddy, 2009) to search for kinase Hidden Markov Model (HMM) profile (PF00069.16) (Sonnhammer et al., 1998) into Arabidopsis and Oryza sequences. We retrieved 3185 proteins containing a kinase motif. On this set of sequences, we again used the hmmsearch program seeking this time EGFs HMM profiles (PF00008.18, PF09120.1, PF07974.4, PF04863.4 and PF07645.6). From this second screen, we retrieved 248 proteins (33 from Arabidopsis thaliana and 215 from Oryza sativa). We extracted the kinase domain sequences of these proteins and aligned them with the E-INS-i program (default parameters) from the MAFFT website ( http://mafft.cbrc.jp/alignment/software/ ). Based on this alignment, we generated a phylogenetic tree by the maximum likelihood method with 100 bootstrap replicates. All the genes with a WAK signature, explicitly containing both EGF motif(s) and kinase domain, were grouped in the tree with a bootstrap value of 86. All other genes outside this clade have been considered as outgroup. All manipulations on phylogenetic trees have been performed with the treedyn program ( http://www.treedyn.org/ ). Empty circles: newly annotated OsWAK genes; black squares: OsWAK genes known to be differentially expressed upon infection; empty squares: WAK genes known to be involved in fungal resistance; asterics: OsWAK genes with an ACF kinase domain. (PDF 59 kb)