Phylogenetic relationships and evolution of the KNOTTED class of plant homeodomain proteins

Knotted-like (KNOX) proteins constitute a group of homeodomain proteins inv olved in pattern formation in developing tissues of angiosperms and other g reen plants, We conducted phylogenetic analyses of nucleotide and amino aci d sequences of all known KNOX proteins in order to examine their evolution. Our analyses reveal two groups of KNOX proteins, classes I and II. Dicot a nd monocot sequences occur in both classes, indicating that the protein cla sses arose prior to the origin of the monocots. A conifer (Picea) sequence is nested within class I, suggesting that there are likely to be other copi es of KNOX genes in this and other conifers. The orthology of several grass genes (including Zen Kn1, ZMKN1) is strongly supported by phylogenetic and synteny analyses. However, no compelling evidence supports the hypothesis of orthology previously proposed for several dicot genes and ZMKN1. Analysi s of expression patterns suggests that the ancestral KNOX gene was expresse d in all plant parts and that the propensity to be downregulated in roots a nd leaves evolved in the class I genes.