title: Phylogenetic relationships and evolution of the KNOTTED class of plant homeodomain proteins.
abstract: Knotted-like (KNOX) proteins constitute a group of homeodomain proteins involved in pattern formation in developing tissues of angiosperms and other green plants. We conducted phylogenetic analyses of nucleotide and amino acid 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 and monocot sequences occur in both classes, indicating that the protein classes 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 copies of KNOX genes in this and other conifers. The orthology of several grass genes (including Zea 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. Analysis of expression patterns suggests that the ancestral KNOX gene was expressed in all plant parts and that the propensity to be downregulated in roots and leaves evolved in the class I genes.
authors.affiliation: Department of Ecology and Evolution, State University of New York at Stony Brook, USA.
authors.forename: G
authors.initials: G
authors.lastname: Bharathan
authors.forename: B J
authors.initials: BJ
authors.lastname: Janssen
authors.forename: E A
authors.initials: EA
authors.lastname: Kellogg
authors.forename: N
authors.initials: N
authors.lastname: Sinha
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019143:Evolution, Molecular; D005801:Genes, Homeobox; D017343:Genes, Plant; D018398:Homeodomain Proteins / Q000235:genetics*; D019684:Magnoliopsida / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D006109:Poaceae / Q000235:genetics; D017386:Sequence Homology, Amino Acid
chemical_list: D018398:Homeodomain Proteins; D010940:Plant Proteins