Ancestry of KNOX genes revealed by bryophyte (Physcomitrella patens) homologs

Structural and phylogenetic studies of KNOX genes identified in the bryophyte Physcomitrella patens are reported here, to provide insights into the evolution of class 1 and class 2 KNOX genes. Three KNOTTED1-like homeobox (KNOX) genomic clones were isolated and sequenced from P. patens. Corresponding cDNAs from a library, prepared from mRNA transcripts isolated from gametophytic tissues, were also sequenced. Conceptual translation and analysis of the bryophyte coding sequences revealed a domain pattern and secondary structures typical of higher plant KNOX proteins. Intron number and positions within the genes were also highly conserved between moss and angiosperm loci, providing further support for their homology. Structural and phylogenetic analyses indicated that moss clones (MKN2 and MKN4) represent class 1 KNOX genes and the remaining clone (MKN1-3) is a class 2 KNOX gene. We conclude that the observed protein domain pattern is encoded by homeobox genes that evolved after separation of the plant lineage from that of fungi and animals, and must have been present in the common ancestor to mosses and seed plants. It is proposed that gene duplication and diversification, which created class 1 and 2 KNOX gene subfamilies, occurred after separation of this common ancestor from its algal progenitor (since a characterized algal KNOX gene cannot be assigned to class 1 or 2), but before the moss and higher plant lineages diverged.