Phylogeny of zebrafish and other vertebrate OR families. (a) Phylogeny of zebrafish receptors. A neighbor joining tree was constructed based on an alignment of the predicted amino acid sequences of 143 intact genes and 4 full-length pseudogenes identified from the zebrafish genome [see Additional file 2]. OR genes are named by subfamily and colored by family. The eight gene families are labeled A-H. The zebrafish melanocortin receptor branch (dotted line labeled "mcr") indicates the root of the tree. Bootstrap scores for each family are indicated in parentheses. (b) Phylogenetic relationship among zebrafish and mouse odorant receptors. The following sets of genes were aligned and used to construct a tree by neighbor joining: the mouse odorant receptors, mORs [8,9]; the subset of 136 intact zebrafish ORs with no disruptions identified in this study (highlighted in red); and mouse melanocortin receptors (mcr). Note the presence of OR gene subfamilies OR112, OR113, and OR114 (Family A) within the Class I clade and zebrafish OR101-1 (Family B) within the Class II clade. Bootstrap scores corresponding to selected nodes are indicated.(c) Phylogeny of the complete OR repertoires of zebrafish, fugu and tetraodon identified in this study. One-hundred-thirty-six non-disrupted genes from zebrafish, 42 non-disrupted genes from fugu, and 42 non-disrupted genes from tetraodon were used in this neighbor joining analysis. Families are labeled A-H and correspond to the zebrafish families shown in panel A. Bootstrap scores corresponding to selected nodes are indicated.