Genomic organizations of ParaHox genes. (A) Phylogenetic tree depicting genomic organization of the P. flava ParaHox cluster (top) compared to the clusters of amphioxus (Branchiostoma floridae) and mouse (Mus musculus) on chromosome (Chr.) 5. Blue, green, red, purple, and yellow boxes are exons of Gsx (Gsh), Xlox (Ipf1), Cdx, PRHOXNB, and Flt1, respectively. The light blue line indicates the fully sequenced PfBS11F10 BAC clone. Bent arrows indicate transcriptional orientations. The bottom line is a zoomed out view showing the neighboring Flt1 gene located near the mouse ParaHox cluster. (B) Evolution of the ParaHox cluster in bilateria. The phylogenetic tree represents the genomic organization of ParaHox genes in several bilateria, including protostomes (Pr) and deuterostomes (De). Protostomes can be further divided into lophotrochozoa (Lo) and ecdysozoa (Ed). The following lophotrochozoa animals were included in the analysis: two polychaete species (Platynereis dumerilii and Capitella teleta) and one leech species (Helobdella robusta) belonging to the Phylum Annelida (An); limpet (Lottia gigantea) and two oyster species (Crassostrea gigas and Pinctada fucata) in the Phylum Mollusca (Mo). Two ecdysozoa species fruit fly Drosophila melanogaster and nematode Caenorhabditis elegans do not contain the full complement of ParaHox genes. In deuterostomes, Phylum Echinodermata (Ec), including sea urchin Strongylocentrotus purpuratus and starfish Patiria miniata, and Phylum Hemichordata (He), including Ptychodera flava and Saccoglossus kowalevskii, constitute Ambulacraria (Am) that is closely related to Phylum Chordata (Ch). ParaHox gene organizations of the three chordate species, amphioxus Branchiostoma floridae, ascidian Ciona intestinalis, and mouse Mus musculus, are presented. IDs of the scaffolds (Sc) on which ParaHox genes are located are indicated beneath the illustrated scaffolds found in the genome databases. Blue, green, and red triangles indicate the orientations of Gsx, Xlox, and Cdx, respectively, in the genome. Double slashes between two genes indicate that although the genes are located on the same chromosome or scaffold they are separated by intervening genes. Species names shown in red contain intact ParaHox clusters.