Genomic organization of the Hox genes identified with HoxPred in the genome-scale analyses. Hox and ParaHox genes are depicted with arrows indicating transcription orientation, over black lines representing the scaffolds. This representation takes into account the relative distance between the genes. The transcription orientation is the same as provided by the JGI genome browser. The color of the arrows relates to HoxPred classification (see color code on the left); white squares are non-Hox genes. The Hox cluster of Strongylocentrotus is from  and the ParaHox genes are from SpBase . The Hox cluster of Branchiostoma is from , with the additional Branchiostoma Hox15 gene found in the genome assembly. Hellobdella genes are not indicated as they span many scaffolds, probably due to poor genome assembly. When available, gene names are specified: in black (from published studies [16, 42, 43, 46]) or in blue (from the JGI genome browser or SpBase). An additional putative Hox gene, showing sequence similarities with Sp-Hox11/13c, lies outside the Hox cluster in Strongylocentrotus. See Additional file 2, Table S4 for the genomic coordinates.