Additional file 1: Figure S1. of Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution

Amino acid sequences used for the analysis of Hox genes of Halocynthia roretzi (Hr) by construction of ML phylogenetic trees. Amino acid sequences include the homeodomain (60 residues in yellow) and the adjacent 20Â N-terminal and seven C-terminal residues. Original accession numbers for these sequences are indicated in brackets. Taxonomic abbreviations are Mm for Mus musculus, Lm for Latimeria menadoensis, Hf for Heterodontus francisci, Ci for Ciona intestinalis, Hr for Halocynthia roretzi, Bl for Branchiostoma lanceolatum and Bf for Branchiostoma floridae. Hr Hox genes, designated according to orthology with Ci-Hox counterparts and according to their classification into paralog groups (PGs) are indicated prior to and in parentheses, respectively. In ascidian sequences, letters in red indicate diagnostic residues for Hox10 homeodomain proteins (see text). (PDF 41Â kb