Li Y , Omori A , Flores RL , Satterfield S , Nguyen C , Ota T , Tsurugaya T , Ikuta T , Ikeo K , Kikuchi M , Leong JCK , Reich A , Hao M , Wan W , Dong Y , Ren Y , Zhang S , Zeng T , Uesaka M , Uchida Y , Li X , Shibata TF , Bino T , Ogawa K , Shigenobu S , Kondo M , Wang F , Chen L , Wessel G , Saiga H , Cameron RA , Livingston B , Bradham C , Wang W , Irie N .

R01 GM125071 NIGMS NIH HHS

	Fig. 1. Echinoderms and their evolutionary diversity.a Echinoderm species of five living classes were analyzed in this study. Pentameral symmetry can also be observed in the transverse section of the sea cucumber (top), which otherwise shows apparent bilaterality. b Evolutionary rate and the phylogenetic tree constructed by RAxML software using the 1196 orthologous protein sequences identified by reciprocal best blast hit (RBBH). The values on branches represent bootstrap values. c Schematic representation of genomic organization of ambulacrarian Hox clusters. Arrows and horizontal lines represent Hox genes and chromosomal DNAs, respectively. Dashed lines indicate the presence of unconnected scaffolds. See Supplementary Fig. 13 for more detailed Hox cluster structures. Hox cluster structures of S. kowalevskii9, A. japonicus56, S. purpuratus7, O. spiculata56 and A. planci8 are according to the previous studies.
	Fig. 2. Evolutionarily conserved echinoderm stages and potential involvement of pitx signal in pentameral body plan development.a Mid-embryonic conservation found in echinoderm species. Based on expression distance (expDists, see also Supplementary Fig. 17) of orthologous groups (defined by orthomcl57), an evolutionary conservation of developmental stages were estimated for three taxonomic levels (Lv-Sp, Lv-Sp-Apj, Lv-Sp-Apj-Anj, see also “methods”). The vertical axis represents percentages of the stage being included in the most (top 1%) conserved stage-combinations13 (Ptop). Changes of the Ptop scores were significant among stages (Friedman test). Error bars represent S.D. of Ptop values. In each species, the developmental phase in which pentameral body plan establishment begins is colored in gray. b Possible evolutionary transition from bilateral symmetry to pentameral symmetric body plan suggested by paleontological studies61. The basal echinoderms had a bilaterally symmetric ambulacral system that is arranged in a 2–1–2 pattern (left); consisting of one unpaired ambulacrum (1) and two ambulacra with a distal bifurcation (2&3, 4&5) and a single unpaired ambulacrum (1). c Feather star development from bilateral symmetry to pentameral symmetry. a.nc aboral nerve center, ar archenteron, ap adhesive pit, dt digestive tract, es enteric sac, hc hydrocoel, l.sc left somatocoel, o.rn oral ring nerve, po podia, r.sc right somatocoel, st stomodeum. d pitx gene expression detected in embryos of attachment stage and cystidean stage. In cystidean embryos, pitx was expressed in the tissues around the gut (arrows) and the inner tissue of the whole stalk (arrowheads). Scale bars: 100 μm. The expression was detected by in situ hybridization with whole mount (left) and sectioned specimens (right).
	Fig. 3. Skeletal element related proteins/domains identified in echinoderms.a SEM image of a skeletal element isolated from the feather star (A. japonica). b Proteins present in the feather star skeletal proteome were isolated from adult skeleton and identified by comparison of LC/MS/MS data to the genes computationally identified in the feather star genome. These proteins were compared to those found in skeletal proteomes of the sea urchin S. purpuratus62–64, the sea star P. miniata36 and the brittle star O. spicullata35. The most prevalent proteins are shown in the figure, along with the number of different proteins from the listed groups present in each species’ proteome. The feather star skeletal proteome contains members of each of the protein families shown. The other echinoderm species are missing some of these proteins in their skeletal proteome and the number of members in each protein family varies between groups.