Conservation of Ciona notochord genes in Oikopleura. (A) Graph showing the distribution of Ci-Bra target genes based on their putative function. Putative functions were ascertained from the published literature [13, 35]. (B) Graph showing the conservation of Ci-Bra target genes in Oikopleura. The x-axis indicates the number of genes in each category. Figure S1. Sequence alignments used for phylogenetic reconstructions. Multiple alignments of the Noto15, Noto9 and Calumenin protein sequences used to construct the phylogenetic trees shown in Figures. 2 and 3. Shaded areas match a cutoff threshold of 80% identity/similarity calculated according to the BLOSUM62 similarity scoring matrix . Abbreviations: Hs: Homo sapiens; Ci: Ciona intestinalis; Bf: Branchiostoma floridae; Cs: Ciona savignyi; Hr: Halocynthia roretzi; Mt: Molgula tectiformis; Dl: Diplosoma listerianum; Od: Oikopleura dioica. Figure S2. Whole-mount in situ hybridization of Oikopleura neurulae. Oikopleura embryos at the neurula stage (1.8 hpf), hybridized in situ with the antisense probes indicated above each panel. Dorsal views, anterior to the top. Red arrowheads indicate notochord precursors. Figure S3. Additional expression patterns in Oikopleura embryos at 7-8 and 10-12 hpf. Oikopleura embryos at 7-8 hpf and 10-12 hpf hybridized in situ with the antisense probes indicated at the bottom right of each row. Insets in (A,B) show high magnification views of the regions of the tail showing hybridization signal. Black arrows indicate subchordal cells, green arrowheads indicate the developing ciliary funnel.