Supplementary methods from Possible co-option of <i>engrailed</i> during brachiopod and mollusc shell development

In molluscs, two homeobox genes, <i>engrailed</i> (<i>en</i>) and <i>distal-less</i> (<i>dlx</i>), are transcription factors that are expressed in correlation with shell development. They are expressed in the regions between shell-forming and non-shell-forming cells, likely defining the boundaries of shell-forming fields. Here we investigate the expression of two transcription factors in the brachiopod <i>Lingula anatina</i>. We find that <i>en</i> is expressed in larval mantle lobes, whereas <i>dlx</i> is expressed in larval tentacles. We also demonstrate that the embryonic shell marker, mantle peroxidase (<i>mpox</i>), is specifically expressed in mantle lobes. Our results suggest that <i>en</i> and <i>mpox</i> are possibly involved in brachiopod embryonic shell development. We discuss the evolutionary developmental origin of lophotrochozoan biomineralization through independent gene co-option

Additional file 1: of Proteome analysis of shell matrix proteins in the brachiopod Laqueus rubellus

RT-PCR analysis of ICP-1 and EF-1ι. M: mantle; L: lophophore. (TIFF 897 kb

Additional file 2: of Proteome analysis of shell matrix proteins in the brachiopod Laqueus rubellus

The depth of the isotigs of shell matrix proteins in this study. (TIFF 597 kb

Additional file 1: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle

Table S1. Summary of Pinctada fucata genome sequence data. Table S2. Summary of the Pinctada fucata genome assemblies. Table S3. Numbers of genes containing functional domains related to heat shock proteins. See also Fig. 3a. Table S4. Numbers of genes containing functional domains related to non-self recognition and signaling. See also Fig. 4a. Table S5. List of biomineralization-related genes tandemly arranged in the genome. See also Fig. 5. Table S6. Hox and neighboring gene models tandemly arranged in the genome. Table S7. ParaHox and neighboring gene models tandemly arranged in the genome. Table S8. Wnt and adjacent gene models tandemly arranged in the genome. (PDF 385 kb