Additional file 1:

OTP annotation. Alignment of Orthopedia transcripts against the assembled genome. Three otp transcripts were mapped against scaffold_62 of the publicly available Nematostella genome assembly. The position relative to the scaffold is indicated to the right of the nucleotide sequence. For transcripts 1-3, identity to the genomic sequence is indicated with a full stop (.). Long introns have been truncated for clarity. Polymorphic positions are highlighted in black. We reconstructed one otp transcript (1) by conceptually splicing overlapping 3' and 5' RACE fragments. This transcript is 1045 nucleotides long and it maps between positions 812065 and 802467 of the scaffold. Another otp transcript (2) was identified among the ESTs sequenced as part of the Nematostella genome project (jgi|Nemev1|205678|fgenesh1_pg.scaffold_62000087). This transcript maps between positions 790736 and 812044 of the scaffold. A third Otp transcript (3) had been previously deposited in the EST database at NCBI [86]; GenBank accession DV090169). This transcript is only 616 nucleotides in length and it appears to be truncated at both ends. The predicted amino acid sequences are shown beneath the nucleotide sequences. Three conserved domains are indicated in bold type; the octapeptide (HSIVGILN), the 60 amino acid homeodomain and the 16 amino acid OAR domain. The OAR domain is downstream and in frame with the homeodomain, but the boxed amino acids are not encoded by any of the three otp transcripts we recovered.

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Additional file 2:

RX annotation. Alignment of rx transcripts against the assembled genome. We reconstructed one rx transcript (1) by conceptually splicing overlapping 3' and 5' RACE fragments (RACE). We also identified two rx sequences among the 150,000 ESTs generated by the Joint Genome Institute Nematostella sequencing project (2: 2664141-1, 3: 2664141-2) and two rx ESTs that were previously deposited at NCBI (4: CAGN10625, 5:CV088198). The RACE product spans nucleotides 785,552 to 790,345 of scaffold_62 in the Joint Genome Institute Nematostella genome assembly. Location relative to the scaffold is indicated to the right of the nucleotide sequence. The long second intron (3713 nucleotides in length) has been truncated for clarity. Polymorphic nucleotides are highlighted in black. Corresponding polymorphic amino acids are boxed. The predicted amino sequence is shown below the nucleotide sequence. Three conserved motifs are shown in bold type: the octapeptide (HSIDAILG), the 60-amino acid homeodomain and the 16-amino acid OAR motif. There are two non-silent polymorphisms within the homeodomain (K/R at position 52 and E/Q at position 59 (see Figure 5 for geographic distribution). The EST CV088198 (5) does not encode the complete OAR motif. It encodes a predicted protein (ending in a phenylalanine) that is 24 residues shorter than the predicted protein encoded by the other transcripts.

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Additional file 3:

RX polymorphism map. Geographic distribution of rx polymorphisms. In total, 95 individual animals were successfully genotyped at each of the two polymorphic positions in the Rx homeodomain from 24 estuaries. Collection sites were as follows: 1, Spurwink River, ME; 2, Odiorne Point, NH; 3, Rye Harbor, NH; 4, Wallis Sands, NH; 5, Old Town Hill, MA; 6, Crane Reserve, MA; 7, Neponset River, MA; 8, Pocasset River, MA; 9, Sippewissett Marsh, MA; 10, Clinton, CT; 11, Kingsport, Nova Scotia; 12, Halifax, NS; 13, Meadowlands, NJ; 14, Rhodes River, MD: 15, Baruch, SC; 16, San Juan Island, WA; 17, Willapa Bay, WA; 18, Coos Bay, OR; 19, Humboldt, CA; 20, Bodega Bay, CA; 21, Tomales Bay, CA; 22, Fort Gillkicker Lagoon, UK; 23, Salterns, UK; 24, Half Moon Lagoon, UK. The overall genotypic frequencies are: position 52: KK = 71.58%, KR = 26.16%, RR = 2.11%; position 59: QQ = 92.55%, QE = 7.45%, EE = 0.00%.

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Additional file 4:

HBN annotation. Annotated Nematostella Homeobrain locus. We reconstructed one hbn transcript (1) by conceptually splicing overlapping 3' and 5' RACE fragments (RACE). We also identified three Hb ESTs that were previously deposited at NCBI (2: DV0879878, 3: DV084683; 4: DV086666). The transcript obtained by RACE is 1139 nucleotides long and comprises three exons, which collectively span nucleotide positions 777,772 to 782,115 of scaffold_62 in the Joint Genome Institute Nematostella genome assembly. The position relative to the scaffold is indicated to the right of the nucleotide sequence. The predicted amino acids are shown below the nucleotides that encode them. Polymorphic nucleotides are highlighted in black. Corresponding polymorphic amino acids are boxed. Long introns have been truncated for clarity. Three conserved protein motifs are shown in bold type; the octapeptide (YTIDMILG), the 60-amino acid homeodomain and the 16-amino acid OAR domain.

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