Additional file 1:

"Alignment of spiggin genes identified in this study (Gaac_spg1-7)". Aligned sequences of the spiggin multi-gene family (Gaac_spg1-7) identified in the threespine stickleback genome. Putative exon regions are shaded in pink and numbered according to the gene structure of Gaac_spg1. Exon-intron boundaries with mutation sites are boxed in green and indels are boxed in red. In Gaac_spg6, repeated regions (two repeat units, 332 bp in length) are boxed in blue. Asterisks indicate sites that are conserved in all of the sequences.

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Additional file 2:

"Sequences of spiggin genes in threespine and ninespine sticklebacks and their homologs in other fishes". Sequences of the spiggin multi-gene family in threespine stickleback (Gaac_spg1, 3, 4, 5, and 7; spg1-4), ninespine stickleback (Pungitius_spgα-γ), and their homologs in torafugu (Takifugu_spiggin_homolog), spotted green pufferfish (Tetraodon_spiggin_homolog), medaka (Oryzias_spiggin_homolog), and zebrafish (Danio_spiggin_homolog) that were used in the phylogenetic analyses. The resulting data matrix, excluding ambiguous regions, was aligned before phylogenetic analyses were performed.

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Additional file 3:

"Expression analysis of spiggin homologs in torafugu and zebrafish". Expression of spiggin homologs in various tissues of torafugu and zebrafish determined by RT-PCR. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a positive control. Plus signs indicate amplification using reverse-transcribed cDNA from each tissue; minus signs indicate negative controls using RNA samples without reverse-transcription.

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Additional file 4:

"Primers used". Sequences of primers that were used in this study.

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Additional file 5:

"Phylogenetic tree using conserved domain structures". Reconstructed phylogenetic tree based on the conserved domain structures (VWD) of spiggins and their homologs. We used translated sequences of threespine and ninespine stickleback spiggin genes that were isolated from the genome sequence (Gaac_spg1, 3, 4, 5, and 7), published spiggin cDNA sequences (spg1-spg4; Pungitius_spgα-γ), and spiggin homologs isolated in torafugu (Takifugu_spg_homolog), spotted green pufferfish (Tetraodon_spg_homolog), medaka (Oryzias_spg_homolog), and zebrafish (Danio_spg_homolog). We extracted conserved domain structures (VWD), numbered them from the N-terminal end, and subjected them to phylogenetic analysis. The ML tree is shown; numbers at nodes in internal branches indicate % bootstrap values (500 replicates). The asterisk indicates the VWD domain of medaka spiggin homolog, for which the relative position is incongruent with those of other domains.

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