exon 13 (cloning primers: 59GGAGCTGCGATCGCTGGTCA- CATG39 and 59CTGAGTTTGATAGTGATGGCTTTGAC39), and a clone containing a medaka aldh1a2 527-nt fragment from exon 12 (cloning primers: 59GGAGGATACAAAATGTCTGG- GAATGG39) to the 39UTR (59CATTAACGTTTCATCCAT- TACTGTCC39) were used to synthesize riboprobes for whole-mount in situ hybridization using standard procedures [108,109], with slight variations: NBT and BCIP were used instead of the BM purple. Supporting Information Figure S1 Phylogenetic trees of the vertebrate Aldh1A gene family, inferred by maximum-likelihood, neighbor-joining, max- imum-parsimony, and Bayesian methods. Found at: doi:10.1371/journal.pgen.1000496.s001 (4.46 MB PDF) Figure S2 High-resolution images of the clusters of the Synteny Database. Found at: doi:10.1371/journal.pgen.1000496.s002 (0.17 MB PDF) Table S1 Supplementary information for dot-plot on Figure 2A. 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