Table S2. Differential expression in gill tissue from Arctic charr (Salvelinus alpinus) family 10 after transfer from freshwater to seawater. AC gill Expression BLASTX alignment Count contig ID P Log2(ER) Sequence description % ID E-Value Score 1 325062 2.5E-06 8.05 gi_301607131, XP_002933173.1, PREDICTED: hypothetical protein LOC100488659 [Xenopus (Silurana) 73 1.1E-10 69 tropicalis] 2 192325 1.5E-05 7.98 gi_410896384, XP_003961679.1, PREDICTED: splicing factor 3B subunit 1-like [Takifugu rubripes] 96 < 1.0E-180 2183 3 258728 2.0E-04 7.52 gi_29841473, AAP06505.1, hypothetical protein [Schistosoma japonicum] 78 2.2E-09 63 4 84094 9.5E-06 7.18 gi_307147580, ADN37680.1, hyopthetical protein [Oncorhynchus mykiss] 71 3.6E-48 179 5 394200 3.7E-04 7.15 gi_198285501, ACH85289.1, hypothetical protein [Salmo salar] 74 2.1E-06 55 6 500590 < 1.0E-10 6.8 gi_76153153, AAX24812.2, SJCHGC04011 protein [Schistosoma japonicum] 83 5.6E-16 87 7 697485 < 1.0E-10 6.72 gi_348542840, XP_003458892.1, PREDICTED: tensin-1-like [Oreochromis niloticus] 72 < 1.0E-180 986 8 277901 < 1.0E-10 6.64 gi_348544791, XP_003459864.1, PREDICTED: CD209 antigen-like [Oreochromis niloticus] 68 1.0E-50 186 9 573774 < 1.0E-10 6.59 gi_348541695, XP_003458322.1, PREDICTED: protein furry homolog [Oreochromis niloticus] 94 < 1.0E-180 4163 10 600452 1.5E-04 6.33 gi_213512967, NP_001133246.1, Epidermis-type lipoxygenase 3 [Salmo salar] >gi_209147549, 67 2.7E-47 172 ACI32895.1, Epidermis-type lipoxygenase 3 [Salmo salar] 11 196145 1.2E-10 6.14 gi_395544590, XP_003774191.1, PREDICTED: liprin-alpha-1 isoform 1 [Sarcophilus harrisii] 84 < 1.0E-180 1527 12 122834 < 1.0E-10 6.09 gi_348538967, XP_003456961.1, PREDICTED: dnaJ homolog subfamily A member 3, mitochondrial-like 86 9.9E-139 431 [Oreochromis niloticus] 13 411052 < 1.0E-10 6.02 gi_225705852, ACO08772.1, GTPase, IMAP family member 7 [Oncorhynchus mykiss] 80 2.9E-43 164 14 278939 1.8E-03 5.98 gi_213515472, NP_001134309.1, Natterin-like protein [Salmo salar] >gi_209153466, ACI33163.1, 95 2.6E-174 497 Natterin-like protein [Salmo salar] >gi_209732252, ACI66995.1, Natterin-like protein [Salmo salar] >gi_209738620, ACI70179.1, Natterin-like protein [Salmo salar] >gi_223647200, ACN10358.1, Natterin- like protein [Salmo salar] >gi_223649054, ACN11285.1, Natterin-like protein [Salmo salar] >gi_223673073, ACN12718.1, Natterin-like protein [Salmo salar] >gi_303667191, ADM16257.1, Natterin-like protein [Salmo salar] 15 97243 < 1.0E-10 5.95 gi_194018427, NP_001123464.1, otolith matrix macromolecule-64 precursor [Oncorhynchus mykiss] 85 9.1E-113 371 >gi_171363649, BAG14384.1, otolith matrix macromolecule-64 [Oncorhynchus mykiss] 16 738412 3.8E-10 5.92 gi_348545386, XP_003460161.1, PREDICTED: hypothetical protein LOC100702240 [Oreochromis 63 1.8E-63 163 niloticus] 17 325057 4.6E-03 5.87 gi_301607131, XP_002933173.1, PREDICTED: hypothetical protein LOC100488659 [Xenopus (Silurana) 73 2.3E-09 69 tropicalis] 18 600471 3.6E-03 5.83 gi_213512967, NP_001133246.1, Epidermis-type lipoxygenase 3 [Salmo salar] >gi_209147549, 74 < 1.0E-180 576 ACI32895.1, Epidermis-type lipoxygenase 3 [Salmo salar] 19 211112 2.3E-05 5.81 gi_363744067, XP_001233210.2, PREDICTED: avidin-related protein 4/5-like [Gallus gallus] 53 4.1E-17 85 20 128003 < 1.0E-10 5.77 gi_291390651, XP_002711849.1, PREDICTED: uromodulin-like [Oryctolagus cuniculus] 55 4.9E-68 153 21 42944 8.0E-03 5.69 gi_348538036, XP_003456498.1, PREDICTED: endonuclease domain-containing 1 protein-like 63 1.1E-44 166 [Oreochromis niloticus] AC gill Expression BLASTX alignment Count contig ID P Log2(ER) Sequence description % ID E-Value Score 22 563916 1.4E-04 5.66 gi_348539876, XP_003457415.1, PREDICTED: heat shock 70 kDa protein 12A-like [Oreochromis 73 2.9E-123 404 niloticus] 23 413191 1.1E-06 5.61 gi_156355451, XP_001623681.1, predicted protein [Nematostella vectensis] >gi_156210403, 46 7.7E-07 55 EDO31581.1, predicted protein [Nematostella vectensis] 24 480420 4.8E-05 5.59 gi_390362987, XP_788663.3, PREDICTED: histamine H3 receptor-like [Strongylocentrotus purpuratus] 65 4.3E-06 54 25 38120 3.3E-02 5.57 gi_348512973, XP_003444017.1, PREDICTED: N-acetyltransferase 10 [Oreochromis niloticus] 91 < 1.0E-180 617 26 60409 1.7E-04 5.43 gi_16549028, CAC82808.1, inducible nitric oxide synthase [Oncorhynchus mykiss] 98 < 1.0E-180 1453 27 153447 3.8E-03 5.4 gi_167963456, NP_001108173.1, uncharacterized protein LOC100137104 [Danio rerio] >gi_194332601, 68 6.5E-152 320 NP_001123789.1, tripartite motif containing 39 [Xenopus (Silurana) tropicalis] >gi_158254035, AAI54145.1, Zgc:173581 protein [Danio rerio] >gi_189441755, AAI67553.1, LOC100170539 protein [Xenopus (Silurana) tropicalis] 28 563824 1.6E-04 5.32 gi_348539878, XP_003457416.1, PREDICTED: heat shock 70 kDa protein 12A-like [Oreochromis 72 2.0E-29 123 niloticus] 29 378629 1.0E-04 5.19 gi_130505373, NP_001076412.1, uncharacterized protein LOC100001227 [Danio rerio] >gi_94732985, 53 1.4E-15 84 CAK04768.1, novel protein [Danio rerio] 30 508214 1.4E-03 5.13 gi_327278390, XP_003223945.1, PREDICTED: interferon-induced very large GTPase 1-like [Anolis 69 1.7E-44 176 carolinensis] 31 669633 3.1E-02 5.13 gi_213514702, NP_001134561.1, Angiogenin-1 precursor [Salmo salar] >gi_209734282, ACI68010.1, 78 5.9E-62 203 Angiogenin-1 precursor [Salmo salar] 32 45834 7.1E-04 5.11 gi_348524546, XP_003449784.1, PREDICTED: protein FAM193A-like [Oreochromis niloticus] 67 3.2E-50 199 33 661818 1.4E-02 5.11 gi_348516981, XP_003446015.1, PREDICTED: hypothetical protein LOC100697337 [Oreochromis 55 1.3E-23 103 niloticus] 34 496824 5.6E-04 5.07 gi_85679686, ABC72122.1, myeloperoxidase [Siniperca chuatsi] 84 < 1.0E-180 1111 35 542772 1.2E-03 5.07 gi_326664433, XP_003197815.1, PREDICTED: GTPase IMAP family member 2-like [Danio rerio] 73 7.5E-62 210 36 570584 1.9E-04 5.05 gi_225869567, YP_002745514.1, collagen-like surface-anchored protein SclG [Streptococcus equi subsp. 43 2.4E-05 55 equi 4047] >gi_37498977, AAQ91579.1, collagen-like protein 3 [Streptococcus equi] >gi_76262845, ABA41497.1, collagen-like protein G [Streptococcus equi subsp. equi] >gi_225698971, CAW92025.1, putative collagen-like surface-anchored protein SclG [Streptococcus equi subsp. equi 4047] 37 401592 2.4E-03 5.03 gi_326665132, XP_003197975.1, PREDICTED: apoptosis-associated speck-like protein containing a 56 3.2E-04 48 CARD-like isoform 1 [Danio rerio] >gi_326665134, XP_003197976.1, PREDICTED: apoptosis-associated speck-like protein containing a CARD-like isoform 2 [Danio rerio] >gi_326665136, XP_003197977.1, PREDICTED: apoptosis-associated speck-like protein containing a CARD-like isoform 3 [Danio rerio] >gi_326665138, XP_003197978.1, PREDICTED: apoptosis-associated speck-like protein containing a CARD-like isoform 4 [Danio rerio] 38 336700 1.9E-03 4.96 gi_223647836, ACN10676.1, Butyrophilin subfamily 1 member A1 precursor [Salmo salar] 89 5.9E-116 346 39 480417 7.7E-04 4.77 gi_357483895, XP_003612234.1, ATP synthase subunit a chloroplastic [Medicago truncatula] 78 5.5E-07 56 >gi_355513569, AES95192.1, ATP synthase subunit a chloroplastic [Medicago truncatula] AC gill Expression BLASTX alignment Count contig ID P Log2(ER) Sequence description % ID E-Value Score 40 708981 1.5E-02 4.75 gi_348506676, XP_003440884.1, PREDICTED: interleukin-17F-like [Oreochromis niloticus] 58 1.9E-22 102 41 413205 6.5E-03 4.7 gi_213514862, NP_001133599.1, Zinc finger protein Gfi-1b [Salmo salar] >gi_209154630, ACI33547.1, 77 9.7E-04 49 Zinc finger protein Gfi-1b [Salmo salar] 42 128002 6.9E-03 4.62 gi_291390651, XP_002711849.1, PREDICTED: uromodulin-like [Oryctolagus cuniculus] 51 4.0E-80 280 43 346911 4.6E-03 4.55 gi_326669328, XP_684086.4, PREDICTED: interferon-induced very large GTPase 1-like [Danio rerio] 66 6.9E-111 377 44 745502 2.5E-02 4.53 gi_325652196, NP_001191714.1, interleukin-17A/F-1 [Oryzias latipes] >gi_313849038, BAJ41371.1, 73 4.4E-37 139 interleukin-17A/F-1 [Oryzias latipes] 45 81546 1.6E-02 4.49 gi_326670011, XP_001338721.3, PREDICTED: tumor necrosis factor receptor superfamily member 5 59 5.4E-13 75 [Danio rerio] 46 498314 3.0E-03 4.4 gi_225716670, ACO14181.1, 3-oxoacyl-acyl-carrier-protein reductase [Esox lucius] 97 5.8E-149 469 47 136874 4.7E-02 4.38 gi_348534761, XP_003454870.1, PREDICTED: P2Y purinoceptor 13-like [Oreochromis niloticus] 71 4.0E-85 272 48 534891 3.5E-02 4.37 gi_76153153, AAX24812.2, SJCHGC04011 protein [Schistosoma japonicum] 65 6.2E-20 93 49 654418 3.5E-02 4.2 gi_219916835, CAQ60110.1, cathelicidin 1 [Salvelinus fontinalis] 97 3.0E-89 276 50 563881 1.9E-02 4.18 gi_348544651, XP_003459794.1, PREDICTED: heat shock 70 kDa protein 12A-like [Oreochromis 74 9.2E-42 153 niloticus] 51 716958 2.0E-02 4.16 gi_348525699, XP_003450359.1, PREDICTED: ELL-associated factor 1-like [Oreochromis niloticus] 90 6.3E-119 374 52 343460 5.1E-02 4.08 gi_156408850, XP_001642069.1, predicted protein [Nematostella vectensis] >gi_156229210, 41 1.7E-17 91 EDO50006.1, predicted protein [Nematostella vectensis] 53 162163 4.2E-02 4 gi_348535132, XP_003455055.1, PREDICTED: hypothetical protein LOC100705794 [Oreochromis 65 8.8E-43 171 niloticus] 54 738388 3.8E-02 3.99 gi_348517678, XP_003446360.1, PREDICTED: interferon-induced very large GTPase 1-like 70 1.4E-56 211 [Oreochromis niloticus] 55 410960 2.8E-05 3.85 gi_156387632, XP_001634307.1, predicted protein [Nematostella vectensis] >gi_156221388, 58 3.1E-11 67 EDO42244.1, predicted protein [Nematostella vectensis] 56 211114 1.3E-02 3.83 gi_93279520, pdb, 2FHL, AChain A, Avidin Related Protein (Avr4)-Bna Complex >gi_93279521, pdb, 57 1.8E-08 59 2FHL, B Chain B, Avidin Related