Table S3. Differential expression in gill tissue from Arctic charr (Salvelinus alpinus) family 12 after transfer from freshwater to seawater. AC gill Expression BLASTX alignment Count Contig ID P Log2(ER) Sequence description % ID E-Value Score 1 510543 < 1.0E-15 8.7 gi_12805155, AAH02035.1, Unknown (protein for MGC:5947) [Mus musculus] 100 1.35E-135 394 2 323017 < 1.0E-15 8.0 gi_213513042, NP_001134270.1, fucosyltransferase 9 [Salmo salar] >gi_209731992, ACI66865.1, 92 4.79E-42 161 Alpha-1,3-fucosyltransferase [Salmo salar] 3 499923 < 1.0E-15 7.9 gi_197631823, ACH70635.1, cytochrome c-like [Salmo salar] >gi_209738490, ACI70114.1, Cytochrome 98 8.02E-64 213 c [Salmo salar] >gi_221219870, ACM08596.1, Cytochrome c [Salmo salar] >gi_221220596, ACM08959.1, Cytochrome c [Salmo salar] >gi_225703780, ACO07736.1, Cytochrome c [Oncorhynchus mykiss] >gi_225705644, ACO08668.1, Cytochrome c [Oncorhynchus mykiss] >gi_303660333, ADM15993.1, Cytochrome c [Salmo salar] 4 99748 < 1.0E-15 7.6 gi_348545563, XP_003460249.1, PREDICTED: hypothetical protein LOC100708591 [Oreochromis 67 2.78E-157 479 niloticus] 5 41921 < 1.0E-15 6.7 gi_209737600, ACI69669.1, Caspase-14 precursor [Salmo salar] 75 1.48E-52 189 6 225544 < 1.0E-15 6.4 gi_83312446, YP_422710.1, Calphotin; microtubule-associated protein 4 [Magnetospirillum magneticum 70 7.52E-05 55 AMB-1] >gi_82947287, BAE52151.1, Calphotin; Microtubule-associated protein 4 [Magnetospirillum magneticum AMB-1] 7 151773 < 1.0E-15 6.3 gi_348517158, XP_003446102.1, PREDICTED: kallikrein-2-like [Oreochromis niloticus] 50 3.49E-28 118 8 293079 < 1.0E-15 6.3 gi_301607131, XP_002933173.1, PREDICTED: hypothetical protein LOC100488659 [Xenopus (Silurana) 56 4.17E-25 64 tropicalis] 9 604942 < 1.0E-15 6.2 gi_394933887, BAM29295.1, Zen 1 [Dermatophagoides farinae] 59 1.47E-09 67 10 511409 5.4E-05 6.2 gi_209734584, ACI68161.1, Caspase-14 precursor [Salmo salar] 76 7.37E-75 246 11 193909 1.4E-04 6.1 gi_209732928, ACI67333.1, NADH dehydrogenase 1 alpha subcomplex subunit 9, mitochondrial 98 1.37E-159 473 precursor [Salmo salar] >gi_223647086, ACN10301.1, NADH dehydrogenase 1 alpha subcomplex subunit 9, mitochondrial precursor [Salmo salar] >gi_223672959, ACN12661.1, NADH dehydrogenase 1 alpha subcomplex subunit 9, mitochondrial precursor [Salmo salar] 12 592962 3.8E-08 5.9 gi_6755574, NP_035544.1, antileukoproteinase precursor [Mus musculus] >gi_2829839, P97430.1, 100 4.05E-100 297 SLPI_MOUSE RecName: Full=Antileukoproteinase; Short=ALP; AltName: Full=Secretory leukocyte protease inhibitor; Flags: Precursor >gi_6606529, AAF19194.1, AF205374_1 secretory leukocyte protease inhibitor [Mus musculus] >gi_1763263, AAC53047.1, secretory leukocyte protease inhibitor [Mus musculus] >gi_1945383, AAC53140.1, secretory leukocyte protease inhibitor [Mus musculus] >gi_1945451, AAC53394.1, secretory leukoprotease inhibitor [Mus musculus] >gi_4100899, AAD09307.1, secretory leukoprotease inhibitor [Mus musculus] >gi_20306996, AAH28509.1, Secretory leukocyte peptidase inhibitor [Mus musculus] >gi_148674431, EDL06378.1, secretory leukocyte peptidase inhibitor, isoform CRA_a [Mus musculus] >gi_148674432, EDL06379.1, secretory leukocyte peptidase inhibitor, isoform CRA_a [Mus musculus] 13 41925 6.2E-05 5.9 gi_209737600, ACI69669.1, Caspase-14 precursor [Salmo salar] 76 1.21E-71 237 14 217197 2.3E-13 5.8 gi_83282445, XP_729774.1, hypothetical protein [Plasmodium yoelii yoelii 17XNL] >gi_23488517, 57 7.23E-13 74 EAA21339.1, hypothetical protein [Plasmodium yoelii yoelii] AC gill Expression BLASTX alignment Count Contig ID P Log2(ER) Sequence description % ID E-Value Score 15 413286 2.4E-11 5.7 gi_156352243, XP_001622673.1, predicted protein [Nematostella vectensis] >gi_156209261, 76 7.38E-09 63 EDO30573.1, predicted protein [Nematostella vectensis] 16 192325 3.8E-04 5.4 gi_410896384, XP_003961679.1, PREDICTED: splicing factor 3B subunit 1-like [Takifugu rubripes] 96 < 1.0E-180 2183 17 590957 1.9E-02 5.4 gi_402869608, XP_003898844.1, PREDICTED: immunoglobulin J chain isoform 1 [Papio anubis] 83 1.73E-56 142 18 563373 2.0E-05 5.4 gi_348525450, XP_003450235.1, PREDICTED: hypothetical protein LOC100694880 [Oreochromis 68 2.61E-52 198 niloticus] 19 522943 1.9E-05 5.4 gi_348500316, XP_003437719.1, PREDICTED: protein LSM14 homolog A-like [Oreochromis niloticus] 77 2.03E-131 424 20 201288 < 1.0E-15 5.4 gi_327287605, XP_003228519.1, PREDICTED: putative adenosylhomocysteinase 3-like [Anolis 97 5.22E-60 220 carolinensis] 21 684033 7.4E-04 5.3 gi_348531282, XP_003453139.1, PREDICTED: pecanex-like protein C14orf135 homolog [Oreochromis 82 < 1.0E-180 722 niloticus] 22 640643 4.8E-05 5.3 gi_229366190, ACQ58075.1, Kallikrein-8 precursor [Anoplopoma fimbria] 50 1.15E-26 89 23 547655 1.7E-02 5.2 gi_148725645, CAN87719.1, novel protein (zgc:91911) [Danio rerio] 98 2.74E-107 327 24 642187 8.1E-03 5.1 gi_410920215, XP_003973579.1, PREDICTED: cell division cycle-associated protein 7-like [Takifugu 70 2.25E-130 394 rubripes] 25 480417 2.5E-03 5.1 gi_357483895, XP_003612234.1, ATP synthase subunit a chloroplastic [Medicago truncatula] 78 5.52E-07 56 >gi_355513569, AES95192.1, ATP synthase subunit a chloroplastic [Medicago truncatula] 26 480420 5.7E-04 4.9 gi_390362987, XP_788663.3, PREDICTED: histamine H3 receptor-like [Strongylocentrotus purpuratus] 65 4.34E-06 54 27 50943 1.2E-02 4.9 gi_259089145, NP_001158610.1, deoxycytidine kinase [Oncorhynchus mykiss] >gi_225705244, 100 2.74E-88 278 ACO08468.1, Deoxycytidine kinase [Oncorhynchus mykiss] 28 60409 1.6E-03 4.9 gi_16549028, CAC82808.1, inducible nitric oxide synthase [Oncorhynchus mykiss] 98 < 1.0E-180 1453 29 89387 1.3E-13 4.9 gi_157278121, NP_001098159.1, transcription factor C-MYB [Oryzias latipes] >gi_40714443, 73 < 1.0E-180 669 BAD06940.1, transcription factor C-MYB [Oryzias latipes] 30 286882 2.9E-03 4.7 gi_260794874, XP_002592432.1, hypothetical protein BRAFLDRAFT_67299 [Branchiostoma floridae] 66 4.18E-04 53 >gi_229277651, EEN48443.1, hypothetical protein BRAFLDRAFT_67299 [Branchiostoma floridae] 31 561397 1.8E-02 4.7 gi_113678175, NP_001038335.1, uncharacterized protein LOC558619 precursor [Danio rerio] 45 5.50E-15 82 >gi_94732333, CAK11037.1, novel protein [Danio rerio] 32 354384 1.5E-06 4.6 gi_303227986, NP_001037801.3, chromosome transmission fidelity protein 8 homolog [Danio rerio] 89 8.39E-43 132 >gi_94733486, CAK04527.1, novel protein [Danio rerio] >gi_213624828, AAI71641.1, Si:ch211-218c6.5 protein [Danio rerio] 33 496824 6.0E-04 4.4 gi_85679686, ABC72122.1, myeloperoxidase [Siniperca chuatsi] 84 < 1.0E-180 1111 34 645707 2.3E-03 4.4 gi_189530913, XP_001339622.2, PREDICTED: hypothetical protein LOC799244 [Danio rerio] 83 < 1.0E-180 653 35 60206 8.2E-05 4.3 gi_225706360, ACO09026.1, Ubiquitin-conjugating enzyme E2 G1 [Osmerus mordax] 98 7.71E-104 332 36 677559 1.0E-02 4.2 gi_410896740, XP_003961857.1, PREDICTED: discoidin, CUB and LCCL domain-containing protein 2- 79 < 1.0E-180 870 like [Takifugu rubripes] AC gill Expression BLASTX alignment Count Contig ID P Log2(ER) Sequence description % ID E-Value Score 37 496803 9.2E-09 4.1 gi_224613258, ACN60208.1, Myeloperoxidase precursor [Salmo salar] 86 1.46E-168 511 38 707813 1.6E-03 4.1 gi_222527286, YP_002571757.1, laminin G, sub domain 2 [Chloroflexus sp. Y-400-fl] >gi_222451165, 40 1.52E-29 136 ACM55431.1, laminin G, sub domain 2 [Chloroflexus sp. Y-400-fl] 39 588379 2.5E-02 4.1 gi_212656619, ACJ36222.1, forkhead box P1b [Ctenopharyngodon idella] 89 < 1.0E-180 716 40 201196 < 1.0E-15 4.1 gi_209736498, ACI69118.1, Transmembrane and TPR repeat-containing protein 4 [Salmo salar] 77 1.21E-18 93 41 201257 < 1.0E-15 3.9 gi_355560983, EHH17669.1, hypothetical protein EGK_14124, partial [Macaca mulatta] 91 < 1.0E-180 586 42 524561 1.9E-02 3.9 gi_348506772, XP_003440931.1, PREDICTED: 2-oxoglutarate receptor 1-like [Oreochromis niloticus] 79 1.03E-119 365 43 586375 4.5E-03 3.8 gi_94732587, CAK05072.1, novel protein similar to vertebrate potassium inwardly-rectifying channel, 98 9.26E-83 263 subfamily J, member 3 (KCNJ3) [Danio rerio] 44 497949 3.2E-05 3.8 gi_348503347, XP_003439226.1, PREDICTED: enhancer of polycomb homolog 1-like [Oreochromis 71 3.34E-78 175 niloticus] 45 666299 5.2E-02 3.7 gi_225716736, ACO14214.1, HRAS-like suppressor 2 [Esox lucius] 55 1.90E-22 102 46 277922 3.8E-02 3.6 gi_225716830, ACO14261.1, CD209 antigen-like protein A [Esox lucius] 68 1.33E-34 136 47 90802 1.6E-06 3.4 gi_410903199, XP_003965081.1, PREDICTED: keratin, type I cytoskeletal 50 kDa-like [Takifugu 84 2.73E-81 195 rubripes] 48 151768 3.3E-02 3.4 gi_308210828, NP_001184098.1, kallikrein-4 precursor [Canis lupus familiaris] >gi_307827342, 47 2.41E-16 84 ADN94676.1, kallikrein-related peptidase 4 precursor [Canis lupus familiaris] 49 754898 9.5E-03 3.4 gi_255982777, CAP08938.1, fish virus induced TRIM protein [Oncorhynchus mykiss] 80 1.67E-116 364 50 617198 9.5E-05 3.3 gi_348517672, XP_003446357.1, PREDICTED: pumilio homolog 2 isoform 1 [Oreochromis niloticus] 91 < 1.0E-180 923 51 584736 3.3E-03 3.3 gi_213514156, NP_001134448.1, E3 ubiquitin-protein ligase RNF138 [Salmo salar] >gi_209733384, 83 6.07E-46 165 ACI67561.1, E3 ubiquitin-protein ligase RNF138 [Salmo salar] 52 316923 2.3E-10 3.2 gi_326677981, XP_002666131.2, PREDICTED: hypothetical protein LOC100331949 [Danio rerio] 57 5.12E-06 57 53 2452 1.6E-13 3.2 gi_292658798, NP_001167620.1, cytochrome P450, family 1, subfamily B, polypeptide 1 [Oncorhynchus 98 < 1.0E-180 1072 mykiss] >gi_290576814, ADD51159.1, cytochrome P450 family 1 subfamily B polypeptide 1 [Oncorhynchus mykiss] 54 338934 1.1E-12 3.1 gi_76153175, AAX24831.2,