Table 1.
Results of quantitative PCR for all candidate genes tested
| Mann–Whitney U-test |
Mean expression level |
|||||
|---|---|---|---|---|---|---|
| Gene ID | Gene annotation | P-value | FDR P-value | Carnivores | Omnivores | FD |
| Carnivore-biased genes (higher expression in carnivores) | ||||||
| btf3 | Basic transcription factor 3 | 0.0002 | 0.0021 | −0.069 | −1.594 | 1.525 |
| c2orf82 | Chromosome 2 open reading frame 82 | 0.0002 | 0.0021 | 1.58 | −0.12 | 1.7 |
| col2a1 | Collagen, type II, α 1 | 0.0003 | 0.0025 | −0.119 | −1.985 | 1.866 |
| col9a1 | Collagen α-1(IX) chain | 0.0003 | 0.0025 | 2.188 | 0.393 | 1.795 |
| csda | Cold shock domain protein A | 0.0006 | 0.0037 | 1.288 | −0.136 | 1.423 |
| des1 | Degenerative spermatocyte homolog 1, lipid desaturase | 0.0006 | 0.0037 | 2.117 | 0.865 | 1.251 |
| eif3c | Eukaryotic translation initiation factor 3, subunit C | 0.0003 | 0.0025 | 2.374 | 1.153 | 1.221 |
| gnb2l1 | Guanine nucleotide-binding protein (G protein), β polypeptide 2-like 1 | 0.0006 | 0.0037 | 2.338 | 1.252 | 1.086 |
| got2 | Glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2) | 0.0002 | 0.0021 | 0.743 | −0.75 | 1.493 |
| krt5.2 | Keratin 5 gene 2 | 0.0006 | 0.0037 | −0.449 | −1.462 | 1.013 |
| krt19 | Keratin 19 | 0.0002 | 0.0021 | 0.204 | −1.121 | 1.325 |
| mrf1 | AT-rich interactive domain 5B (MRF1-like) | 0.0002 | 0.0021 | 1.539 | 0.233 | 1.305 |
| myl1 | Myosin, light chain 1, alkali; skeletal, fast | 0.0104 | 0.0287 | 0.999 | −0.028 | 1.027 |
| pm20d2 | Peptidase M20 domain containing | 0.0011 | 0.0049 | 0.851 | −1.416 | 2.267 |
| reep5 | Receptor accessory protein 5 | 0.0003 | 0.0025 | 1.026 | −0.073 | 1.1 |
| shisa7 | Shisa-7-like | 0.0019 | 0.0068 | 0.091 | −1.101 | 1.191 |
| tbx15 | T-box transcription factor TBX15-like | 0.0002 | 0.0021 | 1.981 | 0.89 | 1.091 |
| tnni2 | Troponin I type 2 (skeletal, fast) | 0.0047 | 0.014 | 1.176 | 0.071 | 1.105 |
| tnnt3 | Troponin T type 3 (skeletal, fast) | 0.0011 | 0.0049 | 0.654 | −0.368 | 1.022 |
| Omnivore-biased genes (higher expression in omnivores) | ||||||
| amy2a | Amylase, α 2A (pancreatic) | 0.003 | 0.0093 | −5.904 | −1.698 | 4.206 |
| c3 | Complement component 3 | 0.0011 | 0.0049 | −1.72 | −0.091 | 1.628 |
| mug1 | Murinoglobulin 1 | 0.0003 | 0.0025 | −3.838 | −1.373 | 2.465 |
| pglyrp1 | Peptidoglycan recognition protein 1 | 0.0003 | 0.0025 | −2.949 | −0.229 | 2.72 |
| pnlip | Pancreatic triacylglycerol lipase-like | 0.0002 | 0.0021 | −5.804 | 1.197 | 7.002 |
| tf | Transferrin | 0.0006 | 0.0037 | −3.302 | −1.63 | 1.671 |
| Unbiased genes | ||||||
| atp5g3 | ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9) | 0.7984 | 0.8487 | −2.824 | −2.905 | 0.081 |
| bicd1 | Bicaudal D homolog 1-like | 1 | 1 | 1.701 | 1.62 | 0.081 |
| cab39l | Calcium-binding protein 39-like | 0.9591 | 0.9735 | −1.216 | −1.201 | 0.016 |
| ccnd2 | Cyclin D2 | 1 | 1 | 1.361 | 1.394 | 0.034 |
| ccni | Cyclin I | 0.5054 | 0.626 | 3.672 | 3.605 | 0.067 |
| col5a1 | Collagen, type V, α 1 | 0.6454 | 0.7322 | 3.879 | 3.795 | 0.085 |
| cox5a | Cytochrome c oxidase subunit Va | 0.8785 | 0.9194 | 0.371 | 0.357 | 0.014 |
| dach1 | Dachshund homolog 1 | 0.1949 | 0.277 | 0.217 | 0.385 | 0.168 |
| ercc3 | Excision repair cross-complementing rodent repair deficiency, complementation group 3 | 0.5737 | 0.6735 | 1.247 | 1.285 | 0.037 |
| faf1 | Fas (TNFRSF6) associated factor 1 | 0.7984 | 0.8487 | 2.257 | 2.262 | 0.006 |
| gas8 | Growth arrest-specific 8 | 0.3823 | 0.4869 | −0.826 | −0.997 | 0.171 |
| gtdc1 | Glycosyltransferase-like domain containing 1 | 0.4418 | 0.5574 | −0.19 | −0.361 | 0.171 |
| krt8 | Keratin 8 | 0.3282 | 0.4302 | 1.818 | 1.657 | 0.161 |
| lyst | Lysosomal trafficking regulator | 0.5737 | 0.6735 | 0.055 | 0.034 | 0.021 |
| mmaa | Methylmalonic aciduria type A protein, mitochondrial-like | 0.1304 | 0.2173 | 0.728 | 0.553 | 0.175 |
| npffr2 | Neuropeptide FF receptor 2-like | 0.5737 | 0.6735 | −1.614 | −1.523 | 0.09 |
| pitx2 | Paired-like homeodomain 2 | 0.3823 | 0.4869 | 1.39 | 1.286 | 0.104 |
| prss8 | Prostasin-like | 0.7209 | 0.7912 | 2.901 | 2.979 | 0.079 |
| psmd1 | Proteasome (prosome, macropain) 26S subunit non-ATPase 1 | 0.7209 | 0.7912 | 1.996 | 1.923 | 0.073 |
| ptafr | Platelet-activating factor receptor | 0.5737 | 0.6735 | −1.115 | −1.254 | 0.139 |
| rasd1 | RAS, dexamethasone-induced 1 | 0.7209 | 0.7912 | 1.626 | 1.557 | 0.068 |
| rbp1 | Retinol-binding protein 1, cellular | 0.9591 | 0.9735 | −1.223 | −1.196 | 0.027 |
| ric8a | Resistance to inhibitors of cholinesterase 8 homolog A | 0.7984 | 0.8487 | 0.73 | 0.68 | 0.051 |
| serbp1 | SERPINE1 mRNA-binding protein 1 | 0.8785 | 0.9194 | 3.021 | 3.073 | 0.052 |
| sgpp1 | Sphingosine-1-phosphate phosphatase 1 | 0.7984 | 0.8487 | 1.203 | 1.191 | 0.012 |
| thrap3 | Thyroid hormone receptor-associated protein 3 | 0.7209 | 0.7912 | 1.754 | 1.73 | 0.024 |
| wapal | Wings apart-like homolog | 0.9591 | 0.9735 | 0.706 | 0.674 | 0.033 |
| zfr | Zinc-finger RNA-binding protein | 0.9591 | 0.9735 | 2.904 | 2.946 | 0.042 |
| Ambiguous genes | ||||||
| a2m | α-2-macroglobulin | 0.007 | 0.0205 | −0.989 | −0.275 | 0.713 |
| abcc4 | ATP-binding cassette, sub-family C member 4 | 0.003 | 0.0093 | 1.242 | 2.051 | 0.809 |
| acp6 | Acid phosphatase 6, lysophosphatidic | 0.0281 | 0.0633 | 1.55 | 1.931 | 0.381 |
| actc1 | Actin, α, cardiac muscle 1 | 0.0499 | 0.1005 | −2.351 | −3.208 | 0.857 |
| aff2 | AF4/FMR2 family member 2-like | 0.065 | 0.1185 | −1.129 | −1.603 | 0.474 |
| aldoa | Aldolase A, fructose-bisphosphate | 0.1949 | 0.277 | 1.335 | 0.936 | 0.4 |
| arhgdig | Rho GDP dissociation inhibitor (GDI) gamma | 0.0379 | 0.0826 | −0.217 | −0.81 | 0.593 |
| arx | Homeobox protein ARX-like | 0.0006 | 0.0037 | 0.721 | −0.17 | 0.892 |
| atp2a1 | ATPase, Ca++ transporting, cardiac muscle, fast twitch 1 | 0.065 | 0.1185 | −1.207 | −2.023 | 0.816 |
| barx2 | Homeobox protein BarH-like 2-like | 0.0019 | 0.0068 | 2.38 | 1.504 | 0.875 |
| BC157756.1 | Novel protein similar to prothymosin, α | 0.1605 | 0.2408 | −0.647 | −0.904 | 0.257 |
| cbfb | Core-binding factor, β subunit, transcript variant 2 | 0.0011 | 0.0049 | 1.546 | 1.032 | 0.514 |
| cct8 | Chaperonin containing TCP1, subunit 8 (θ) | 0.0104 | 0.0287 | −0.023 | −0.55 | 0.527 |
| chchd1 | Coiled–coil–helix–coiled–coil–helix | 0.065 | 0.1185 | −0.485 | −0.181 | 0.303 |
| cirbp | Cold inducible RNA-binding protein | 0.083 | 0.1494 | −0.71 | −0.51 | 0.2 |
| clptm1 | Cleft lip and palate transmembrane protein 1 | 0.0148 | 0.0383 | 0.109 | 0.599 | 0.49 |
| cnn1 | Calponin 1, basic, smooth muscle | 0.0499 | 0.1005 | −0.147 | 0.169 | 0.316 |
| cryba4 | Crystallin, β A4 | 0.2786 | 0.3761 | −0.759 | −1.229 | 0.469 |
| crybb2 | Crystallin, β B2 | 0.065 | 0.1185 | −1.322 | −0.334 | 0.988 |
| crybb3 | Crystallin, β B3 | 0.1605 | 0.2408 | 0.435 | −0.299 | 0.733 |
| ddx1 | DEAD (Asp−Glu−Ala−Asp) box polypeptide 1 | 0.0281 | 0.0633 | 1.434 | 0.875 | 0.559 |
| ddx21 | DEAD (Asp−Glu−Ala−Asp) box polypeptide 21 | 0.0011 | 0.0049 | 1.089 | 0.556 | 0.533 |
| det1 | De-etiolated homolog 1 | 0.003 | 0.0093 | 0.272 | 0.822 | 0.55 |
| eef1b2 | Eukaryotic translation elongation factor 1 β 2 | 0.1605 | 0.2408 | −0.132 | −0.541 | 0.409 |
| eif3b | Eukaryotic translation initiation factor 3, subunit B | 0.003 | 0.0093 | −0.675 | −1.184 | 0.509 |
| eif3l | Eukaryotic translation initiation factor 3, subunit L | 0.0207 | 0.049 | −2.033 | −2.534 | 0.501 |
| elmod1 | ELMO/CED-12 domain containing 1 | 0.0499 | 0.1005 | 3.628 | 3.281 | 0.347 |
| eno3 | Enolase 3 β muscle | 0.1049 | 0.1816 | 2.258 | 2.662 | 0.404 |
| fam49a | Family with sequence similarity 49, member A | 0.2345 | 0.323 | −0.424 | −0.71 | 0.286 |
| fam73a | Family with sequence similarity 73, member A | 0.1949 | 0.277 | 2.814 | 2.453 | 0.361 |
| foxn3 | Forkhead box N3 | 0.0011 | 0.0049 | 1.791 | 2.652 | 0.86 |
| gak | Cyclin G-associated kinase | 0.1605 | 0.2408 | 1.489 | 1.729 | 0.24 |
| galntl6 | Polypeptide N-acetylgalactosaminyltransferase 6-like | 0.1605 | 0.2408 | −0.78 | −0.527 | 0.253 |
| gpm6a | Glycoprotein M6A | 0.0148 | 0.0383 | −1.423 | −1.902 | 0.479 |
| hoxa1 | Homeobox A1 | 0.0379 | 0.0826 | −0.087 | −0.543 | 0.455 |
| hpcal1 | Hippocalcin-like 1 | 0.0019 | 0.0068 | −1.25 | −0.706 | 0.544 |
| hsp90ab1 | Heat shock protein 90 kDa α (cytosolic), class B member 1 | 0.6454 | 0.7322 | 0.749 | 0.511 | 0.238 |
| htatsf1 | HIV-1 Tat specific factor 1 | 0.3282 | 0.4302 | −0.067 | −0.312 | 0.245 |
| itgb1bp3 | Integrin β 1-binding protein 3 | 0.0019 | 0.0068 | 0.171 | −0.703 | 0.874 |
| krt12 | Keratin 12 | 0.1605 | 0.2408 | −1.214 | −0.926 | 0.288 |
| kti12 | KTI12 homolog, chromatin associated | 0.0104 | 0.0287 | −0.735 | −0.464 | 0.271 |
| lyzc | Lysozyme C-like | 0.5054 | 0.626 | −1.851 | −1.573 | 0.278 |
| mdh2 | Malate dehydrogenase 2, NAD (mitochondrial) | 0.0003 | 0.0025 | 0.685 | 0.075 | 0.61 |
| myh2 | Myosin, heavy chain 2, skeletal muscle, adult | 0.065 | 0.1185 | 0.189 | −0.517 | 0.706 |
| myh8 | Myosin, heavy chain 8, skeletal muscle, perinatal | 0.6454 | 0.7322 | 1.361 | 1.028 | 0.332 |
| myl3 | Myosin, light chain 3, alkali; ventricular, skeletal, slow | 0.0011 | 0.0049 | −0.07 | −1.05 | 0.98 |
| mylpf | Myosin, light chain, phosphorylatable, fast skeletal muscle | 0.1605 | 0.2408 | 0.388 | 0.629 | 0.241 |
| nbeal2 | Neurobeachin-like protein 2-like | 0.0002 | 0.0021 | 1.499 | 2.252 | 0.753 |
| ndufab1 | NADH dehydrogenase (ubiquinone) 1, α/β subcomplex, 1, 8 kDa | 0.0019 | 0.0068 | −1.46 | −1.911 | 0.451 |
| neb | Nebulin-like | 0.6454 | 0.7322 | 1.449 | 1.171 | 0.278 |
| ngly1 | Peptide-N(4)-(N-acetyl-β-glucosaminyl)asparagine amidase-like | 0.1949 | 0.277 | −0.644 | −0.903 | 0.259 |
| nono | Non-POU domain containing, octamer-binding | 0.0207 | 0.049 | 2.179 | 2.653 | 0.474 |
| nsa2 | Ribosome biogenesis homolog | 0.3282 | 0.4302 | −1.369 | −1.065 | 0.304 |
| peli1 | Pellino homolog 1 | 0.1304 | 0.2173 | 1.219 | 1.519 | 0.3 |
| pgc | Progastricsin (pepsinogen C) | 0.0499 | 0.1005 | −0.252 | 0.17 | 0.422 |
| pif1 | PIF1 5′-to-3′ DNA helicase homolog | 0.3823 | 0.4869 | −1.224 | −0.742 | 0.482 |
| pou6f1 | POU class 6 homeobox 1 | 0.065 | 0.1185 | 2.109 | 2.352 | 0.243 |
| psmc6 | Proteasome (prosome, macropain) 26S subunit ATPase 6 | 0.0002 | 0.0021 | −0.864 | −1.676 | 0.813 |
| ptprs | Protein tyrosine phosphatase, receptor type, S | 0.003 | 0.0093 | −0.292 | −1.007 | 0.715 |
| rho | Rhodopsin | 0.0207 | 0.049 | −1.563 | −2.307 | 0.744 |
| sfxn5 | Sideroflexin 5 | 0.0207 | 0.049 | 1.652 | 0.914 | 0.738 |
| slc3a2 | Solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 | 0.1605 | 0.2408 | −1.286 | −1.658 | 0.372 |
| slc25a3 | Solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 3 | 0.2786 | 0.3761 | −1.278 | −1.644 | 0.365 |
| sox21 | SRY (sex determining region Y)-box 21 | 0.1304 | 0.2173 | 2.188 | 1.858 | 0.33 |
| ssg1 | Steroid sensitive gene 1 | 0.003 | 0.0093 | 0.963 | 0.042 | 0.921 |
| taf15 | TAF15 RNA polymerase II, TATA box-binding protein (TBP)-associated factor, 68 kDa | 0.0207 | 0.049 | −0.299 | −0.56 | 0.262 |
| tbc1d13 | TBC1 domain family, member 13 | 0.0002 | 0.0021 | 3.606 | 2.747 | 0.86 |
| tmem147 | Transmembrane protein 147 | 0.0047 | 0.014 | −1.153 | −0.717 | 0.436 |
| tmsb4 | Thymosin β 4 | 0.1605 | 0.2408 | −0.683 | −0.995 | 0.312 |
| tnnc2 | Troponin C type 2 (fast) | 0.1049 | 0.1816 | 0.076 | −0.301 | 0.377 |
| tpm1 | Tropomyosin 1 (α) | 0.1049 | 0.1816 | 0.48 | 0.136 | 0.343 |
| tpt1 | Tumor protein, translationally-controlled 1 | 0.2345 | 0.323 | −1.09 | −1.407 | 0.317 |
| trim63 | Tripartite motif-containing 63 | 0.0281 | 0.0633 | 2.713 | 1.249 | 1.464 |
| ttn | Titin | 0.0499 | 0.1005 | 1.248 | 0.326 | 0.922 |
| ubn2 | Ubinuclein 2 | 0.0148 | 0.0383 | 1.903 | 2.178 | 0.274 |
| ush2a | Usherin-like, Usher syndrome 2A | 0.0019 | 0.0068 | 2.072 | 1.127 | 0.945 |
| ybx1 | Y box-binding protein 1 | 0.0019 | 0.0068 | −0.98 | −0.254 | 0.726 |
| zbtb46 | Zinc-finger and BTB domain containing 46 | 0.1949 | 0.277 | 3.319 | 3.549 | 0.23 |
| znf326 | Zinc-finger protein 326 | 0.2345 | 0.323 | −0.204 | −0.462 | 0.258 |
| znf451 | Zinc-finger protein 451-like | 0.065 | 0.1185 | 2.313 | 2.731 | 0.419 |