Table 1.
List of Genes that Were Consistently Upregulated in Sulfide Spring Fishes of All Drainages.
| Gene ID | Accession Number | Gene Name | Xmac Annotation | Number of Transcripts |
|---|---|---|---|---|
| TCONS_00000049 | O75452 | Retinol dehydrogenase 16 | rdh1 | 1 |
| TCONS_00002627 | Q16878 | Cysteine dioxygenase type 1 | CDO1 | 1 |
| TCONS_00002704 | Q00610 | Clathrin heavy chain 1 | CLTCL1 | 2 |
| TCONS_00002706 | P53007 | Tricarboxylate transport protein | si:dkey-178e17.1 | 1 |
| TCONS_00002887 | n/a | XLOC_002625 | 1 | |
| TCONS_00004013 | Q9Y6N5 | Sulfide:quinone oxidoreductase | sqrdl | 1 |
| TCONS_00004833 | Q5BKX6 | Solute carrier family 45 member 4 | SLC45A4 (2 of 2) | 1 |
| TCONS_00005215 | Q9BRT3 | Migration and invasion enhancer 1 | XLOC_004459 | 1 |
| TCONS_00006194 | P02144 | Myoglobin | Mb | 1 |
| TCONS_00006595 | Q8NHV1 | GTPase IMAP family member 7 | zgc:152658 | 1 |
| TCONS_00006596 | P10620 | Microsomal glutathione S-transferase 1 | mgst1.2 | 1 |
| TCONS_00006640 | P52294 | Importin subunit alpha-5 | kpna1 | 1 |
| TCONS_00006715 | Q5T6X4 | Protein FAM162B | fam162a | 3 |
| TCONS_00007401 | B7ZAP0 | RAB GTPase activating protein 1-like | rabgap1l2 | 1 |
| TCONS_00008470 | P15121 | Aldose reductase | akr1b1 | 1 |
| TCONS_00010008 | O00483 | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex | ndufa4l2 | 1 |
| TCONS_00010278 | P41236 | Protein phosphatase inhibitor 2 | ppp1r2 | 1 |
| TCONS_00010396 | Q7KZN9 | Cytochrome c oxidase assembly protein COX15 | cox15 | 1 |
| TCONS_00011484 | Q96PR1 | Potassium voltage-gated channel subfamily C member 2 | kcnc2 | 1 |
| TCONS_00011526 | P58743 | Prestin | slc26a5 | 1 |
| TCONS_00011778 | P21266 | Glutathione S-transferase Mu 3 | ENSXMAG00000009961 | 1 |
| TCONS_00012045 | Q12805 | EGF-containing fibulin-like extracellular matrix protein 1 | EFEMP1 | 1 |
| TCONS_00012336 | Q9H628 | Ras-related and estrogen-regulated growth inhibitor-like protein | zgc:171704 | 2 |
| TCONS_00012508 | P53985 | Monocarboxylate transporter 1 | slc16a1 | 1 |
| TCONS_00012770 | P00390 | Glutathione reductase | Gsr | 1 |
| TCONS_00013706 | P99999 | Cytochrome c | XLOC_011171 | 1 |
| TCONS_00014743 | Q6ZQY3 | Acidic amino acid decarboxylase GADL1 | GADL1 (1 of 2) | 1 |
| TCONS_00014769 | Q6ZQY3 | Acidic amino acid decarboxylase GADL1 | GADL1 (2 of 2) | 1 |
| TCONS_00014831 | Q96P48 | Arf-GAP with Rho-GAP domain, ANK repeat, and PH domain-containing protein 1 | ENSXMAG00000006436 | 1 |
| TCONS_00014991 | Q16822 | Phosphoenolpyruvate carboxykinase | pck2 | 1 |
| TCONS_00015284 | P27144 | Adenylate kinase 4 | ak4 | 2 |
| TCONS_00015294 | Q9BYD5 | Cornifelin | ponzr10 (4 of 5) | 1 |
| TCONS_00015352 | Q8TDN7 | Alkaline ceramidase 1 | acer1 | 1 |
| TCONS_00015381 | Q96B33 | Claudin-23 | cldn23 | 2 |
| TCONS_00016368 | Q16831 | Uridine phosphorylase 1 | upp1 | 1 |
| TCONS_00016470 | P60174 | Triosephosphate isomerase | tpi1a | 1 |
| TCONS_00017022 | Q9UBX3 | Mitochondrial dicarboxylate carrier | SLC25A10 | 2 |
| TCONS_00017053 | Q86WA9 | Sodium-independent sulfate anion transporter | slc26a11 | 1 |
| TCONS_00017057 | O15525 | Transcription factor MafG | MAFG (2 of 2) | 1 |
| TCONS_00017983 | P09972 | Fructose-bisphosphate aldolase C | aldocb | 2 |
| TCONS_00018345 | P25325 | 3-mercaptopyruvate sulfurtransferase | zgc:162544 (1 of 2) | 1 |
| TCONS_00018346 | P25325 | 3-mercaptopyruvate sulfurtransferase | zgc:162544 (2 of 2) | 1 |
| TCONS_00018398 | Q9UQK1 | Protein phosphatase 1 regulatory subunit 3C | ppp1r3ca | 2 |
| TCONS_00019672 | Q9UPQ4 | Tripartite motif-containing protein 35 | TRIM35 (2 of 15) | 1 |
| TCONS_00020083 | P10599 | Thioredoxin | ENSXMAG00000001739 | 1 |
| TCONS_00020502 | P35558 | Phosphoenolpyruvate carboxykinase | pck1 | 1 |
| TCONS_00021089 | Q684P5 | Rap1 GTPase-activating protein 2 | rap1gap2a | 1 |
| TCONS_00021347 | P07339 | Cathepsin D | ctsd | 1 |
| TCONS_00021997 | O95571 | Persulfide dioxygenase ETHE1 | ETHE1 | 2 |
| TCONS_00022001 | O95571 | Persulfide dioxygenase ETHE1 | ETHE1 | 3 |
| TCONS_00022084 | Q86YN6 | Peroxisome proliferator-activated receptor gamma coactivator 1-beta | ENSXMAG00000019179 | 1 |
| TCONS_00022105 | Q5VV67 | Peroxisome proliferator-activated receptor gamma coactivator-related protein 1 | XLOC_017890 | 1 |
| TCONS_00022352 | n/a | XLOC_018095 | 1 | |
| TCONS_00022678 | P09105 | Hemoglobin subunit theta-1 | ENSXMAG00000000181 | 2 |
| TCONS_00022913 | Q7L5N7 | Lysophosphatidylcholine acyltransferase 2 | LPCAT4 (1 of 2) | 1 |
| TCONS_00022971 | P00918 | Carbonic anhydrase | cahz | 2 |
| TCONS_00023196 | Q53RY4 | Keratinocyte-associated protein 3 | tmem54 | 1 |
| TCONS_00023347 | Q9Y241 | HIG1 domain family member 1A | hig1 | 1 |
| TCONS_00023958 | Q15120 | Pyruvate dehydrogenase kinase, isozyme 3 | pdk3a | 1 |
| TCONS_00024060 | Q56VL3 | OCIA domain-containing protein 2 | ociad2 | 1 |
| TCONS_00025513 | P25325 | 3-mercaptopyruvate sulfurtransferase | ENSXMAG00000008042 | 1 |
| TCONS_00025981 | P06733 | Alpha-enolase | eno1a | 1 |
| TCONS_00026107 | n/a | abch1 | 1 | |
| TCONS_00026499 | O60675 | Transcription factor MafK | maff | 1 |
| TCONS_00026767 | P0CG29 | Glutathione S-transferase theta-2 | ENSXMAG00000006919 | 4 |
| TCONS_00026929 | P48506 | Glutamate-cysteine ligase catalytic subunit | gclc | 1 |
| TCONS_00028224 | n/a | XLOC_022849 | 1 | |
| TCONS_00028623 | n/a | XLOC_023166 | 1 | |
| TCONS_00028908 | n/a | XLOC_023394 | 1 | |
| TCONS_00030449 | Q9Y6M7 | Sodium bicarbonate cotransporter 3 | SLC4A7 (1 of 2) | 2 |
| TCONS_00030815 | Q96FC7 | Phytanoyl-CoA hydroxylase-interacting protein-like | ENSXMAG00000007363 | 1 |
| TCONS_00033175 | Q06830 | Peroxiredoxin 1 | prdx1 | 3 |
| TCONS_00034020 | Q8N4X5 | Actin filament-associated protein 1-like 2 | si:dkey-220o5.5 | 1 |
| TCONS_00034143 | O15394 | Neural cell adhesion molecule 2 | ENSXMAG00000017303 | 1 |
| TCONS_00034516 | n/a | XLOC_028149 | 1 | |
| TCONS_00034517 | P07911 | Uromodulin | XLOC_028150 | 1 |
Note.—Provided are the GenBank accession number for the top BLAST hit, the gene name, the corresponding identifier in the Xiphophorus maculatus (Xmac) reference genome, and the number of transcripts with evidence for upregulation for each gene. For additional information, see supplementary table S4, Supplementary Material online.
n/a, not applicable.