Table 1.
Samples Used in the Study and Results of the Opsin Gene Expression in the Eyes or Retina.
| Species | Order | Median Species Depth (m)a | Stage | Code | Size (mm) | Date of Collection | Raw Reads | Reads After Bacteria Filtering | Gene Expression |
Accession No. | Source | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RH1 | RH2 | SWS1 | SWS2 | |||||||||||
| Anoplogaster cornuta | Trachichthyiformes | 1000–2000 | Larva | 39016 | 4 | April 2015 | 36,373,372 | 36,125,630 | <0.01 | 0.99 | <0.01 | SAMN10473242 | GenBank | |
| Larva | 39017 | 4 | April 2015 | 34,712,538 | 34,604,364 | <0.01 | 0.99 | <0.01 | SAMN10473243 | GenBank | ||||
| Larva | 4_23 | 9 | April 2015 | 41,592,840 | 41,519,070 | 0.02 | 0.98 | <0.01 | SAMN10473246 | GenBank | ||||
| Larva | 4_22 | 11 | April 2015 | 75,109,270 | 74,990,214 | 0.11 | 0.89 | <0.01 | SAMN10473245 | GenBank | ||||
| Larva | 4_21 | 11-12 | April 2015 | 28,945,804 | 28,869,552 | 0.22 | 0.78 | <0.01 | SAMN10473244 | GenBank | ||||
| Larva | 261s03 | 12 | 30.3.2017 | 48,458,044 | 48,457,472 | 0.47 | 0.53 | <0.01 | SAMN20741930 | This study | ||||
| Larva | 126A1 | 20 | 1.3.2020 | 79,371,594 | 79,347,702 | 0.28 | 0.72 | SAMN20746021 | This study | |||||
| Adult | 56H6 | 102 | 6.-7.4.2017 | 11,658,040 | 11,635,610 | 1 | SAMN20748547 | This study | ||||||
| Ceratoscopelus warmingii | Myctophiformes | 400–500 | Adult | 300s03 | 63 | 7.-8.4.2017 | 49,078,974 | 44,114,639 | 0.66 RH1-1 | SAMN20752508 | This study | |||
| 0.01 RH1-2 | ||||||||||||||
| 0.33 RH1-3 | ||||||||||||||
| Adult | S1 | n/a | June 2014 | 8,796,786 | 8,789,961 | 0.94 RH1-1 | SAMN10473255 | GenBank | ||||||
| 0.02 RH1-2 | ||||||||||||||
| 0.04 RH1-3 | ||||||||||||||
| Adult | S2 | n/a | June 2014 | 8,655,248 | 8,649,342 | 0.93 RH1-1 | SAMN10473256 | GenBank | ||||||
| 0.02 RH1-2 | ||||||||||||||
| 0.05 RH1-3 | ||||||||||||||
| Adult | S3 | n/a | June 2014 | 7,904,714 | 7,899,617 | 0.94 RH1-1 | SAMN10473257 | GenBank | ||||||
| 0.01 RH1-2 | ||||||||||||||
| 0.05 RH1-3 | ||||||||||||||
| Chauliodus sloani | Stomiiformes | 800–900 | Larva | 67I2_2 | 11 | 3.4.2017 | 34,445,252 | 34,371,394 | 0.01 | 0.99 | SAMN20769443 | This study | ||
| Larva | 67I1 | 17 | 3.4.2017 | 20,701,686 | 20,683,764 | <0.01 | 0.99 | SAMN20769824 | This study | |||||
| Juvenile | 109B6 | 20 | 5.4.2017 | 24,854,866 | 24,835,646 | 1 | SAMN20771653 | This study | ||||||
| Chauliodus danae | Stomiiformes | 800–900 | Juvenile | 109C7 | 24 | 30.3.2017 | 32,865,334 | 32,834,300 | 1 | SAMN20771814 | This study | |||
| Juvenile | 109A2 | 20 | 5.4.2017 | 25,389,318 | 25,344,182 | 1 | SAMN20777471 | This study | ||||||
| Juvenile | 109D7 | 96 | 30.3.2017 | 18,540,248 | 18,533,484 | 1 | SAMN20777490 | This study | ||||||
| Coccorella atlantica | Aulopiformes | 300–400 | Larva | 109G8 | 21 | 30.3.2017 | 26,376,620 | 26,359,060 | 0.01 | 0.99 RH2-1 | SAMN20793157 | This study | ||
| Adult | 56C7 | 77 | 25.3.2017 | 36,794,070 | 36,790,854 | 0.69 | 0.31 RH2-2 | SAMN20793158 | This study | |||||
| Adult | 297_7 | 68 | 6.-7.4.2017 | 43,948,534 | 40,511,279 | 0.96 | 0.04 RH2-2 | SAMN20793260 | This study | |||||
| Grammatostomias flagellibarba | Stomiiformes | 500–600 | Adult | 56H8 | 138 | 6.-7.4.2017 | 9,775,520 | 9,742,864 | 1 | SAMN20794729 | This study | |||
| Gyrinomimus myersi | Beryciformes | 1000–2000 | Larva | S25 | n/a | April 2015 | 19,270,096 | 19,122,986 | <0.01 | 0.45 RH2-1 | 0.07 | <0.01 | SAMN10473271 | GenBank |
| 0.13 RH2-2 | ||||||||||||||
| 0.08 RH2-3 | ||||||||||||||
| 0.11 RH2-4 | ||||||||||||||
| 0.15 RH2-5 | ||||||||||||||
| Howella brodiei | Pempheriformes | 500–600 | Adult | 56D8 | 76 | 25.3.2017 | 56,905,264 | 43,936,178 | 0.17 RH1-1 | SAMN20797093 | This study | |||
| 0.83 RH1-2 | ||||||||||||||
| Adult | 56D9 | 68 | 25.3.2017 | 61,909,674 | 61,590,270 | 0.07 RH1-1 | SAMN20799523 | This study | ||||||
| 0.93 RH1-2 | ||||||||||||||
| Hygophum reinhardtii | Myctophiformes | 100–200 | Larva | 67I2_1 | 5 | 3.4.2017 | 17,222,626 | 17,122,880 | 0.26 RH2-1 | SAMN20799641 | This study | |||
| 0.68 RH2-2 | ||||||||||||||
| 0.06 RH2-3 | ||||||||||||||
| Idiacanthus fasciola | Stomiiformes | 600–700 | Larva | 71C2 | 22 | 22.3.2017 | 23,382,468 | 23,379,360 | 1 | SAMN20800764 | This study | |||
| Larva | 67D2 | 22 | 31.3.2017 | 6,647,384 | 6,623,496 | 1 | SAMN20800770 | This study | ||||||
| Larva | 71C1 | 18 | 22.3.2017 | 23,632,774 | 23,497,715 | 1 | SAMN20800774 | This study | ||||||
| Larva | 67I7 | 25 | 5.4.2017 | 25,713,960 | 25,701,768 | 1 | SAMN20800775 | This study | ||||||
| Larva | 71B9 | 14 | 22.3.2017 | 43,695,620 | 43,633,424 | 1 | SAMN20801851 | This study | ||||||
| Larva | 67B8 | 17 | 29.3.2017 | 28,333,642 | 28,313,024 | 1 | SAMN20804813 | This study | ||||||
| Larva | 109A1 | 41 | 5.4.2017 | 27,834,274 | 27,818,750 | 1 | SAMN20804946 | This study | ||||||
| Adult | 228s01 | 210 | 22.-23.3.2017 | 21,704,528 | 21,622,274 | 1 | SAMN20805116 | This study | ||||||
| Adult | 67F8 | 178 | 1.4.2017 | 15,744,604 | 15,739,004 | 1 | SAMN20805515 | This study | ||||||
| Adult | 67B6 | 75 | 29.3.2017 | 15,439,954 | 11,368,044 | 1 | SAMN20834669 | This study | ||||||
| Melamphaes sp. | Beryciformes | 600–700 | Juvenile | 4_26 | n/a | April 2015 | 38,583,370 | 38,534,507 | 1 | SAMN10473273 | GenBank | |||
| Juvenile | 4_28 | n/a | April 2015 | 35,489,970 | 35,431,421 | 1 | SAMN10473274 | GenBank | ||||||
| Melanolagus bericoides | Argentiniformes | 800–900 | Larva | 71H3 | 7 | 26.3.2017 | 26,219,646 | 26,210,402 | 1 | SAMN20834672 | This study | |||
| Pteraclis aesticola | Scombriformes | 0–300 | Larva | 109H4 | 8 | 30.3.2017 | 19,918,922 | 19,870,484 | 0.22 | 0.78 | SAMN20844147 | This study | ||
| Pollichthys mauli | Stomiiformes | 300–400 | Adult | 109I2 | 34 | 30.3.2017 | 55,767,498 | 54,875,747 | 1 | SAMN20845044 | This study | |||
| Adult | 109I3 | 36 | 30.3.2017 | 68,655,686 | 67,082,709 | 1 | SAMN20848441 | This study | ||||||
| Scombrolabrax heterolepis | Scombriformes | 800–900 | Adult | ,56E3 | 91 | 25.3.2017 | 65,770,014 | 65,527,135 | 0.98 | 0.02 | SAMN20857047 | This study | ||
| Adult | ,56E4 | 77 | 25.3.2017 | 60,643,652 | 60,472,479 | 0.93 | 0.07 | SAMN20857932 | This study | |||||
| Scopelarchus guentheri | Aulopifoformes | 200–300 | Larva | 109H1 | 21 | 30.3.2017 | 37,542,802 | 37,416,486 | 0.96 RH2_larval | SAMN20859427 | This study | |||
| 0.04RH2-2_larval | ||||||||||||||
| Scopelarchus michaelsarsi | Aulopifoformes | 300–400 | Larva | 109B9 | 21 | 5.4.2017 | 9,971,250 | 9,919,148 | 1 RH2_larval | SAMN20860823 | This study | |||
| Larva | 71B7 | 20 | 22.3.2017 | 43,695,620 | 43,682,534 | <0.01 RH1a | 0.96 RH2_larval | SAMN20865446 | This study | |||||
| <0.01 RH1b | 0.03RH2-2_larval | |||||||||||||
| Adult | 272_10 | 66 | 2.4.2017 | 45,565,202 | 43,729,338 | 0.80 RH1a | 0.10 RH2_adult | SAMN20867027 | This study | |||||
| 0.10 RH1b | ||||||||||||||
| Scopelogadus mizolepis | Beryciformes | 800–900 | Adult | ,57E2 | 43 | 5.4.2017 | 5,160,876 | 5,160,672 | 1 | SAMN20867114 | This study | |||
| Adult | 300s01 | 62 | 7.-8.4.2017 | 15,448,240 | 15,420,650 | 1 | SAMN20867573 | This study | ||||||
| Scopelosaurus hoedti | Aulopiformes | 500–600 | Adult | 297_9 | 69 | 6.-7.4.2017 | 43,948,534 | 42,248,053 | 0.98 | 0.02 | SAMN20872996 | This study | ||
| Vinciguerria poweriae | Stomiiformes | 100–300 | Larva | 109H2 | 18 | 30.3.2017 | 25,863,628 | 25,755,100 | 1 | SAMN20878005 | This study | |||
| Larva | 109C8 | 16 | 30.3.2017 | 22,914,004 | 22,858,398 | 1 | SAMN20882114 | This study | ||||||