Table 1:
Primer and probe sequences of genes used as molecular biomarkers to determine stress levels in late-larval delta smelt (Hypomesus transpacificus)
| Gene name | Gene code | Primer sequences | Function | Probe no. | Percentage efficiency |
|---|---|---|---|---|---|
| Glutathione-S-transferase | gst | 5′ → 3′ AATCTCCCTGGCAGACATTGTT 3′ → 5′ GGCCGGCTCTCAAACACAT | Cellular detoxification, osmotic stress | 127 | 108 |
| Mineralocorticoid receptor 1 | mr1 | 5′ → 3′ TTTCTACACTTTCCGCGAGTCA 3′ → 5′ TGATGATCTCCACCAGCATCTC | Mediator for cortisol signalling; HPI axis | 39 | 99 |
| Glucocorticoid receptor 2 | gr2 | 5′ → 3′ CATCGTGAAGCGTGAGGAGAA 3′ → 5′ TGCATGGAGTCCAGTAGTTTGG | Mediator for cortisol signalling; HPI axis | 129 | 98 |
| Pro-opiomelanocortin | pomc | 5′ → 3′ TGTTCACCTGTGCAGGTCTGA 3′ → 5′ GAGAAGCTCTCTTCCGTGGACA | Precursor of adrenocorticotrophic hormone; HPI axis | 127 | 102 |
| 11-beta-hydroxyteroid-dehydrogenase type 1 | 11-beta-hsd-1 | 5′ → 3′ CGTGTCGTCTCTGCTGGCTA 3′ → 5′ GGCGAACTTGGTGGAGGAG | Cortisol conversion; HPI axis | 55 | 109 |
| 11-beta-hydroxyteroid-dehydrogenase type 2 | 11-beta-hsd-2 | 5′ → 3′ TCCTGCCATCCTCCTACAAGAC 3′ → 5′ TCTGGACCAGGTGTTTGAACTG | Cortisol conversion; HPI axis | 14 | 106 |
| Beta actin | β-actin | 5′ → 3′ TGCCACAGGACTCCATACC 3′ → 5′ CATCGGCAACGAGAGGTT | Housekeeping gene, reference gene | 11 | 107 |
| Glyceraldehyde 3-phosphate dehydrogenase | gapdh | 5′ → 3′ TCCACGAGAAAGACCCAACT 3′ → 5′ CACGCCAGTAGACTCAACCA | Housekeeping gene, reference gene | 159 | 95 |
| Insulin like growth factor | igf | 5′ → 3′ GACACGCTGCAGTTTGTATGTG 3′ → 5′ CCATAGCCTGCCGGTTTGT | Development, somatic growth, interaction with growth hormone | 110 | 100 |
| Serum/glucocorticoid regulated kinase | sgk3 | 5′ → 3′ TTATTGAGATCAAAGCGCATGAC 3′ → 5′ GGTGTGAAGGGAGGTGGAATC | Ion homeostasis, stimulates sodium transport via epithelial sodium channel | 85 | 107 |
| Hypoxia inducible factor 1 alpha | hif1a | 5′ → 3′ GCCATGGCCAAGCTCCTTA 3′ → 5′ ATTCAGCATTGGCACTAAGCAC | Transcription factor, oxygen homeostasis | 41 | 105 |
| Glucose transporter 2 | glut2 | 5′ → 3′ GCCATGTCAGTTGGCCTCAT 3′ → 5′ GACATGCTGACGTAGCTCATCC | Glucose homeostasis, energy metabolism | 130 | 109 |
| Heat shock protein 70 kD | hsp70 | 5′ → 3′ AAGATTCTGGAGAAGTGCAACGA 3′ → 5′ CCTTCTCAGCGGTCTGGTTCT | General stress, heat stress | 20 | 107 |
| Nuclear factor k-beta | nfkb | 5′ → 3′ TGCACGGATGAACACATTGTC 3′ → 5′ CCAAAGTCCAGAGGCTTGTCA | Transcription factor, host defense, chronic inflammatory diseases | 123 | 103 |
| Ammonium transporter | NH4 trans | 5′ → 3′ CAGGCTGTCTTATCGCTTACGG 3′ → 5′ CAGCGTCATGACTAACAGCTGAA | Excesss ammonia elimination across gills and skin | 61 | 95 |
| Catalase | catalase | 5′ → 3′ GACCAGGGCATCAAGAACCTTA 3′ → 5′ GGATGGCGTAGTCTGGGTCA | Antioxidant enzyme, protects cell from oxidative damage by reactive oxygen species | 88 | 97 |
| Sodium potassium ATPase | Na K atpase | 5′ → 3′ GTCATCCCAATCTACTGCACCA 3′ → 5′ CATGATGTCGCCAATCTTGC | Ion transport during osmoregulation, osmoregulatory stress | 88 | 109 |
Abbreviations: HPI axis, hypothalamic–pituitary–interrenal axis.