Table 1. Top 20 downregulated and 10 upregulated candidate genes from the RNA-seq analysis, and efficiencies for candidate hypoxia stress genes. Genes are presented in order of the significance of the correlation with PC1, which separated normoxia and hypoxia (data are in Table S1). Species abbreviations for efficieny: CK= Chinook salmon (Oncorhynchus tshawytscha), CO= Coho salmon (O. kisutch), CM= Chum salmon (O. keta), PK= Pink salmon (O. gorbuscha), SX= Sockeye salmon (O. nerka), AS= Atlantic salmon (Salmo salar), AC= Artic charr (Salvelinus alpinus), RT= Rainbow trout (O. mykiss), and BT= Bull trout (Salvelinus confluentus).

Gene name	Function of gene	Assay name	PCR Efficiency
			CK	CO	CM	PK	SX	AS	AC	RT	BT
Down-regulated genes
Anillin-like	Cell division	Anillin	1.20	1.30	1.27	1.20	1.12	1.29	1.00	0.99	1.56
Ribonucleoside-diphosphate reductase subunit M2-like	DNA synthesis	RRM2	1.28	1.38	1.27	1.07	1.15	1.34	1.10	1.00	1.47
Aurora kinase B-like	Cell division	AURKB	1.26	1.42	1.29	1.14	1.21	1.37	1.00	1.07	1.50
Ribonucleoside-diphosphate reductase large subunit-like	DNA synthesis	RRM1	1.04	1.16	1.16	0.99	1.10	1.19	1.02	1.00	1.31
Kinesin-like protein KIF2C	Cell division	KIF2C	1.11	1.20	1.18	1.09	1.05	1.24	0.98	1.02	1.27
Non-SMC condensin II complex subunit D3	Cell division	Ncapd3	1.09	1.19	1.11	1.08	1.01	1.17	0.99	1.00	1.33
Histone H2A.V	Cell division	H2AFV	1.08	1.22	1.29	1.11	1.05	1.31	1.00	1.05	0.71
Kinesin family member 15-like	Cell division	Kif15	1.17	1.22	1.15	1.01	1.03	1.21	0.99	1.02	1.31
Rho GTPase-activating protein 11A-like	Cell division	ARHGAP11A	1.22	1.28	1.20	1.03	1.10	1.33	1.05	0.98	1.42
Rab9 effector protein with kelch motifs-like	Cell division	Rab9	1.26	1.16	1.26	1.03	1.05	1.08	1.02	1.03	1.03
ERCC excision repair 6 like, spindle assembly checkpoint helicase	Cell division	ERCC6L	1.13	1.22	1.18	1.10	1.06	1.16	1.02	1.01	1.29
Tonsoku-like protein	DNA synthesis	Tonsl	1.15	1.39	1.26	1.03	1.13	1.30	1.02	0.86	1.52
Citron Rho-interacting kinase-like	Cell division	CIT	1.16	1.28	1.14	1.10	1.08	1.21	1.01	1.02	1.38
Proliferating cell nuclear antigen	DNA synthesis	PCNA	1.11	1.20	1.12	1.11	1.26	1.17	1.04	0.99	1.26
Claspin-like	DNA synthesis	Claspin	1.16	1.25	1.04	1.03	1.04	1.15	0.81	0.93	1.18
NDC80, kinetochore complex component	Cell division	Ndc80	1.13	1.25	1.21	1.03	0.99	1.19	1.01	0.99	1.30
Lamin B1	Cell division	Lmnb1	1.22	1.33	1.22	1.06	1.10	1.27	1.00	1.03	1.45
Condensin-2 complex subunit G2-like	Cell division	NCAPG2	1.21	1.17	—	1.31	—	1.70	1.20	0.99	1.36
Chromosome-associated kinesin KIF4-like	Cell division	Kif4	1.28	1.24	1.35	1.01	1.06	1.28	1.13	1.02	1.38
Structural maintenance of chromosomes protein 4-like	Cell division	SMC4		1.83	1.99	1.66	1.48	1.55	—	1.07	1.85
Up-regulated genes
Malignant fibrous histiocytoma-amplified sequence 1 homolog	Cell cycle arrest	MFHAS1	1.13	1.23	1.29	0.99	1.14	1.17	0.95	1.02	1.36
Receptor activity-modifying protein 1-like	Ion transport	RAMP1	0.99	1.19	1.14	1.06	1.04	1.08	1.02	—	1.17
Peptidylglycine alpha-amidating monooxygenase_106571984	Peptide amidation	PAM	1.16	1.19	1.12	1.01	1.04	1.15	1.01	1.03	1.22
protein family with sequence similarity 214, A	Cell division	FAM214A	1.21	1.34	1.19	0.98	1.05	1.18	1.01	0.98	1.12
Calphotin	Cellular calcium regulation	Calphotin	1.10	1.21	1.18	0.99	1.03	1.12	1.01	1.00	1.48
Gutathione peroxidase 3	Oxidative stress	GPX3	1.25	1.16	1.11	1.08	1.05	1.20	0.85	0.92	1.21
Endothelin-converting enzyme 2	Neuropeptide processing	ECE-2	1.16	1.25	1.20	1.10	1.09	1.20	1.04	1.02	1.38
Cyclin dependent kinase inhibitor 1B	Cell cycle arrest	CDKN1B	1.23	1.31	1.20	1.07	1.07	1.21	1.04	—	1.38
Transcription factor SOX-5	Cell cycle arrest	SOX-5	1.04	1.12	1.42	1.17	0.98	1.10	1.01	1.01	1.43
Acyl-coenzyme A thioesterase 9, mitochondrial	Oxidative stress	ACOT9	1.13	1.25	1.45	1.15	1.07	1.27	1.01	1.01	1.37