Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system

Pulgar, Rodrigo; Hödar, Christian; Travisany, Dante; Zuñiga, Alejandro; Domínguez, Calixto; Maass, Alejandro; González, Mauricio; Cambiazo, Verónica

doi:10.1186/s12864-015-1716-9

Table 1 Representative probe sets differentially expressed between infected and non-infected fish

From: Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system

GeneBank ID^a	Fold change^b		Tentative annotation^c	Adj. P value^d
Up-regulated in LS and HS families	LS	HS		LS	HS
Immune response
CB511680	1.468	1.642	Lysozyme C II	0.000	0.000
CA050178	0.171	0.497	MHC class I (hla-UBA)	0.022	0.008
CA063704	0.114	0.171	CD97 antigen	0.045	0.030
CB508464	0.329	0.311	Canopy 4 (cnpy4)	0.028	0.032
CA044420	0.408	0.293	Aminopeptidase N	0.024	0.044
CB493358	0.288	0.373	Microsomal glutathione S-transferase 2	0.048	0.011
Energetic metabolism
CB500248	0.266	0.378	ATP synthase subunit e, mitochondrial	0.023	0.007
CA768741	0.273	0.301	ATP synthase subunit epsilon, mitochondrial	0.008	0.013
CA045510	0.252	0.252	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1	0.009	0.013
CK991263	0.169	0.219	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8	0.039	0.007
CB493482	0.251	0.276	Glucagon-1	0.014	0.005
CB492183	0.289	0.243	Succinyl-CoA ligase beta-chain	0.007	0.040
CB497724	0.225	0.280	Mitochondrial import receptor subunit TOM7	0.041	0.046
Organization and regulation of actin cytoskeleton
CA770217	0.160	0.345	Actin, cytoplasmic 1	0.019	0.005
CB508611	0.264	0.293	Thymosin beta-4	0.015	0.018
EG804880	0.231	0.294	Tropomyosin alpha-3 chain	0.037	0.012
EG783905	0.605	0.381	Myosin light chain 3	0.026	0.009
BU965651	0.326	0.337	Myosin light chain 4	0.010	0.012
DW564371	0.174	0.193	Ras GTPase-activating protein nGAP (ngap)	0.044	0.032
CB508887	0.248	0.306	Ral guanine nucleotide dissociation stimulator	0.021	0.021
Cell metabolism and regulation
CB507177	0.237	0.356	Cell division protein kinase 10	0.018	0.015
DW577024	0.198	0.304	Anaphase-promoting complex subunit 13	0.048	0.009
CB500559	0.227	0.251	Casein kinase II subunit alpha	0.009	0.017
CB492123	0.276	0.196	Trafficking protein particle complex subunit 5	0.025	0.040
CA042337	0.156	0.174	Charged multivesicular body protein 3	0.034	0.041
CB486725	0.202	0.326	Vacuolar ATP synthase subunit S1	0.029	0.009
CB490914	0.252	0.309	Fumarylacetoacetase	0.040	0.008
CB492396	0.199	0.277	Cytosolic 5-nucleotidase III	0.046	0.024
Stress response
CA045475	0.313	0.407	Pro-opiomelanocortin	0.026	0.004
CA047150	0.334	0.292	Pro-opiomelanocortin A2s	0.013	0.009
CA054693	0.157	0.246	Alcohol dehydrogenase class-3	0.048	0.020
EG824838	0.184	0.297	Microsomal glutathione S-transferase 3	0.033	0.022
CB498572	0.245	0.246	Gamma-glutamyl hydrolase	0.017	0.027
Gene expression
EG812701	0.579	0.809	Histone deacetylase complex subunit SAP30L	0.000	0.020
CA045554	0.310	0.332	Neurogenic differentiation factor 1	0.026	0.012
CB493607	0.313	0.219	Small nuclear ribonucleoprotein-associated protein B	0.002	0.013
CA058810	0.231	0.243	Eukaryotic translation initiation factor 1A	0.014	0.011
CA060458	0.297	0.449	Eukaryotic translation initiation factor 5A-1	0.023	0.012
Down-regulated in LS and HS families	LS	HS		LS	HS
Synthesis of proteins
CA045933	−0.703	−0.707	40S ribosomal protein S27	0.000	0.002
CA051651	−0.562	−0.403	40S ribosomal protein S5	0.008	0.026
CB497637	−0.610	−0.409	40S ribosomal protein S19	0.017	0.025
CA037570	−0.590	−0.840	60S ribosomal protein L27	0.002	0.000
CA768633	−0.585	−0.318	60S ribosomal protein L38	0.005	0.031
CB501170	−0.629	−0.517	60S ribosomal protein L36	0.002	0.001
Glycolysis, Oxidative Phosphorylation and mitochondrial transport
CA768062	−0.318	−0.654	Glyceraldehyde-3-phosphate dehydrogenase	0.005	0.017
CA052837	−0.424	−0.497	Phosphoglycerate mutase 1	0.006	0.025
CN442520	−1.051	−1.070	Cytochrome oxidase subunit 2	0.001	0.000
CB493612	−0.461	−0.909	Cytochrome oxidase subunit 3	0.014	0.001
CN442526	−0.311	−0.420	Cytochrome b	0.029	0.009
CA063030	−0.708	−0.311	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6	0.038	0.048
CN442551	−0.826	−1.058	NADH-ubiquinone oxidoreductase chain 1	0.001	0.008
CN442556	−0.416	−0.476	NADH-ubiquinone oxidoreductase chain 2	0.000	0.043
BU965678	−0.926	−1.207	NADH-ubiquinone oxidoreductase chain 3	0.000	0.008
CN442494	−0.320	−0.528	NADH-ubiquinone oxidoreductase chain 4	0.043	0.019
CA042906	−0.454	−0.746	ADP/ATP translocase 2	0.027	0.014
CA058445	−0.187	−0.313	ADP/ATP translocase 2	0.034	0.009
CB502545	−0.399	−0.595	Mitochondrial import inner membrane translocase subunit Tim23	0.043	0.000
CB498852	−0.402	−0.828	Heat shock cognate 70 kDa protein	0.031	0.000
Plasma transport of oxygen and selenium
CB492263	−1.300	−1.249	Hemoglobin subunit alpha-4	0.013	0.009
BU965636	−1.140	−1.657	Hemoglobin subunit beta	0.044	0.003
CA049300	−1.540	−1.691	Hemoglobin subunit beta-1	0.016	0.010
CB498665	−1.140	−1.164	Hemoglobin subunit beta-4	0.035	0.042
CA044104	−1.227	−1.947	Selenoprotein Pa	0.000	0.000
CB510462	−0.463	−0.867	Selenoprotein Pb	0.015	0.000
Extracellular matrix organization and collagen biosynthesis
CA047568	−0.216	−0.223	Collagen alpha-1(I) a chain	0.024	0.046
CB488336	−0.427	−0.272	Collagen alpha-1(I) a chain	0.010	0.026
CA061635	−0.568	−0.239	Collagen alpha-1(I) b chain	0.001	0.046
CB493159	−0.296	−0.309	Collagen alpha-2(I) chain	0.005	0.021
CB492428	−0.246	−0.478	Secreted protein acidic and rich in cysteine (SPARC)	0.042	0.030
Homeostasis of metals (iron and copper)
CB509708	−0.353	−0.443	Ferritin, heavy subunit	0.002	0.005
CB510731	−0.376	−0.634	Ferritin, middle subunit	0.001	0.006
CA039497	−0.337	−0.736	Hemopexin	0.005	0.041
CB508872	−0.767	−0.712	Metallothionein A	0.009	0.029
CB507722	−0.245	−0.328	Metallothionein B	0.048	0.009

^aGenBank accession numbers of probes
^bFold change between infected and non-infected fish represented as log₂ of expression ratio
^cTentative annotation of the best match according to blastx or blastn against nr GenBank database
^dAn adjusted p < 0.05 indicated that gene expression level was significantly altered following bacterial infection. Complete list of differentially expressed probes is available in Additional file 2

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ISSN: 1471-2164

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