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Background: Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking.

BackgroundWarmer seawater as a result of climate change may impose environmental challenges for Atlantic salmon aquaculture in its southernmost geographic range. Seawater temperatures above optimal level for growth may be reached in the warmest summer weeks. Caged fish can experience temperature and low oxygen saturation stress during such episodes, raising fish welfare and productivity concerns. In this work we compare the transcriptional responses in Atlantic salmon exposed to chronic high temperature (19°C) and low oxygen saturation (4-5 mg/L) stress.ResultsWe used next-generation sequencing and RT-qPCR to screen for effects, and focused on growth regulation and oxidative stress in fish exposed to sub-optimal conditions. Both prolonged temperature (45 days) and low oxygen (120 days) stress had a significant negative effect on growth. The main effect of heat stress appears to be a general reduced transcriptional rate in salmon liver, while mechanisms typically associated with responses induced by chemical drugs were stimulated. Heat stress significantly down-regulated several transcripts encoding proteins involved in the protection against oxidative stress, including CuZn SOD, Mn SOD, GPx1 and GR, as well as additional stress markers HIF1A, CYP1A, MTOR and PSMC2 (RT-qPCR data). In salmon held at low oxygen concentration for four months protein ubiquitination (protein catabolism) was the most strongly affected pathway. According to the RT-qPCR data, low oxygen stress significantly up-regulated the transcriptional levels of IGFBP1B and down-regulated the levels of GR. Pathway analysis suggests that high temperature and low oxygen saturation stress affects many similar mechanisms in Atlantic salmon. Based on the gene lists, six out of the top ten predicted upstream transcriptional regulators, 1,2-dithiol-3-thione sirolimus, CD437, 5-fluorouracil, HNF4A and NFE2L2, were similar between the two treatments.ConclusionsIn conclusion, temperature and low oxygen saturation stress affect many identical mechanisms in liver cells resulting in a metabolic depression, but these effects are not necessarily mediated through altered transcription of the same genes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-817) contains supplementary material, which is available to authorized users.

Little is known about the digestion of nutrients in stomachless (agastric) fishes with short intestines, such as wrasse. This study describes the digestion, absorption and evacuation rates in ballan wrasse (Labrus bergylta) fed either dry or pre-soaked diets. Ballan wrasse juveniles received either dry or pre-soaked diets containing inert markers to determine intestinal evacuation rates over a 4-14 h period after ingestion. The digestive tract evacuation was completed in 12-14 h, and was not affected by dietary moisture level. Within the different segments of the intestine, 90% of the digesta moved from the foregut to the midgut after 4-8 h, and over 7% of the digesta had arrived in the hindgut 4 h after feeding. The foregut was a major site of digestion, where 86% of carbohydrates, 74% of proteins, and 50% of lipids, were absorbed from the diet. The absorption of carbohydrates and lipids increased until the hindgut (98 and 80%, respectively). Protein absorption continued along the length of the intestine reaching 90% absorption at the hindgut. Protein and carbohydrate absorption was slightly higher in the foregut for fish fed dry versus moist diets, but this difference disappeared in the midgut. The moisture levels of diet had no effect on the digesta moisture levels, expression of metabolic genes, the levels of nutrients in plasma, or intestinal health. Nine aquaporins were found to be expressed in the wrasse intestinal tissue. Vertebrate aquaporins are involved in water transport from the intestinal lumen into the body and may play a role in maintaining stable moisture level of the digesta in the intestine of ballan wrasse regardless of the initial dietary moisture levels.

In the present study, IgT genes of Atlantic salmon were cloned and characterised. Analysis of our sequence data as well as ESTs reported to the databases revealed three distinct IgT heavy chain sub-variants in salmon, as opposed to two of IgM and IgD. The IgT sub-variants in salmon are 76-80% identical to each other, and 75-82% identical to the reported rainbow trout sequences, whereas the similarity to the orthologous molecules in zebrafish, grass carp, mandarin fish, and grouper is 25-41%. The heavy chains of both secreted and membrane anchored forms of salmon IgT include four constant Ig domains, τ1-τ4. This parallels the IgM heavy chains in elasmobranch fish and higher vertebrates, but differs from IgM in teleost fish where the membrane anchored form include only three constant Ig domains, μ1-μ3. The similarity between τ1 and μ1 in salmon is relatively high (52%) when compared to the remaining part of the molecules (τ2-τ4 and μ2-μ4 are 13-24% similar). To compare τ, μ and δ expressions in different tissues (head kidney, thymus, spleen, gill, skin, hind gut, brain and muscle) of Atlantic salmon, RT-qPCR assays were designed and evaluated. The analyses revealed that IgM transcripts are most abundant (up to 200 times more than IgD) followed by IgT (up to 20 times more than IgD) in most tissues. Highest expression of IgM, IgT, and IgD was in head kidney and spleen.

BackgroundThe ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach loss has occurred independently multiple times in the course of evolution. By assembling the ballan wrasse genome and transcriptome we aimed to determine the genetic basis for its digestive system function and appetite regulation. Among other, this knowledge will aid the formulation of aquaculture diets that meet the nutritional needs of agastric species.ResultsLong and short read sequencing technologies were combined to generate a ballan wrasse genome of 805 Mbp. Analysis of the genome and transcriptome assemblies confirmed the absence of genes that code for proteins involved in gastric function. The gene coding for the appetite stimulating protein ghrelin was also absent in wrasse. Gene synteny mapping identified several appetite-controlling genes and their paralogs previously undescribed in fish. Transcriptome profiling along the length of the intestine found a declining expression gradient from the anterior to the posterior, and a distinct expression profile in the hind gut.ConclusionsWe showed gene loss has occurred for all known genes related to stomach function in the ballan wrasse, while the remaining functions of the digestive tract appear intact. The results also show appetite control in ballan wrasse has undergone substantial changes. The loss of ghrelin suggests that other genes, such as motilin, may play a ghrelin like role. The wrasse genome offers novel insight in to the evolutionary traits of this large family. As the stomach plays a major role in protein digestion, the lack of genes related to stomach digestion in wrasse suggests it requires formulated diets with higher levels of readily digestible protein than those for gastric species.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4570-8) contains supplementary material, which is available to authorized users.

Background: Extensive sequencing efforts have been taking place for the Atlantic cod (Gadus morhua) in recent years, the number of ESTs in the Genbank has reached more than 140.000. Despite its importance in North Atlantic fisheries and potential use in aquaculture, relatively few gene expression examination exists for this species, and systematic evaluations of reference gene stability in quantitative real-time RT-PCR (qRT-PCR) studies are lacking.

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