Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons from Multi-site Sampling

ABSTRACT: The experiment focused on the transcriptomic changes associated with gill inflammation in sea farmed Atlantic salmon (Salmo salar). To ensure the multifactorial aspect of gill inflammation, fish were sampled at three marine production sites (A on Isle of Mull, B in Shetland and C in Shetland) between October 2017 and March 2018. All fish were of strain Fanad and originated from the same egg fertilisation batch. They were reared in different hatcheries (Couldoran, Pettigo-Damph and Knock-Frisa for sites A, B and C, respectively) for one year and entered the sea in spring 2017. The resultant gill tissues (44 samples in total with 1 gill sample per fish) were first scored for proliferative gill disease (PGD), using gross morphology PGD scores from 0 with no visual pathology to 5 with severe visual pathology, and then subjected to RNA-seq and histopathological (microscopic) examination. One RNA-seq sample (fish 95) was identified as an outlier and removed from the subsequent analysis. As a result, the analysis aiming to integrate gill transcriptome, gross morphology and histopathology was performed on 43 gill samples, classified either as PGD score 1 (n = 26) or PGD score 3 (n = 17). In total, 20 gill samples originated from site A (10 with PGD1 and 10 with PGD 3, 10 samples from site B (7 with PGD1 and 3 with PGD 3) and 13 samples from site C (9 with PGD1 and 4 with PGD 3).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Salmo salar

SUBMITTER: Elzbieta Krol

PROVIDER: E-MTAB-8855 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The aim of this experiment was to explore transcriptomic changes in the gills of Altantic salmon (Salmo salar) following a model lab based parr smolt transformation from fresh water (FW) to salt water (SW). The process of smoltification (migration from FW to SW) is stimulated by long day photoperiod, which acts on the tissue-specific levels of active thyroid hormone (triiodothyronine, T3) through the expression of thyroid hormone type 2 deiodinase (dio2), responsible for conversion of inactive thyroxine (T4) to T3. To gain insight into the functional significance of dio2 induction, we performed a SW-challenge experiment in which we inhibited dio2 activity by addition of iopanoic acid (IOP) to the SW. We also assessed the ability of co-treatment with T3 to override IOP effects. Juvenile fish maintained in FW were subjected to a standard smolt photoperiod regime known to stimulate smoltification, after which they were randomly allocated to one of the four treatments: SW, SW+IOP, SW+IOP+T3 and FW as a control. Fish (n = 8-10 per treatment) were exposed to these conditions for 6 h and then sacrificed to obtain gill tissue for microarray analysis, carried out using a custom-designed Agilent oligonucleotide microarray platform Salar_2 (one glass slide with 4 x 44K arrays, Agilent design ID: 025520, array design A-MEXP-2065), developed and validated for Atlantic salmon (for details, see specific protocols) . In total, 36 hybridisations were performed on gills from individual fish, with 8-10 replicate fish per treatment. We identified 1939 genes whose expression was significantly increased or decreased by transfer from FW to SW. For a subset of 259 genes, this SW response was abolished if IOP was added to the SW, but maintained if T3 was also present during IOP treatment. This group of genes constitutes a candidate list, for which SW-inducibility appears to be dependent on locally mediated changes in gill T3 availability. The results of this experiment have been submitted for publication in Current Biology and are currently under review.

Dataset Information

Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons from Multi-site Sampling

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