Bioproject ID: PRJNA659524

bioproject id PRJNA659524      to NCBI
key word Challenge, strain, high growth rates, immune performance, Flavobacterium psychrophilum
experiment type challenge
publication nan
description Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during baterial infection with Flavobacterium psychrophilum (rainbow trout)
abstract Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain’s superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental bacterial infection with Flavobacterium psychrophilum (Fp) (CSF 259-93), the causative agent of bacterial cold water disease (BCWD) in salmonids. At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with Fp by intramuscular injection and one control tank was mock challenged by sham injection. Sampling was conducted at 5 days post challenge (dpc) (Early Infection) and 21 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. The select strain of trout showed significantly better survival rates (Log-Rank Test, p < 0.0001) over the 21 day infection period, with 70 and 95 % mortality among the select and commercial strain, respectively. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status. Overall design: At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. There were three infected tanks and one mock challenged tank per strain. Intestinal samples were collected from all tanks at 5 days post challenge (dpc) and 21 dpc. Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. At each time point, there are 6 pooled samples of infected fish and 2 pooled samples of mock challenged fish per strain. However, due to high mortality in the commercial strain, only one tank of infected commercial trout was sampled at 21 dpc.

Sample Information

sample id sample name tissue strain treatment description
1. SRR12523305 GSM4748358 intestine Flavobacterium psychrophilum TF1-21dpc-1: Commercial 21dpc BCWD TF1 BiologicalRep1 nan
2. SRR12523306 GSM4748359 intestine Flavobacterium psychrophilum TF1-21dpc-2: Commercial 21dpc BCWD TF1 BiologicalRep2 nan
3. SRR12523307 GSM4748360 intestine Flavobacterium psychrophilum TFC-21dpc-1: Commercial 21dpc BCWD_Sham TFControl BiologicalRep1 nan
4. SRR12523308 GSM4748361 intestine Flavobacterium psychrophilum TFC-21dpc-2: Commercial 21dpc BCWD_Sham TFControl BiologicalRep2 nan
5. SRR12523309 GSM4748362 intestine Flavobacterium psychrophilum CF1-21dpc-1: Select 21dpc BCWD CF1 BiologicalRep1 nan
6. SRR12523310 GSM4748363 intestine Flavobacterium psychrophilum CF1-21dpc-2: Select 21dpc BCWD CF1 BiologicalRep2 nan
7. SRR12523311 GSM4748364 intestine Flavobacterium psychrophilum CF2-21dpc-1: Select 21dpc BCWD CF2 BiologicalRep1 nan
8. SRR12523312 GSM4748365 intestine Flavobacterium psychrophilum CF2-21dpc-2: Select 21dpc BCWD CF2 BiologicalRep2 nan
9. SRR12523313 GSM4748366 intestine Flavobacterium psychrophilum CF3-21dpc-1: Select 21dpc BCWD CF3 BiologicalRep1 nan
10. SRR12523314 GSM4748367 intestine Flavobacterium psychrophilum CF3-21dpc-2: Select 21dpc BCWD CF3 BiologicalRep2 nan
11. SRR12523315 GSM4748368 intestine Flavobacterium psychrophilum CFC-21dpc-1: Select 21dpc BCWD_Sham CFControl BiologicalRep1 nan
12. SRR12523316 GSM4748369 intestine Flavobacterium psychrophilum CFC-21dpc-2: Select 21dpc BCWD_Sham CFControl BiologicalRep2 nan
13. SRR12523317 GSM4748370 intestine Flavobacterium psychrophilum TF1-5dpc-1: Commercial 5dpc BCWD TF1 BiologicalRep1 nan
14. SRR12523318 GSM4748371 intestine Flavobacterium psychrophilum TF1-5dpc-2: Commercial 5dpc BCWD TF1 BiologicalRep2 nan
15. SRR12523319 GSM4748372 intestine Flavobacterium psychrophilum TF2-5dpc-1: Commercial 5dpc BCWD TF2 BiologicalRep1 nan
16. SRR12523320 GSM4748373 intestine Flavobacterium psychrophilum TF2-5dpc-2: Commercial 5dpc BCWD TF2 BiologicalRep2 nan
17. SRR12523321 GSM4748374 intestine Flavobacterium psychrophilum TF3-5dpc-1: Commercial 5dpc BCWD TF3 BiologicalRep1 nan
18. SRR12523322 GSM4748375 intestine Flavobacterium psychrophilum TF3-5dpc-2: Commercial 5dpc BCWD TF3 BiologicalRep2 nan
19. SRR12523323 GSM4748376 intestine Flavobacterium psychrophilum TFC-5dpc-1: Commercial 5dpc BCWD_Sham TFControl BiologicalRep1 nan
20. SRR12523324 GSM4748377 intestine Flavobacterium psychrophilum TFC-5dpc-2: Commercial 5dpc BCWD_Sham TFControl BiologicalRep2 nan
21. SRR12523325 GSM4748378 intestine Flavobacterium psychrophilum CF1-5dpc-1: Select 5dpc BCWD CF1 BiologicalRep1 nan
22. SRR12523326 GSM4748379 intestine Flavobacterium psychrophilum CF1-5dpc-2: Select 5dpc BCWD CF1 BiologicalRep2 nan
23. SRR12523327 GSM4748380 intestine Flavobacterium psychrophilum CF2-5dpc-1: Select 5dpc BCWD CF2 BiologicalRep1 nan
24. SRR12523328 GSM4748381 intestine Flavobacterium psychrophilum CF2-5dpc-2: Select 5dpc BCWD CF2 BiologicalRep2 nan
25. SRR12523329 GSM4748382 intestine Flavobacterium psychrophilum CF3-5dpc-1: Select 5dpc BCWD CF3 BiologicalRep1 nan
26. SRR12523330 GSM4748383 intestine Flavobacterium psychrophilum CF3-5dpc-2: Select 5dpc BCWD CF3 BiologicalRep2 nan
27. SRR12523331 GSM4748384 intestine Flavobacterium psychrophilum CFC-5dpc-1: Select 5dpc BCWD_Sham CFControl BiologicalRep1 nan
28. SRR12523332 GSM4748385 intestine Flavobacterium psychrophilum CFC-5dpc-2: Select 5dpc BCWD_Sham CFControl BiologicalRep2 nan