Bioproject ID: PRJNA268960

bioproject id PRJNA268960      to NCBI
key word Migration; RNAseq; transcriptome; PARR-SMOLT TRANSFORMATION; RNA-SEQ DATA; ATLANTIC SALMON; CANDIDATE GENES; CHINOOK SALMON; GROWTH-HORMONE; RAINBOW-TROUT; THYROID-HORMONES; PACIFIC SALMON; COHO SALMON
experiment type migration
publication Mckinney, G. J. , et al. "Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss." Molecular Ecology 24.8(2015).
description RNAseq used to examine gene expression in divergent migrant and resident populations of rainbow trout that share a recent coancestry
abstract Little information has been gathered regarding the ontogenetic changes that contribute to differentiation between resident and migrant individuals, particularly before the onset of gross morphological and physiological changes in migratory individuals. The aim of this study was to evaluate gene expression during early development in Oncorhynchus mykiss populations with different life histories, in a tissue known to integrate environmental cues to regulate complex developmental processes and behaviours. We sampled offspring produced from migrant and resident parents, collecting whole embryos prior to the beginning of first feeding, and brain tissue at three additional time points over the first year of development. RNA sequencing for 32 individuals generated a reference transcriptome of 30177 genes that passed count thresholds. Differential gene expression between migrant and resident offspring was observed for 1982 genes. The greatest number of differentially expressed genes occurred at 8months of age, in the spring a full year before the obvious physiological transformation from stream-dwelling parr to sea water-adaptable smolts begins for migrant individuals. Sex and age exhibited considerable effects on differential gene expression between migrants and resident offspring. Differential gene expression was observed in genes previously associated with migration, but also in genes previously unassociated with early life history divergence. Pathway analysis revealed coordinated differential expression in genes related to phototransduction, which could modulate photoperiod responsiveness and variation in circadian rhythms. The role for early differentiation in light sensitivity and biological rhythms is particularly intriguing in understanding early brain processes involved in differentiation of migratory and resident life history types.

Sample Information

sample id sample name tissue strain treatment description
1. SRR1692327 Hatch_116-3 Embryo nan Sashin Lake nan
2. SRR1692348 June_29-3 Brain nan Sashin Lake nan
3. SRR1692351 Oct_3-1 Brain nan Sashin Creek nan
4. SRR1692345 June_20-1 Brain nan Sashin Lake nan
5. SRR1692300 Feb_2-3 Brain nan Sashin Creek nan
6. SRR1692343 June_3-1 Brain nan Sashin Creek nan
7. SRR1692311 Hatch_69-9 Embryo nan Sashin Creek nan
8. SRR1692341 June_1-1 Brain nan Sashin Creek nan
9. SRR1692344 June_6-1 Brain nan Sashin Creek nan
10. SRR1692346 June_21-3 Brain nan Sashin Lake nan
11. SRR1692302 Feb_3-5 Brain nan Sashin Creek nan
12. SRR1692304 Feb_21-4 Brain nan Sashin Lake nan
13. SRR1692308 Feb_29-5 Brain nan Sashin Lake nan
14. SRR1692355 Oct_28-3 Brain nan Sashin Lake nan
15. SRR1692299 Feb_1-2 Brain nan Sashin Creek nan
16. SRR1692349 Oct_1-2 Brain nan Sashin Creek nan
17. SRR1692354 Oct_21-3 Brain nan Sashin Lake nan
18. SRR1692306 Feb_28-2 Brain nan Sashin Lake nan
19. SRR1692312 Hatch_74-8 Embryo nan Sashin Creek nan
20. SRR1692313 Hatch_106-4 Embryo nan Sashin Lake nan
21. SRR1692325 Hatch_107-3 Embryo nan Sashin Lake nan
22. SRR1692352 Oct_6-4 Brain nan Sashin Creek nan
23. SRR1692360 Oct_29-4 Brain nan Sashin Lake nan
24. SRR1692347 June_28-3 Brain nan Sashin Lake nan
25. SRR1692353 Oct_20-2 Brain nan Sashin Lake nan
26. SRR1692305 Feb_21-5 Brain nan Sashin Lake nan
27. SRR1692309 Hatch_66-3 Embryo nan Sashin Creek nan
28. SRR1692340 Hatch_117-4 Embryo nan Sashin Lake nan
29. SRR1692342 June_2-3 Brain nan Sashin Creek nan
30. SRR1692310 Hatch_69-8 Embryo nan Sashin Creek nan
31. SRR1692350 Oct_2-2 Brain nan Sashin Creek nan
32. SRR1692303 Feb_6-5 Brain nan Sashin Creek nan