Bioproject ID: PRJNA478787

bioproject id PRJNA478787      to NCBI
key word temperature;Cold stress;Multiple tissues;Tropical stenothermal fish;Ubiquitin-mediated protein degradation;Heat shock 70 KDa protein;Cold-induced RNA-binding protein;RNA-BINDING PROTEIN;TILAPIA OREOCHROMIS-NILOTICUS;DIFFERENTIAL GENE-EXPRESSION;HSP70 MESSENGER-RNA;HEAT-SHOCK RESPONSE;GILTHEAD SEA BREAM;NILE TILAPIA;PHYSIOLOGICAL-RESPONSES;THERMAL-STRESS;COMMON CARP
experiment type temperature
publication Liu, Lili , et al. "Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb ( Puntius tetrazona )." BMC Genomics 21.1(2020).
description tiger barb Raw sequence reads
abstract Background Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. The tiger barb Puntius tetrazona is a tropical stenothermal fish, with great popularity in aquarium trade and research. Results To investigate the response mechanism of P. tetrazona to low temperature, fish were exposed to increasing levels of acute cold stress. Histopathological analysis showed that the brain, gill, liver and muscle tissues appeared serious damage after cold stress (13 degrees C). Brain, gill, liver and muscle tissues from control (CTRL) groups (27 degrees C) and COLD stress groups (13 degrees C) of eight-month fish (gender-neutral) were sampled and assessed for transcriptomic profiling by high-throughput sequencing. 83.0 Gb of raw data were generated, filtered and assembled for de novo transcriptome assembly. According to the transcriptome reference, we obtained 392,878 transcripts and 238,878 unigenes, of which 89.29% of the latter were annotated. There were 23,743 differently expressed genes (DEGs) been filtered from four pairs of tissues (brain, gill, liver and muscle) between these cold stress and control groups. These DEGs were mainly involved in circadian entrainment, circadian rhythm, biosynthesis of steroid and fatty acid. There were 64 shared DEGs between the four pairs of groups, and five were related to ubiquitylation/deubiquitylation. Our results suggested that ubiquitin-mediated protein degradation might be necessary for tropical stenothermal fish coping with acute cold stress. Also, the significant cold-induced expression of heat shock 70 kDa protein (HSP70) and cold-induced RNA-binding protein (CIRBP) was verified. These results suggested that the expression of the molecular chaperones HSP70 and CIRBP in P. tetrazona might play a critical role in coping with acute cold stress. Conclusions This is the first transcriptome analysis of P. tetrazona using RNA-Seq technology. Novel findings about tropical stenothermal fish under cold stress (such as HSP70 and CIRBP genes) are presented here. This study contributes new insights into the molecular mechanisms of tropical stenothermal species response to acute cold stress.

Sample Information

sample id sample name tissue strain treatment description
1. SRR7507732 27muscleB muscle nan 27C RNA-seq of tiger barb: adult muscle-27C
2. SRR7507733 27liverD liver nan 27C RNA-seq of tiger barb: adult liver-27C
3. SRR7507734 27gillA gill nan 27C RNA-seq of tiger barb: adult gill-27C
4. SRR7507735 27brainC brain nan 27C RNA-seq of tiger barb: adult brain-27C
5. SRR7507736 27brainB brain nan 27C RNA-seq of tiger barb: adult brain-27C
6. SRR7507737 27brainA brain nan 27C RNA-seq of tiger barb: adult brain-27C
7. SRR7507738 27liverB liver nan 27C RNA-seq of tiger barb: adult liver-27C
8. SRR7507739 27liverA liver nan 27C RNA-seq of tiger barb: adult liver-27C
9. SRR7507740 27gillC gill nan 27C RNA-seq of tiger barb: adult gill-27C
10. SRR7507741 27gillB gill nan 27C RNA-seq of tiger barb: adult gill-27C
11. SRR7507742 13liverC liver nan 13C RNA-seq of tiger barb: adult liver-13C
12. SRR7507743 13muscleA muscle nan 13C RNA-seq of tiger barb: adult muscle-13C
13. SRR7507744 13muscleB muscle nan 13C RNA-seq of tiger barb: adult muscle-13C
14. SRR7507745 13muscleC muscle nan 13C RNA-seq of tiger barb: adult muscle-13C
15. SRR7507746 13liverB liver nan 13C RNA-seq of tiger barb: adult liver-13C
16. SRR7507747 13liverA liver nan 13C RNA-seq of tiger barb: adult liver-13C
17. SRR7507748 27muscleD muscle nan 27C RNA-seq of tiger barb: adult muscle-27C
18. SRR7507749 27muscleC muscle nan 27C RNA-seq of tiger barb: adult muscle-27C
19. SRR7507750 13brainB brain nan 13C RNA-seq of tiger barb: adult brain-13C
20. SRR7507751 13brainA brain nan 13C RNA-seq of tiger barb: adult brain-13C
21. SRR7507752 13gillA gill nan 13C RNA-seq of tiger barb: adult gill-13C
22. SRR7507753 13brainC brain nan 13C RNA-seq of tiger barb: adult brain-13C
23. SRR7507754 13gillC gill nan 13C RNA-seq of tiger barb: adult gill-13C
24. SRR7507755 13gillB gill nan 13C RNA-seq of tiger barb: adult gill-13C