Transcriptomic response to heat stress among ecologically divergent populations of redband trout

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Narum, Shawn R ^a   Campbell, Nathan R ^a  

^a Columbia River Inter Tribal Fish Commission ^*  (United States)

Author keywords

Climate change; Oncorhynchus mykiss gairdneri; Redband trout; RNA seq; Thermal adaptation; Transcriptome

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME; HEAT SHOCK PROTEIN;

ARTICLE; DESERT; DOWN REGULATION; ENVIRONMENTAL EXPOSURE; ENVIRONMENTAL IMPACT ASSESSMENT; GENE EXPRESSION; GILL; HEAT STRESS; NONHUMAN; POPULATION RESEARCH; RAINBOW TROUT; SEQUENCE ALIGNMENT; TEMPERATURE STRESS; UPREGULATION; WATER TEMPERATURE; ADAPTATION; ANIMAL; BIOSYNTHESIS; ECOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HEAT; HEAT SHOCK RESPONSE; ONCORHYNCHUS MYKISS; PHYSIOLOGY;

ONCORHYNCHUS MYKISS;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; ECOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HEAT-SHOCK PROTEINS; HEAT-SHOCK RESPONSE; HOT TEMPERATURE; ONCORHYNCHUS MYKISS;

EID: 84924905683     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1246-5     Document Type: Article

References (47)

1. Angilleta MJ. Thermal Adaptation: a Theoretical and Empirical Synthesis. Oxford: Oxford University Press; 2009.
2. Whitehead A, Galvez F, Zhang S, Williams LM, Oleksiak MF. Functional genomics of physiological plasticity and local adaptation in killifish. J Hered. 2011;102:499-511.
3. Dahlhoff EP, Rank NE. Functional and physiological consequences of genetic variation at phosphoglucose isomerase: Heat shock protein expression is related to enzyme genotype in a montane beetle. Proc Natl Acad Sci. 2000;97:10056-61.
4. Hoffman AA, Sorensen JG, Loeschcke V. Adaptation of Drosophila to temperature extremes: bringing together quantitative and molecular approaches. J Therm Biol. 2003;28:175-216.
5. Kavanagh KD, Haugen TO, Gregersen F, Jernvall J, Vollestad LA. Contemporary temperature-driven divergence in a Nordic freshwater fish under conditions commonly thought to hinder adaptation. BMC Evol Biol. 2010;10:350.
6. Keller I, Seehausen O. Thermal adaptation and ecological speciation. Mol Ecol. 2012;21:782-99.
7. Wolf JBW. Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial. Mol Ecol Res. 2013;13:559-72.
8. Morimoto RI, Sarge KD, Abravaya K. Transcriptional regulation of heat shock genes. J Biol Chem. 1992;267:21987-90.
9. Sørensen JG, Kristensen TN, Loeschcke V. The evolutionary and ecological role of heat shock proteins. Ecol Lett. 2003;6:1025-37.
10. Sørensen JG, Dahlgaard J, Loeschcke V. Genetic variation in thermal tolerance among natural populations of Drosophila buzzatii: down regulation of Hsp70 expression and variation in heat stress resistance traits. Funct Ecol. 2001;15:289-96.
11. Sørensen JG, Norry FM, Scannapieco AC, Loeschcke V. Altitudinal variation for stress resistance traits and thermal adaptation in adult Drosophila buzzatii from the New World. J Evol Biol. 2005;18:829-37.
12. Kassahn KS, Crozier RH, Ward AC, Stone G, Caley MJ. From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis. BMC Genomics. 2007;8:358.
13. Narum SR, Campbell NR, Kozfkay CC, Meyer KA. Adaptation of redband trout in desert and montane environments. Mol Ecol. 2010;19:4622-37.
14. Narum SR, Campbell NR, Meyer KA, Miller MR, Hardy RW. Thermal adaptation and acclimation of ectotherms from differing aquatic climates. Mol Ecol. 2013;22:3090-9097.
15. Pörtner HO, Knust R. Climate change affects marine fishes through the oxygen limitation of thermal tolerance. Science. 2007;315:95-7.
16. Gamperl AK, Rodnick KJ, Faust HA, Venn EC, Bennett MT, Crawshaw LI, et al. Metabolism, swimming performance, and tissue biochemistry of high desert redband trout (Oncorhynchus mykiss ssp.): evidence for phenotypic differences in physiological function. Physiol Biochem Zool. 2002;75:413-31.
17. Rodnick KJ, Gamperl AK, Lizars KR, Bennett MT, Rausch RN, Keeley ER. Thermal tolerance and metabolic physiology among redband trout populations in south-eastern Oregon. J Fish Biol. 2004;64:310-35.
18. Hornett EA, Wheat CW. Quantitative RNA-seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. BMC Genomics. 2012;13:361.
19. De Woody JA, Abts KC, Fahey AL, Ji Y, Kimble SJA, Marra NJ, et al. Of contig and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies. Mol Ecol Res. 2013;13:551-8.
20. Singal S. De novo transcriptomic analyses for non-model organisms: an evaluation of m ethods across a multi-species data set. Mol Ecol Res. 2013;13:403-16.
21. Sánchez CC, Weber GM, Gao G, Cleveland BM, Yao J, Rexroad CR. Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors. BMC Genomics. 2011;12:626.
22. Eliason EJ, Clark TD, Hague MJ, Hanson LM, Gallagher ZS, Jeffries KM, et al. Differences in thermal tolerance among sockeye salmon populations. Science. 2011;332:109-12.
23. Pörtner HO. Climate variations and the physiological basis of temperature dependent biogeography: systemic to molecular hierarchy of thermal tolerance in animals. Comp Biochem Physiol. 2002;132A:739-61.
24. Farrell AP. Environment, antecedants and climate change: lessons from the study of temperature physiology and river migration of salmonids. J Exp Biol. 2009;212:3771-80.
25. Cassinelli JD, Moffitt CM. Comparison of growth and stress in resident redband trout held in laboratory simulations of montane and desert summer temperature cycles. Trans Am Fish Soc. 2010;139:339-52.
26. Somero GN. The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine "winners" and "losers.". J Exp Biol. 2010;213:912-20.
27. Fangue NA, Nann AF, Hofmeister M, Schulte PM. Intraspecific variation in thermal tolerance and heat shock protein gene expression in common killifish, Fundulus heteroclitus. J Exp Biol. 2006;209:2859-72.
28. Dong Y, Somero GN. Temperature adaptation of cytosolic malate dehydrogenases of limpets (genus Lottia): differences in stability and function due to minor changes in sequence correlate with biogeographic and vertical distributions. J Exp Biol. 2008;212:169-77.
29. Miller KM, Li S, Kaukinen KH, Ginther N, Hammill E, Curtis JMR, et al. Genomic signatures predict migration and spawning failure in wild Canadian salmon. Science. 2011;331:214-7.
30. Fausch KD, Torgersen CE, Baxter CV, Li HW. Landscapes to riverscapes: bridging the gap between research and conservation of stream fishes. Bioscience. 2002;52:483-98.
31. Ficke AD, Myrick CA, Hansen LJ. Potential impacts of global climate change of freshwater fisheries. Rev Fish Biol Fisher. 2007;17:581-613.
32. Gustafson RG, Waples RS, Myers JM, Weitkamp LA, Bryant GJ, Johnson OW, et al. Pacific salmon extinctions: quantifying lost and remaining diversity. Conserv Biol. 2007;21:1009-20.
33. Perry AL, Low PJ, Ellis JR, Reynolds JD. Climate change and distribution shifts in marine fishes. Science. 2005;308:1912-5.
34. Wenger SJ, Isaak DJ, Luce C, Neville HM, Fausch KD, Dunham JB, et al. Flow regime, temperture, and biotic interactions drive differential declines of trout species under climate change. Proc Nat Acad Sci. 2011;108:14175-80.
35. Isaak DJ, Rieman BE. Stream isotherm shifts from climate change and implications for distributions of ectothermic organisms. Glob Change Biol. 2013;19:742-51.
36. Allendorf FW, Hohenlohe PA, Luikart G. Genomics and the future of conservation genetics. Nat Rev. 2010;11:697-709.
37. Cooke SJ, Sack L, Franklin CE, Farrell AP, Beardall J, Wikelski M, et al. What is conservation physiology? Perspectives on an increasingly integrated and essential science. Conserv Physiol. 2013;1:1-23.
38. Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA. Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol. 2013;22:2841-7.
39. Hoffmann AA, Sgro CM. Climate change and evolutionary adaptation. Nature. 2011;470:479-85.
40. Portner HO. Oxygen- and capacity-limitation of thermal tolerance: a matrix for integrating climate-related stressor effects in marine ecosystems. J Exp Biol. 2010;213:881-93.
41. Pandey RV, Franssen SU, Futschik A, Schlotterer C. Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data. Mol Ecol Res. 2013;13:740-5.
42. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
43. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40.
44. Dillies M-A, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform. 2012;10:1093.
45. McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40:4288-97.
46. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57:289-300.
47. Conesa A, Götz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674-6.