Open Access Highly Accessed Research article

RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species

Steve Smith13, Louis Bernatchez2 and Luciano B Beheregaray1*

Author Affiliations

1 Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia

2 Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada

3 Current address: Department für Integrative Biologie und Evolution, Veterinärmedizinische Universität Wien, Vienna 1160, Austria

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BMC Genomics 2013, 14:375  doi:10.1186/1471-2164-14-375

Published: 5 June 2013

Abstract

Background

Identifying genes of adaptive significance in a changing environment is a major focus of ecological genomics. Such efforts were restricted, until recently, to researchers studying a small group of model organisms or closely related taxa. With the advent of next generation sequencing (NGS), genomes and transcriptomes of virtually any species are now available for studies of adaptive evolution. We experimentally manipulated temperature conditions for two groups of crimson spotted rainbowfish (Melanotaenia duboulayi) and measured differences in RNA transcription between them. This non-migratory species is found across a latitudinal thermal gradient in eastern Australia and is predicted to be negatively impacted by ongoing environmental and climatic change.

Results

Using next generation RNA-seq technologies on an Illumina HiSeq2000 platform, we assembled a de novo transcriptome and tested for differential expression across the treatment groups. Quality of the assembly was high with a N50 length of 1856 bases. Of the 107,749 assembled contigs, we identified 4251 that were differentially expressed according to a consensus of four different mapping and significance testing approaches. Once duplicate isoforms were removed, we were able to annotate 614 up-regulated transfrags and 349 that showed reduced expression in the higher temperature group.

Conclusions

Annotated blast matches reveal that differentially expressed genes correspond to critical metabolic pathways previously shown to be important for temperature tolerance in other fish species. Our results indicate that rainbowfish exhibit predictable plastic regulatory responses to temperature stress and the genes we identified provide excellent candidates for further investigations of population adaptation to increasing temperatures.

Keywords:
Rainbowfish; Melanotaenia duboulayi; Transcriptomes; Climate change; Thermal adaptation