Transcriptomic characterization of tambaqui (Colossoma macropomum, Cuvier, 1818) exposed to three climate change scenarios

Abstract

Climate change substantially affects biodiversity around the world, especially in the Amazon region, which is home to a significant portion of the world's biodiversity. Freshwater fishes are susceptible to increases in water temperature and variations in the concentrations of dissolved gases, especially oxygen and carbon dioxide. It is important to understand the mechanisms underlying the physiological and biochemical abilities of fishes to survive such environmental changes. In the present study, we applied RNA-Seq and de novo transcriptome sequencing to evaluate transcriptome alterations in tambaqui when exposed to five or fifteen days of the B1, A1B and A2 climate scenarios foreseen by the IPCC. The generated ESTs were assembled into 54,206 contigs. Gene ontology analysis and the STRING tool were then used to identify candidate protein domains, genes and gene families potentially responsible for the adaptation of tambaqui to climate changes. After sequencing eight RNA-Seq libraries, 32,512 genes were identified and mapped using the Danio rerio genome as a reference. In total, 236 and 209 genes were differentially expressed at five and fifteen days, respectively, including chaperones, energetic metabolism-related genes, translation initiation factors and ribosomal genes. Gene ontology enrichment analysis revealed that mitochondrion, protein binding, protein metabolic process, metabolic processes, gene expression, structural constituent of ribosome and translation were the most represented terms. In addition, 1,202 simple sequence repeats were detected, 88 of which qualified for primer design. These results show that cellular response to climate change in tambaqui is complex, involving many genes, and it may be controlled by different cues and transcription/translation regulation mechanisms. The data generated from this study provide a valuable resource for further studies on the molecular mechanisms involved in the adaptation of tambaqui and other closely related teleost species to climate change.