Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel

Abstract

BackgroundGenomic and transcriptomic approaches have the potential for unveiling the genome-wide response to environmental perturbations. The abundance of the catadromous European eel (Anguilla anguilla) stock has been declining since the 1980s probably due to a combination of anthropogenic and climatic factors. In this paper, we explore the transcriptomic dynamics between individuals from high (river Tiber, Italy) and low pollution (lake Bolsena, Italy) environments, which were measured for 36 PCBs, several organochlorine pesticides and brominated flame retardants and nine metals.ResultsTo this end, we first (i) updated the European eel transcriptome using deep sequencing data with a total of 640,040 reads assembled into 44,896 contigs (Eeelbase release 2.0), and (ii) developed a transcriptomic platform for global gene expression profiling in the critically endangered European eel of about 15,000 annotated contigs, which was applied to detect differentially expressed genes between polluted sites. Several detoxification genes related to metabolism of pollutants were upregulated in the highly polluted site, including genes that take part in phase I of the xenobiotic metabolism (CYP3A), phase II (glutathione-S-transferase) and oxidative stress (glutathione peroxidase). In addition, key genes in the mitochondrial respiratory chain and oxidative phosphorylation were down-regulated at the Tiber site relative to the Bolsena site.ConclusionsTogether with the induced high expression of detoxification genes, the suggested lowered expression of genes supposedly involved in metabolism suggests that pollution may also be associated with decreased respiratory and energy production.

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

“…Therefore, it is not surprising that RNA-seq has become the technology of choice for quantifying differential gene expression (Deng et al, 2011;Smith et al, 2013). Gene expression analyses have allowed the identification of key molecular mechanisms underlying desired traits in farmed fish (Roberge et al, 2006;Ferraresso et al, 2008Ferraresso et al, , 2013, but have also been successfully applied to natural populations of marine fishes (Whitehead and Crawford, 2006;Larsen et al, 2007Larsen et al, , 2011Pujolar et al, 2012Pujolar et al, , 2013bCôté et al, 2014). Finally, transcriptomic analyses can be complemented and integrated with protein expression analysis to investigate the responses at the proteomic level for a deeper understanding of functional implications (Nie et al, 2007;Dalziel and Schulte, 2012).…”

Detecting genome-wide gene transcription profiles associated with high pollution burden in the critically endangered European eel

“…However, largescale transcriptomic approaches in eels have been limited to the study of osmoregulation (Kalujnaia et al, 2007) and a comparative gene transcription analysis between larvae of European and American eels ) using a 6000-probe microarray. Only recently a preliminary study has been conducted using an eel-specific microarray of 14,913 annotated cDNAs to compare two groups of silver eel males at two Italian sites with varying levels of pollution (Pujolar et al, 2012). In the present study, we extend the analysis to investigate the molecular responses to bioaccumulation levels in female silver eels across habitats with different levels of exposure to environmental pollutants.…”

Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa

“…Under extreme environmental stress, the immune system of fish is greatly compromised, and thus, genes with functions related to immune response such as AEBP1 are expected to be under strong positive selection in stressful environments. Members of the CYP family (including CYP3A40 with the highest dN/dS of 2.606 in our study) have been associated with detoxification processes such as in the European eel (Pujolar et al 2012). Owing to high levels of ROS and other free radicals associated with numerous stresses in Lake Magadi (Johannsson et al 2014), genes that promote their destruction would be selectively propagated in the genome.…”