title: Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel.
abstract: BACKGROUND
  Genomic 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.
  
  
  RESULTS
  To 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.
  
  
  CONCLUSIONS
  Together 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.
authors.affiliation: Department of Biology, University of Padova, Italy. martipujolar@gmail.com
authors.forename: Jose Martin
authors.initials: JM
authors.lastname: Pujolar
authors.forename: Ilaria A M
authors.initials: IA
authors.lastname: Marino
authors.forename: Massimo
authors.initials: M
authors.lastname: Milan
authors.forename: Alessandro
authors.initials: A
authors.lastname: Coppe
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Maes
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Capoccioni
authors.forename: Eleonora
authors.initials: E
authors.lastname: Ciccotti
authors.forename: Lieven
authors.initials: L
authors.lastname: Bervoets
authors.forename: Adrian
authors.initials: A
authors.lastname: Covaci
authors.forename: Claude
authors.initials: C
authors.lastname: Belpaire
authors.forename: Gordon
authors.initials: G
authors.lastname: Cramb
authors.forename: Tomaso
authors.initials: T
authors.lastname: Patarnello
authors.forename: Luca
authors.initials: L
authors.lastname: Bargelloni
authors.forename: Stefania
authors.initials: S
authors.lastname: Bortoluzzi
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Zane
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D051544:Cytochrome P-450 CYP3A / Q000235:genetics / Q000378:metabolism; D004524:Eels / Q000235:genetics*; D004579:Electron Transport / Q000235:genetics; D056727:Endangered Species; D004787:Environmental Pollution; D005411:Flame Retardants / Q000633:toxicity*; D015870:Gene Expression / Q000187:drug effects*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects*; D055106:Genome-Wide Association Study; D005979:Glutathione Peroxidase / Q000235:genetics / Q000378:metabolism; D005982:Glutathione Transferase / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D007558:Italy; D008969:Molecular Sequence Data; D010085:Oxidative Phosphorylation / Q000187:drug effects; D010575:Pesticides / Q000633:toxicity*; D059467:Transcriptome; D014874:Water Pollutants, Chemical / Q000633:toxicity*; D015027:Zebrafish / Q000235:genetics
chemical_list: D005411:Flame Retardants; D010575:Pesticides; D014874:Water Pollutants, Chemical; D005979:Glutathione Peroxidase; D051544:Cytochrome P-450 CYP3A; D005982:Glutathione Transferase