Journal Article

Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress

Coutellec, Marie-Agnès, Besnard, Anne-Laure, Klopp, Christophe, Bouetard, Anthony, Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Laboratoire de Génétique Cellulaire (LGC), Noirot, Celine, Écologie et santé des écosystèmes (ESE), Choisne, Damien, Bouchez, Olivier, Robe, Eugénie, Lagadic, Laurent

2012

Overview

Due to their ability to explore whole genome response to drugs and stressors, omics-based approaches are widely used in toxicology and ecotoxicology, and identified as powerful tools for future ecological risk assessment and environmental monitoring programs. Understanding the long-term effects of contaminants may indeed benefit from the coupling of genomics and eco-evolutionary hypotheses. Next-generation sequencing provides a new way to investigate pollutants impact, by targeting early responses, screening chemicals, and directly quantifying gene expression, even in organisms without reference genome. Lymnaea stagnalis is a freshwater mollusk in which access to genomic resources is critical for many scientific issues, especially in ecotoxicology. We used 454-pyrosequencing to obtain new transcriptomic resources in L. stagnalis and to preliminarily explore gene expression response to a redox-cycling pesticide, diquat. We obtained 151,967 and 128,945 high-quality reads from control and diquat-exposed individuals, respectively. Sequence assembly provided 141,999 contigs, of which 124,387 were singletons. BlastX search revealed significant match for 34.6% of the contigs (21.2% protein hits). KEGG annotation showed a predominance of hits with genes involved in energy metabolism and circulatory system, and revealed more than 400 putative genes involved in oxidative stress, cellular/molecular stress and signaling pathways, apoptosis, and metabolism of xenobiotics. Results also suggest that diquat may have a great diversity of molecular effects. Moreover, new genetic markers (putative SNPs) were discovered. We also created a Ensembl-like web-tool for data-mining ( http://genotoul-contigbrowser.toulouse.inra.fr:9095/Lymnaea_stagnalis/index.html ). This resource is expected to be relevant for any genomic approach aimed at understanding the molecular basis of physiological and evolutionary responses to environmental stress in L. stagnalis.

• Publisher: Springer Verlag,CCSD,Springer US,Springer,Springer Nature B.V
• Subject: Animals / apoptosis / circulatory system / Contaminants / Data mining / Databases, Genetic / Diquat / Diquat - pharmacology / DNA sequencing / drug effects / Earth and Environmental Science / Ecology / Ecotoxicology / energy metabolism / Environment / environmental assessment / Environmental impact / Environmental Management / Environmental monitoring / Environmental stress / Ethylenediaminetetraacetic acid / Expressed Sequence Tags / Freshwater / freshwater molluscs / Freshwater mollusks / Gene expression / Gene Expression Profiling / Genes / Genetic markers / Genetic research / genetics / Genomes / Genomics / Herbicides / Herbicides - pharmacology / Life Sciences / long term effects / Lymnaea / Lymnaea - drug effects / Lymnaea - genetics / Lymnaea stagnalis / Marine / Mollusca / Mollusks / Nucleotide sequencing / Oxidative stress / Pesticides / pharmacology / pollutants / Risk assessment / screening / Sequence Analysis, DNA / single nucleotide polymorphism / snails / Toxicology / Transcriptome / Xenobiotics
• ISBN: 0003126649000