Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress
Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress
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DOI：
10.1007/s10646-012-0977-1
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发表时间：
2012-11-01
期刊：
影响因子：
2.7
通讯作者：
Coutellec, Marie-Agnes
中科院分区：
文献类型：
--
作者：
Bouetard, Anthony;Noirot, Celine;Coutellec, Marie-Agnes
由于能够探索全基因组对药物和压力源的反应，基于组学的方法被广泛应用于毒理学和生态毒理学，并被确定为未来生态风险评估和环境监测计划的有力工具。了解污染物的长期影响可能确实受益于基因组学和生态进化假设的结合。下一代测序提供了一种研究污染物影响的新方法，通过靶向早期反应，筛选化学物质，直接量化基因表达，甚至在没有参考基因组的生物体中也是如此。海扁豆是一种淡水软体动物，其基因组资源的获取对许多科学问题至关重要，特别是在生态毒理学方面。我们利用454焦磷酸测序技术获得了停滞L.的新的转录组资源，并初步探讨了对氧化还原循环农药diquat的基因表达响应。我们分别从对照组和暴露于diquat的个体中获得了151,967和128,945个高质量的reads。序列组装提供了141,999个contigs，其中124,387个是单例。BlastX搜索显示34.6%的contigs（21.2%的protein hits）显著匹配。KEGG注释显示，与能量代谢和循环系统相关的基因占主导地位，并发现了400多个可能与氧化应激、细胞/分子应激和信号通路、细胞凋亡和外源代谢有关的基因。结果还表明，diquat可能具有多种分子效应。此外，还发现了新的遗传标记（假定的snp）。我们还创建了一个类似于ensembl的数据挖掘web工具（http://genotoul-contigbrowser.toulouse.inra.fr:9095/Lymnaea_stagnalis/index.html）。这一资源有望为任何旨在了解L.停滞藻对环境胁迫的生理和进化反应的分子基础的基因组方法提供相关信息。
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.