A viral metagenomics strategy on a non-metagenomics experiment: mining next generation sequencing datasets from pig DNA pools.. Reduced Representation Libraries in pigs

In this study, we mined Ion Torrent reads obtained by sequencing DNA isolated from archived blood samples collected from 100 performance tested Italian Large White pigs. Two reduced representation libraries were prepared from two DNA pools constructed each from 50 equimolar DNA samples. A specific bioinformatics pipeline was designed to mine unmapped reads on the reference pig genome that were obtained from the two NGS datasets. Our approach identified sequences matching several viruses of the Parvoviridae family. This study demonstrated the potential of mining NGS datasets non originally derived by metagenomics experiments for viral metagenomics analyses in a livestock species.

本研究针对100头经性能测定的意大利大白猪的存档血液样本，提取其DNA并开展离子激流（Ion Torrent）测序，获取测序读段后进行挖掘分析。我们以50份等摩尔浓度的DNA样本分别构建两个DNA混合池，由此制备了两个简化基因组文库（reduced representation library）。针对这两个下一代测序（Next Generation Sequencing, NGS）数据集，我们设计了专属的生物信息学分析流程，用于筛选并挖掘在猪参考基因组上未比对上的测序读段。通过本研究的分析策略，我们成功鉴定出与细小病毒科（Parvoviridae）内多种病毒匹配的序列。本研究证实，将原本并非用于宏基因组实验的下一代测序数据集应用于畜禽物种的病毒宏基因组学分析具有可观的应用潜力。