Using Illumina Next Generation Sequencing Technologies to sequence multigene families in de novo species

The advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene family, for species with and without a reference genome. We develop novel assembly methods to annotate and filter these data, which can be utilized for any gene family or any species. We find no significant difference between the ratio of genes within their respective gene families of our data compared with available genomic data. Using simulated data we explore the limitations of short-read sequence data and our assembly in recovering this gene family. We highlight...

下一代测序技术（Next Generation Sequencing Technology, NGST）的问世革新了分子生物学研究领域，使我们能够快速对众多不同物种的基因或基因组开展测序工作。随着高通量测序技术愈发普及，亟需开发更高效的分析流程以应对其产出的海量数据，并更好地完成对从头构建谱系的基因组组装工作。本研究将传统实验室实验方法与Illumina下一代测序技术相结合，针对携带参考基因组与未携带参考基因组的物种，对哺乳动物中规模最大的多基因家族——嗅觉受体基因家族（Olfactory Receptor gene family）进行扩增与测序。我们开发了全新的组装方法用于注释与过滤上述测序数据，该方法可推广应用于任意基因家族或任意物种的相关研究。经对比发现，本研究数据中各基因家族内的基因占比与现有公开基因组数据相比无显著差异。本研究借助模拟测序数据，探究了短读长测序数据以及本研究采用的组装方法在复原该基因家族过程中存在的局限性，并着重阐明了……