Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms

The Cyclophyllidea is the most diverse order of tapeworms, encompassing species that infect all classes of terrestrial tetrapods including humans and domesticated animals. Available phylogenetic reconstructions based either on morphology or molecular data lack the resolution to allow scientists to either propose a solid taxonomy or infer evolutionary associations. Molecular markers available for the Cyclophyllidea mostly include ribosomal DNA and mitochondrial loci. In this study, we identified 3,641 single-copy nuclear coding loci by comparing the genomes of Hymenolepis microstoma, Echinococcus granulosus, and Taenia solium. We designed RNA baits based on the sequence of H. microstoma, and applied target enrichment and Illumina sequencing to test the utility of those baits to recover loci useful for phylogenetic analyses. We captured DNA from five species of tapeworms representing two families of cyclophyllideans. We obtained an average of 3,284 (90%) of the targets from the test sampl...圆叶目（Cyclophyllidea）是多样性最高的绦虫目，其物种可感染包括人类与家养动物在内的所有陆生四足类类群。现有基于形态学或分子数据的系统发育重建分辨率不足，既无法为科研人员构建可靠的分类学体系，亦难以准确推断演化关联。目前适用于圆叶目绦虫的分子标记多为核糖体DNA与线粒体基因座。本研究通过对比缩小膜壳绦虫（Hymenolepis microstoma）、细粒棘球绦虫（Echinococcus granulosus）与猪带绦虫（Taenia solium）的基因组，共鉴定出3641个单拷贝核编码基因座。我们以缩小膜壳绦虫的序列为基础设计RNA诱饵，并通过靶向富集结合Illumina测序技术，验证了该类诱饵用于获取系统发育分析所需基因座的实用性。我们从代表圆叶目2个科的5种绦虫样本中成功捕获DNA。本次实验平均从待测样本中获取了3284个目标基因座（占比90%）……