Location: Animal Parasitic Diseases LaboratoryTitle: Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms
|YUAN, HAO - Shanghai Ocean University|
|JIANG, JAIMEI - Shanghai Ocean University|
|JIMINEZ, F.A. - Southern Illinois University|
|COOK, J.A. - University Of New Mexico|
|GALBREATH, K.E. - Northern Michigan University|
|LI, CHENGHONG - Shanghai Ocean University|
Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/6/2016
Publication Date: 1/6/2016
Citation: Yuan, H., Jiang, J., Jiminez, F., Hoberg, E.P., Cook, J., Galbreath, K., Li, C. 2016. Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms. Molecular Ecology Resources. 16:1095-1106.
Interpretive Summary: The Cyclophyllidea is the most diverse order of tapeworms, encompassing species that infect all classes of terrestrial tetrapods including humans and domesticated food and companion animals. This group of tapeworms contains the most significant pathogens of humans, and notably the taeniid tapeworms that include Taenia solium regarded as the most important food-borne parasite globally. Understanding phylogeny (evolutionary relationships) for these parasites is an essential cornerstone in developing measures for control and mitigation of infections on the global stage. Available phylogenetic reconstructions based either on morphology or molecular data lack the resolution to allow scientists to either propose a solid taxonomy or infer their evolutionary associations. In a pilot study using next generation DNA protocols we applied target gene enrichment and Illumina methods to capture new genetic data among this group of tapeworm parasites. Our results showed that our target gene tools could be applied to both phylogenetic and phylogeographic (distributions of populations and species) studies in the Cyclophyllidea. Methods developed and validated will be expected to have broad generality across the parasitological community in demonstrating a pathway for development of new critical data for resolution of questions about diversity by a broad spectrum of academic and governmental organizations and scientists.
Technical Abstract: 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 their evolutionary associations. Molecular markers available for the phylogenetic reconstruction of the Cyclophyllidea are mostly ribosomal DNA and mitochondrial loci. In this study, we identified 3,641 single-copy nuclear coding loci through the comparison of the genomes of Hymenolepis microstoma, Echinococcus granulosus, and Taenia solium. We designed RNA baits based on the sequence of H. microstoma, and tested the utility of those markers for phylogenetic analyses by applying target gene enrichment and Illumina sequencing methods to capture genetic data from five species of tapeworms representing two families and genera of cyclophyllideans , Schizorchis and Arostrilepis. We obtained an average of 3,284 (90%) targets from the test samples and then used captured sequences (2,181,361 bp in total; fragment size ranging from 301 bp to 6,969 bp) to reconstruct a phylogeny for the five test species along with the three species for which genomic data are available. The results corroborated the current consensus regarding cyclophyllidean relationships. To assess the potential for our method to yield informative genetic variation at intraspecific scales, we extracted 14,074 single nucleotide polymorphism (SNP) sites from alignments of four Arostrilepis macrocirrosa and two Arostrilepis cooki and successfully inferred their relationships across space. The results showed that our target gene tools could be applied to both phylogenetic and phylogeographic studies in the Cyclophyllidea.