title: Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms.
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 evolutionary associations. Molecular markers available for the Cyclophyllidea mostly include ribosomal DNA and mitochondrial loci. In this study, we identified 3641 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 3284 (90%) of the targets from the test samples and then used captured sequences (2 181 361 bp in total; fragment size ranging from 301 to 6969 bp) to reconstruct a phylogeny for the five test species plus the three species for which genomic data are available. The results were consistent with 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 polymorphisms (SNPs) from alignments of four Arostrilepis macrocirrosa and two A. cooki and successfully inferred their relationships. The results showed that our target gene tools yield data sets that provide robust inferences at a range of taxonomic scales in the Cyclophyllidea.
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Yuan
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
authors.forename: Jiamei
authors.initials: J
authors.lastname: Jiang
authors.affiliation: Department of Zoology, Southern Illinois University, Carbondale, IL, 62901, USA.
authors.forename: Francisco Agustín
authors.initials: FA
authors.lastname: Jiménez
authors.affiliation: US National Parasite Collection and Animal Parasitic Disease Laboratory, USDA Agricultural Research Service, BARC East No. 1180, 10300 Baltimore Avenue, Beltsville, MD, 20705, USA.
authors.forename: Eric P
authors.initials: EP
authors.lastname: Hoberg
authors.affiliation: Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Cook
authors.affiliation: Department of Biology, Northern Michigan University, Marquette, MI, 49855, USA.
authors.forename: Kurt E
authors.initials: KE
authors.lastname: Galbreath
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
authors.forename: Chenhong
authors.initials: C
authors.lastname: Li
mesh_terms: D000818:Animals; D002589:Cestoda / Q000145:classification* / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D019143:Evolution, Molecular; D005091:Exons; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D009693:Nucleic Acid Hybridization / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D013048:Specimen Handling / Q000379:methods*; D059467:Transcriptome
chemical_list: D015345:Oligonucleotide Probes; D004247:DNA
keywords: cestodes; gene capture; next-generation sequencing; nuclear markers; phylogenetics; phylogeography