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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Parasitic Diseases Laboratory » Research » Research Project #430794

Research Project: Developing a Pipeline for Helminth Parasite Genomics

Location: Animal Parasitic Diseases Laboratory

Project Number: 8042-32000-105-06-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 15, 2016
End Date: Dec 31, 2017

(1) Characterize and interpret genomes of a diverse assemblage of parasitic helminths. (2) Whole genome sequencing (~80X coverage, utilizing Illumina HiSeq technology) will be explored for the first time in order to better understand genetic diversity among poorly studied mammalian and avian tapeworms belonging to the Hymenolepididae and Anoplocephalidae and to other groups including mammalian nematodes. (3) Our aim is develop high-coverage genome sequencing and assembly that can lead to the first reference genomes for these parasite taxa serving as a foundation and resource for future studies in comparative biology, host-parasite associations and disease dynamics. (4) Identify loci and larger genomic regions experiencing special regimes of selection in parasitic taxa. (5) Construct a foundation for understanding patterns of diversity, host-parasite associations, faunal assembly, and historical responses to climate change and environmental perturbation for parasitic helminths. By extension, these data provide a model framework for exploring more general concepts about effects of climate change on the distribution of parasites and disease across managed and wild systems. (6) Our aim is to provide genome assemblies which contain or represent orders of magnitude more information than is presently available for most parasitic helminths and nematodes. Due to high species diversity this system will be developed as a model for phylogenomic work in this nascent field. (7) Our aim is to develop detailed phylogenomic data enabling us, and others, to explore how environmental disruption influences biological diversity.

Novel whole genome sequences of non-medical tapeworms and nematodes provide a considerable expansion of knowledge about fundamental processes of evolution and elucidation of species limits and historical biogeography of complex host-parasite systems. Understanding genomic structure across an assemblage of parasite taxa contributes directly to a foundation and resource to explore patterns of biodiversity, host-parasite associations, faunal assembly and historical responses to climate change in complex biological systems. Whole genome sequencing will be achieved for 40-50 parasite species (focusing on poorly known taxa of mammalian and avian parasites) with estimated 80X coverage through Ilumina HiSeq technology. Specimens are derived from field-based and cryo-preserved collections, not replicated in any museum archive, representing the culmination of 20 years of NSF sponsored field inventories in North America, Eurasia, Africa and SE Asia conducted in collaboration between Museum of Southwestern Biology (MSB) and ARS scientists. Specimens for inclusion in sequencing and analyses are selected according to protocols and criteria developed by MSB and ARS. In the pipeline- (1) general laboratory work, DNA extractions, and development of the NGS (next gen sequencing) library will be completed at MSB; (2) Sequencing runs on an Ilumina Hi-Seq 2500 instrument will be completed at the Keck Center at University of Illinois (UI); (3) Data analysis will be shared among MSB, UI and ARS and completed on the UNM super computer (Center for Advanced Research Computing) including quality control, trimming, genomic assembly and bioinformatics analysis pipelines; (4) Interpretation relative to comparative informatics, evolution and biogeography will emerge through collaboration with ARS, MSB and UI, leading to co-authored publications.