title: Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia.
abstract: In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans. Here, we present a method using next generation sequencing to provide high-resolution genomic data from S. japonicum for population-based studies.
  
  
  
  We applied whole genome amplification followed by double digest restriction site associated DNA sequencing (ddRADseq) to individual S. japonicum miracidia preserved on Whatman FTA cards. We found that we could effectively and consistently survey hundreds of thousands of variants from 10,000 to 30,000 loci from archived miracidia as old as six years. An analysis of variation from eight miracidia obtained from three hosts in two villages in Sichuan showed clear population structuring by village and host even within this limited sample.
  
  
  
  This high-resolution sequencing approach yields three orders of magnitude more information than microsatellite genotyping methods that have been employed over the last decade, creating the potential to answer detailed questions about the sources of human infections and to monitor drug resistance. Costs per sample range from $50-$200, depending on the amount of sequence information desired, and we expect these costs can be reduced further given continued reductions in sequencing costs, improvement of protocols, and parallelization. This approach provides new promise for using modern genome-scale sampling to S. japonicum surveillance, and could be applied to other schistosome species and other parasitic helminthes.
authors.affiliation: Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Shortt
authors.affiliation: Department of Biology, University of Texas Arlington, Arlington, TX, United States of America.
authors.forename: Daren C
authors.initials: DC
authors.lastname: Card
authors.affiliation: Department of Biology, University of Texas Arlington, Arlington, TX, United States of America.
authors.forename: Drew R
authors.initials: DR
authors.lastname: Schield
authors.affiliation: Institute of Parasitic Disease, Sichuan Center for Disease Control and Prevention, Chengdu, The People's Republic of China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Institute of Parasitic Disease, Sichuan Center for Disease Control and Prevention, Chengdu, The People's Republic of China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhong
authors.affiliation: Department of Biology, University of Texas Arlington, Arlington, TX, United States of America.
authors.forename: Todd A
authors.initials: TA
authors.lastname: Castoe
authors.affiliation: Department of Environmental and Occupational Health, University of Colorado, Colorado School of Public Health, Aurora, CO, United States of America.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Carlton
authors.affiliation: Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: David D
authors.identifier: 0000-0002-7627-4214
authors.initials: DD
authors.lastname: Pollock
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D005260:Female; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D018895:Microsatellite Repeats; D010865:Pilot Projects; D012549:Schistosoma japonicum / Q000235:genetics*; D012554:Schistosomiasis japonica / Q000453:epidemiology; D017422:Sequence Analysis, DNA