Schistosoma japonicum ddRADseq raw sequence reads

Schistosomiasis is a devastating tropical disease that affects more than 200 million people worldwide. Over the past several decades, transmission control strategies implemented in China have reduced the prevalence and morbidity of Schistosoma japonicum in many areas. Infections still persist, however, and it is therefore of great interest to determine the sources of recurring infections and genetic analysis is a promising means to achieve this. Towards this aim, we conducted a pilot study to assess the feasibility of using high throughput sequencing to assess the geographic distribution of schistosome genetic variants. Because DNA yields from miracidia, the most easily accessible life stage, are insufficient for high throughput sequencing, we first employed whole genome amplification to obtain sufficient quantities of DNA. We then employed a technique, double digest restriction-site associated DNA sequencing, that reproducibly sequences the same fraction of a genome across numerous samples. We successfully sequenced eight 6-year old S. japonicum samples from Sichuan Province, China and a single adult worm sample originating from Anhui Province, China, easily and economically identifying tens of thousands of variable loci, a sufficient number to discriminate fine-scale population structure. Further population sampling will help answer important questions concerning the persistence of infections, the sources of new infections, and whether parasite populations have undergone incipient evolution of drug resistance.