A specific PCR assay for the identification and differentiation of Schistosoma japonicum geographical isolates in mainland China based on analysis of mitochondrial genome sequences

► Eight mt genome sequences for Schistosoma japonicum samples from seven provinces in China were analyzed. ► The S. japonicum mt genomes from lower Yangtze provinces were 2 bp shorter than those from SW China. ► Sequence differences among the eight mt genomes of S. japonicum samples were 0.20-2.51%. ► A specific PCR assay was developed for the differentiation of S. japonicum geographical isolates. ► This PCR assay would provide a useful tool for tracing the source of S. japonicum infection in China.