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Background   Schistosoma japonicum  is a pathogen of the phylum Platyhelminthes that causes zoonotic schistosomiasis in China and Southeast Asian countries where a lack of efficient measures has hampered disease control. The development of tools for diagnosis of acute and chronic infection and for novel antiparasite reagents relies on understanding the biological mechanisms that the parasite exploits.    Results  In this study, the polyadenylated transcripts from the male and female  S. japonicum  were sequenced using a high-throughput RNA-seq technique. Bioinformatic and experimental analyses focused on post-transcriptional RNA processing, which revealed extensive alternative splicing events in the adult stage of the parasite. The numbers of protein-coding sequences identified in the transcriptomes of the female and male  S. japonicum  were 15,939 and 19,501 respectively, which is more than predicted from the annotated genome sequence. Further, we identified four types of post-transcriptional processing, or alternative splicing, in both female and male worms of  S. japonicum : exon skipping, intron retention, and alternative donor and acceptor sites. Unlike mammalian organisms, in  S. japonicum , the alternative donor and acceptor sites were more common than the other two types of post-transcriptional processing. In total, respectively 13,438 and 16,507 alternative splicing events were predicted in the transcriptomes of female and male  S. japonicum .    Conclusions  By using RNA-seq technology, we obtained the global transcriptomes of male and female  S. japonicum . These results further provide a comprehensive view of the global transcriptome of  S. japonicum.  The findings of a substantial level of alternative splicing events dynamically occurring in  S. japonicum  parasitization of mammalian hosts suggest complicated transcriptional and post-transcriptional regulation mechanisms employed by the parasite. These data should not only significantly improve the re-annotation of the genome sequences but also should provide new information about the biology of the parasite.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-715) contains supplementary material, which is available to authorized users.

Genome-wide transcriptome analysis shows extensive alternative RNA splicing in the zoonotic parasite Schistosoma japonicum