Schistosomiasis is a neglected tropical disease that affects more than 200 million people in the developing world. Currently only a single drug (praziquantel) is available to treat this disease, highlighting the importance of developing new techniques to study these parasites. Although important tools exist to study Schistosoma (e.g. genome sequences and RNA interference), the complexity of the schistosome life cycle continues to hinder progress towards developing novel therapeutics. Specifically, large-scale, unbiased functional genomic screens to identify new drug targets are currently not possible. With the long-term goal of identifying novel therapeutic targets in Schistosoma, our current objective is to use the experimentally tractable free-living flatworm S. mediterranea as a model to identify and decipher the function of flatworm-specific genes. Despite their divergent lifestyles (free-living vs. parasitic), these animals share many fundamental similarities, both at the anatomic and genomic levels. Given these similarities, our hypothesis is that many processes essential for physiology, reproduction, and viability are deeply conserved between these flatworms. To address this hypothesis we propose the following two specific aims: (1) Identify flatworm-specific genes required for viability or reproduction and (2) Develop novel techniques to disrupt adult schistosome gene function in vivo. In the first aim, we will use high-throughput in situ hybridization to compare the tissue-specific expression of 108 flatworm-specific genes in Schistosoma mansoni and S. mediterranea. We will also determine the loss-of-function phenotype for these genes in S. mediterranea using RNA interference. These studies will provide a candidate gene list for in vivo functional studies proposed in specific aim #2. Since it is presently not possible to genetically manipulate adult schistosomes in vivo, our second aim will determine if vivo-morpholinos can induce gene knockdown in adult schistosome tissues inside infected mice. These approaches will be used to examine if genes identified in specific aim #1 have important roles in schistosome biology in vivo. These studies are innovative because they (i) introduce S. mediterranea as a model to accelerate functional genomic studies of Schistosoma and (ii) develop morpholino-based techniques to genetically manipulate adult schistosomes in the mammalian host. These studies are significant since they describe a potentially potent workflow for anti-schistosomal target discovery: large-scale screening in S. mediterranea and in vivo candidate validation using vivo-morpholinos. Collectively, our studies will attempt to fill important gaps in functional genomic studies of parasitic flatworms and have the potential to identify new therapeutic targets in Schistosoma.