14Background 15 The full scope of the genes expressed by schistosomes during intramolluscan development 16 has yet to be characterized. Understanding the gene products deployed by larval schistosomes 17 in their snail hosts will provide insights into their establishment, maintenance, asexual 18 reproduction, ability to castrate their hosts, and their prolific production of human-infective 19 cercariae. Using the Illumina platform, the intramolluscan transcriptome of Schistosoma 20 mansoni was investigated in field-derived specimens of the prominent vector species 21 Biomphalaria pfeifferi at 1 and 3 days post infection (d) and from snails shedding cercariae. 22 These S. mansoni samples were derived from the same snails used in our complementary B. 23 pfeifferi transcriptomic study. We supplemented this view with microarray analyses of S. 24 mansoni from B. glabrata at 2d, 4d, 8d, 16d, and 32d. 25 Principal Findings 26 Transcripts representing at least 7,740 (66%) of known S. mansoni genes were expressed 27 during intramolluscan development, with the greatest number expressed in snails shedding 28 cercariae. Many transcripts were constitutively expressed throughout development featuring 29 membrane transporters, and metabolic enzymes involved in protein and nucleic acid synthesis 30 and cell division. Several proteases and protease inhibitors were expressed at all stages, 31 including some proteases usually associated with cercariae. Transcripts associated with G-32 protein coupled receptors, germ cell perpetuation, and stress responses and defense were well 33 represented. We noted transcripts homologous to planarian anti-bacterial factors, several neural 34 development or neuropeptide transcripts including neuropeptide Y, and receptors that may be 2 35 associated with schistosome germinal cell maintenance and that could also impact host 36 reproduction. In at least one snail the presence of larvae of another digenean species (an 37 amphistome) was associated with repressed S. mansoni transcriptional activity. 38 Conclusions/Significance 39 This in vivo study, particularly featuring field-derived snails and schistosomes, provides a 40 distinct view from previous studies of development of cultured intramolluscan stages from lab-41 maintained organisms. We found many highly represented transcripts with suspected or 42 unknown functions, with connection to intramolluscan development yet to be elucidated. 43 44 AUTHOR SUMMARY 45 Schistosoma mansoni is one of the most important schistosome species causing the 46 neglected tropical disease human intestinal schistosomiasis. By focusing on S. mansoni in vivo 47 58 59 65 responsible for causing human disease -pose fundamental questions of interest for 66 parasitologists, evolutionary biologists, ecologists, developmental biologists and comparative 67 immunologists. 3 68 There is much about digenean-gastropod associations worthy of study: the host specificity 69 often shown; the manner by which digeneans establish intimate infections without provoking 70 ...