C. King, K. Dickman, and D. Tisch, Reassessment of the cost of chronic helmintic infection: a meta-analysis of disability-related outcomes in endemic schistosomiasis, The Lancet, vol.365, issue.9470, pp.1561-1569, 2005.
DOI : 10.1016/S0140-6736(05)66457-4

P. Steinmann, J. Keiser, R. Bos, M. Tanner, and J. Utzinger, Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk, The Lancet Infectious Diseases, vol.6, issue.7, pp.411-425, 2006.
DOI : 10.1016/S1473-3099(06)70521-7

C. King, Parasites and poverty: The case of schistosomiasis, Acta Tropica, vol.113, issue.2, pp.95-104, 2010.
DOI : 10.1016/j.actatropica.2009.11.012

C. King, Schistosomiasis: challenges and opportunities Institute of Medicine (US) Forum on Microbial Threats. The Causes and Impacts of Neglected Tropical and Zoonotic Diseases: Opportunities for Integrated Intervention Strategies National Academies Press (US), p.21977543, 2011.

M. Doenhoff, P. Hagan, D. Cioli, V. Southgate, and L. Pica-mattoccia, Praziquantel: its use in control of schistosomiasis in sub-Saharan Africa and current research needs, Parasitology, vol.101, issue.13, pp.1825-1835, 2009.
DOI : 10.1007/BF00547377

P. Fallon and M. Doenhoff, Drug resistant schistosomiasis: Resistance to praziquantel and oxaminquine induced in Schistosoma mansoni in mice is drug specific, Am J Trop Med Hyg, vol.51, pp.83-88, 1994.

S. Melman, M. Steinauer, C. Cunningham, L. Kubatko, and I. Mwangi, Reduced susceptibility of Kenyan Schistosoma mansoni to praziquantel following repeated exposures: origin, measurement , and likelihood of persistence, PLoS Negl Trop Dis, vol.3, 2009.

A. Fenwick, J. Webster, E. Bosque-oliva, L. Blair, and F. Fleming, The Schistosomiasis Control Initiative (SCI): rationale, development and implementation from 2002???2008, Parasitology, vol.97, issue.13, pp.1719-1730, 2002.
DOI : 10.1186/1741-7015-5-27

K. Esvelt, A. Smidler, F. Catteruccia, and G. Church, Author response, eLife, vol.106, p.25035423, 2014.
DOI : 10.7554/eLife.03401.019

M. Berriman, B. Haas, P. Loverde, R. Wilson, and G. Dillon, The genome of the blood fluke Schistosoma mansoni, Nature, vol.46, issue.7253, pp.352-358, 2009.
DOI : 10.1038/nature08160

A. Lockyer, J. Spinks, R. Kane, K. Hoffmann, and J. Fitzpatrick, Biomphalaria glabrata transcriptome: cDNA microarray profiling identifies resistant- and susceptible-specific gene expression in haemocytes from snail strains exposed to Schistosoma mansoni, BMC Genomics, vol.9, issue.1, pp.634-644, 2008.
DOI : 10.1186/1471-2164-9-634

C. Adema, P. Hanington, C. Lun, G. Rosenberg, and A. Aragon, Differential transcriptomic responses of Biomphalaria glabrata (Gastropoda, Mollusca) to bacteria and metazoan parasites, Schistosoma mansoni and Echinostoma paraensei (Digenea, Platyhelminthes), Molecular Immunology, vol.47, issue.4, 2010.
DOI : 10.1016/j.molimm.2009.10.019

C. Richards and P. Shade, The Genetic Variation of Compatibility in Biomphalaria glabrata and Schistosoma mansoni, The Journal of Parasitology, vol.73, issue.6, pp.1146-1151, 1987.
DOI : 10.2307/3282295

C. Richards, M. Knight, and F. Lewis, Genetics of Biomphalaria glabrata and its effect on the outcome of Schistosoma mansoni infection, Parasitology Today, vol.8, issue.5, pp.171-174, 1992.
DOI : 10.1016/0169-4758(92)90015-T

J. Webster and M. Woolhouse, Selection and Strain Specificity of Compatibility between Snail Intermediate Hosts and Their Parasitic Schistosomes, Evolution, vol.52, issue.6, pp.1627-1643, 1998.
DOI : 10.2307/2411336

M. Knight, A. Miller, C. Patterson, C. Rowe, and G. Michaels, The identification of markers segregating with resistance to Schistosoma mansoni infection in the snail Biomphalaria glabrata, Proceedings of the National Academy of Sciences, vol.96, issue.4, pp.1510-1515, 1999.
DOI : 10.1073/pnas.96.4.1510

J. Webster, C. Gower, and L. Blair, System, The American Naturalist, vol.164, issue.S5, pp.33-51, 2004.
DOI : 10.1086/424607

C. Bayne, Successful parasitism of vector snail Biomphalaria glabrata by the human blood fluke (trematode) Schistosoma mansoni: A 2009 assessment, Molecular and Biochemical Parasitology, vol.165, issue.1, pp.8-18, 2009.
DOI : 10.1016/j.molbiopara.2009.01.005

E. Loker, Gastropod Immunobiology, Adv Exp Med Biol, vol.708, pp.17-43, 2010.
DOI : 10.1007/978-1-4419-8059-5_2

G. Mitta, C. Adema, B. Gourbal, E. Loker, and A. Théron, Compatibility polymorphism in snail/schistosome interactions: From field to theory to molecular mechanisms, Developmental & Comparative Immunology, vol.37, issue.1, p.21945832, 2012.
DOI : 10.1016/j.dci.2011.09.002

URL : https://hal.archives-ouvertes.fr/halsde-00631055

R. Waterhouse, E. Kriventseva, S. Meister, Z. Xi, and K. Alvarez, Evolutionary Dynamics of Immune-Related Genes and Pathways in Disease-Vector Mosquitoes, Science, vol.316, issue.5832, pp.1738-1743, 2007.
DOI : 10.1126/science.1139862

D. Severson and S. Behura, Mosquito Genomics: Progress and Challenges, Annual Review of Entomology, vol.57, issue.1, pp.143-166, 2012.
DOI : 10.1146/annurev-ento-120710-100651

P. Hanington, M. Forys, J. Dragoo, S. Zhang, and C. Adema, Role for a somatically diversified lectin in resistance of an invertebrate to parasite infection, Proceedings of the National Academy of Sciences, vol.107, issue.49, pp.21087-21092, 2010.
DOI : 10.1073/pnas.1011242107

P. Hanington, M. Forys, and E. Loker, A Somatically Diversified Defense Factor, FREP3, Is a Determinant of Snail Resistance to Schistosome Infection, PLoS Neglected Tropical Diseases, vol.9, issue.Pt 4, p.22479663, 2012.
DOI : 10.1371/journal.pntd.0001591.s001

W. Ittiprasert and M. Knight, Reversing the Resistance Phenotype of the Biomphalaria glabrata Snail Host Schistosoma mansoni Infection by Temperature Modulation, PLoS Pathogens, vol.55, issue.3, p.22577362, 2012.
DOI : 10.1371/journal.ppat.1002677.g007

C. Goodall, R. Bender, J. Brooks, and C. Bayne, Biomphalaria glabrata cytosolic copper/zinc superoxide dismutase (SOD1) gene: Association of SOD1 alleles with resistance/susceptibility to Schistosoma mansoni, Molecular and Biochemical Parasitology, vol.147, issue.2, pp.207-210, 2006.
DOI : 10.1016/j.molbiopara.2006.02.009

K. Bonner, C. Bayne, M. Laurson, and M. Blouin, Effects of Cu/Zn Superoxide Dismutase (sod1) Genotype and Genetic Background on Growth, Reproduction and Defense in Biomphalaria glabrata, PLoS Neglected Tropical Diseases, vol.21, issue.6, p.22724037, 2012.
DOI : 10.1371/journal.pntd.0001701.s001

P. Basch, An interpretation of snail-trematode infection rates: Specificity based on concordance of compatible phenotypes, International Journal for Parasitology, vol.5, issue.4, pp.449-452, 1975.
DOI : 10.1016/0020-7519(75)90012-0

C. Richards, Genetic factors in susceptibility of Biomphalaria glabrata for different strains of Schistosoma mansoni, Parasitology, vol.70, issue.02, pp.231-241, 1975.
DOI : 10.1017/S0031182000049696

J. Webster and M. Woolhouse, Selection and Strain Specificity of Compatibility between Snail Intermediate Hosts and Their Parasitic Schistosomes, Evolution, vol.52, issue.6, pp.1627-1634, 1998.
DOI : 10.2307/2411336

A. Théron, A. Rognon, B. Gourbal, and G. Mitta, Multi-parasite host susceptibility and multi-host parasite infectivity: A new approach of the Biomphalaria glabrata/Schistosoma mansoni compatibility polymorphism, Infection, Genetics and Evolution, vol.26, pp.80-88, 2014.
DOI : 10.1016/j.meegid.2014.04.025

A. Théron, C. Coustau, A. Rognon, S. Gourbiere, and M. Blouin, Effects of laboratory culture on compatibility between snails and schistosomes, Parasitology, vol.60, issue.10, pp.1179-1188, 2008.
DOI : 10.2307/3285775

S. Nuismer and S. Otto, Host-parasite interactions and the evolution of ploidy, Proceedings of the National Academy of Sciences, vol.101, issue.30, pp.11036-11039, 2004.
DOI : 10.1073/pnas.0403151101

J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko, Stacks: an analysis tool set for population genomics, Molecular Ecology, vol.61, issue.Suppl 1, pp.3124-3140, 2013.
DOI : 10.1111/mec.12354

M. Pahl, O. Askinazi, C. Hamilton, I. Cheng, and K. Cichewicz, Signalling via Single-Pass Transmembrane Proteins, 2013.
DOI : 10.1002/9780470015902.a0025160

C. Adema, M. Luo, B. Hanelt, L. Hertel, and J. Marshall, A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni, Mem??rias do Instituto Oswaldo Cruz, vol.101, pp.167-177, 2006.
DOI : 10.1590/S0074-02762006000900027

R. Sawada and S. Mitaku, How are exons encoding transmembrane sequences distributed in the exon-intron structure of genes?, Genes to Cells, vol.20, issue.1, pp.115-136, 2011.
DOI : 10.1111/j.1365-2443.2010.01468.x

A. Skerra, Engineered protein scaffolds for molecular recognition, Journal of Molecular Recognition, vol.2, issue.4, pp.167-187, 2000.
DOI : 10.1002/1099-1352(200007/08)13:4<167::AID-JMR502>3.0.CO;2-9

E. Roger, C. Grunau, R. Pierce, H. Hirai, and B. Gourbal, Controlled Chaos of Polymorphic Mucins in a Metazoan Parasite (Schistosoma mansoni) Interacting with Its Invertebrate Host (Biomphalaria glabrata), PLoS Neglected Tropical Diseases, vol.20, issue.23, 2008.
DOI : 10.1371/journal.pntd.0000330.s002

URL : https://hal.archives-ouvertes.fr/halsde-00344615

C. Adema, L. Hertel, R. Miller, and E. Loker, A family of fibrinogen-related proteins that precipitates parasite-derived molecules is produced by an invertebrate after infection, Proceedings of the National Academy of Sciences, vol.94, issue.16, pp.8691-8696, 1997.
DOI : 10.1073/pnas.94.16.8691

Y. Moné, B. Gourbal, D. Duval, D. Pasquier, L. Kieffer-jaquinod et al., A Large Repertoire of Parasite Epitopes Matched by a Large Repertoire of Host Immune Receptors in an Invertebrate Host/Parasite Model, PLoS Neglected Tropical Diseases, vol.462, issue.Pt 3, p.20838648, 2010.
DOI : 10.1371/journal.pntd.0000813.t004

D. Charlesworth, Balancing Selection and Its Effects on Sequences in Nearby Genome Regions, PLoS Genetics, vol.88, issue.4, pp.64-16683038, 2006.
DOI : 0016-6731(1978)088[0149:HAAEFL]2.0.CO;2

K. Nam and H. Ellegren, Recombination Drives Vertebrate Genome Contraction, PLoS Genetics, vol.10, issue.5, p.22570634, 2012.
DOI : 10.1371/journal.pgen.1002680.s009

C. Sire, P. Durand, J. Pointier, and A. Théron, Genetic Diversity and Recruitment Pattern of Schistosoma mansoni in a Biomphalaria glabrata Snail Population: A Field Study Using Random-Amplified Polymorphic DNA Markers, The Journal of Parasitology, vol.85, issue.3, pp.436-441, 1999.
DOI : 10.2307/3285775

D. Begun, A. Holloway, K. Stevens, L. Hillier, and Y. Poh, Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans, PLoS Biology, vol.302, issue.11, pp.310-17988176, 2007.
DOI : 10.1371/journal.pbio.0050310.sd021

S. Meagher and W. Potts, A Microsatellite-Based MHC Genotyping System for House Mice (Mus domesticus), Hereditas, vol.10, issue.1-2, pp.75-82, 1997.
DOI : 10.1111/j.1601-5223.1997.00075.x

C. Roux, M. Pauwels, M. Ruggiero, D. Charlesworth, and V. Castric, Recent and Ancient Signature of Balancing Selection around the S-Locus in Arabidopsis halleri and A. lyrata, Molecular Biology and Evolution, vol.30, issue.2, pp.435-447, 2013.
DOI : 10.1093/molbev/mss246

URL : https://hal.archives-ouvertes.fr/hal-00860473

P. Hedrick, PATHOGEN RESISTANCE AND GENETIC VARIATION AT MHC LOCI, Evolution, vol.2, issue.10, pp.1902-1908, 2002.
DOI : 10.1146/annurev.mi.33.100179.001221

L. Desprès, D. Imbert-establet, and M. Monnerot, Molecular characterization of mitochondrial DNA provides evidence for the recent introduction of Schistosoma mansoni into America, Molecular and Biochemical Parasitology, vol.60, issue.2, pp.221-230, 1993.
DOI : 10.1016/0166-6851(93)90133-I

D. Blair, G. Davis, and B. Wu, Evolutionary relationships between trematodes and snails emphasizing schistosomes and paragonimids, Parasitology, vol.123, issue.07, pp.229-243, 2001.
DOI : 10.1017/S003118200100837X

N. Takahata, Y. Satta, and J. Klein, Polymorphism and balancing selection at major histocompatibility complex loci, Genetics, vol.130, pp.925-938, 1992.

J. Tennessen and M. Blouin, Balancing Selection at a Frog Antimicrobial Peptide Locus: Fluctuating Immune Effector Alleles?, Molecular Biology and Evolution, vol.25, issue.12, p.18799711, 2008.
DOI : 10.1093/molbev/msn208

A. Andrés, M. Hubisz, A. Indap, D. Torgerson, and J. Degenhardt, Targets of Balancing Selection in the Human Genome, Molecular Biology and Evolution, vol.26, issue.12, pp.2755-2764, 2009.
DOI : 10.1093/molbev/msp190

M. Riehle, K. Markianos, O. Niaré, J. Xu, and J. Li, Natural Malaria Infection in Anopheles gambiae Is Regulated by a Single Genomic Control Region, Science, vol.312, issue.5773, pp.577-579, 2006.
DOI : 10.1126/science.1124153

D. Obbard, D. Callister, F. Jiggins, D. Soares, and G. Yan, The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiae, BMC Evolutionary Biology, vol.8, issue.1, pp.274-18840262, 2008.
DOI : 10.1186/1471-2148-8-274

S. Rottschaefer, M. Riehle, B. Coulibaly, M. Sacko, and O. Niaré, Exceptional Diversity, Maintenance of Polymorphism, and Recent Directional Selection on the APL1 Malaria Resistance Genes of Anopheles gambiae, PLoS Biology, vol.5, issue.3, p.21408087, 2011.
DOI : 10.1371/journal.pbio.1000600.s006

S. Hulbert, C. Webb, S. Smith, and Q. Sun, : Evolution and Utilization, Annual Review of Phytopathology, vol.39, issue.1, pp.285-312, 2001.
DOI : 10.1146/annurev.phyto.39.1.285

J. Trowsdale and S. Powis, The MHC: relationship between linkage and function, Current Opinion in Genetics & Development, vol.2, issue.3, pp.492-497, 1992.
DOI : 10.1016/S0959-437X(05)80163-7

M. Marrelli, C. Li, J. Rasgon, and M. Jacobs-lorena, Transgenic malaria-resistant mosquitoes have a fitness advantage when feeding on Plasmodium-infected blood, Proceedings of the National Academy of Sciences, vol.104, issue.13, pp.5580-5583, 2007.
DOI : 10.1073/pnas.0609809104

M. Wise-de-valdez, D. Nimmo, J. Betz, H. Gong, and A. James, Genetic elimination of dengue vector mosquitoes, Proceedings of the National Academy of Sciences, vol.108, issue.12, pp.4772-4775, 2011.
DOI : 10.1073/pnas.1019295108

B. Garcia, A. Pierce, R. Gourbal, B. Werkmeister, E. Colinet et al., Involvement of the cytokine MIF in the snail host immune response to the parasite Schistosoma mansoni, PLoS Pathog, vol.6, p.20886098, 2010.
URL : https://hal.archives-ouvertes.fr/halsde-00608628

M. Knight, A. Miller, Y. Liu, P. Scaria, and M. Woodle, Polyethyleneimine (PEI) Mediated siRNA Gene Silencing in the Schistosoma mansoni Snail Host, Biomphalaria glabrata, PLoS Neglected Tropical Diseases, vol.2, issue.7, p.21765961, 2011.
DOI : 10.1371/journal.pntd.0001212.g006

N. Baird, P. Etter, T. Atwood, M. Currey, and A. Shiver, Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers, PLoS ONE, vol.428, issue.10, p.18852878, 2008.
DOI : 10.1371/journal.pone.0003376.g003

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009.
DOI : 10.1093/bioinformatics/btp324

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234

L. Zhivotovsky, Estimating population structure in diploids with multilocus dominant DNA markers, Molecular Ecology, vol.18, issue.6, pp.907-913, 1999.
DOI : 10.1017/S0953756297003791

G. Marçais and C. Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, vol.27, issue.6, pp.764-770, 2001.
DOI : 10.1093/bioinformatics/btr011

J. Simpson, K. Wong, S. Jackman, J. Schein, and S. Jones, ABySS: A parallel assembler for short read sequence data, Genome Research, vol.19, issue.6, pp.1117-1123, 2009.
DOI : 10.1101/gr.089532.108

G. Boratyn, A. Schäffer, R. Agarwala, S. Altschul, and D. Lipman, Domain enhanced lookup time accelerated BLAST, Biology Direct, vol.7, issue.1, p.22510480, 2012.
DOI : 10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7

C. Bayne, A convention for naming molluscan genes, Curr Top in Genet, vol.5, pp.45-48, 2012.

C. Cole, J. Barber, and G. Barton, The Jpred 3 secondary structure prediction server, Nucleic Acids Research, vol.36, issue.Web Server, pp.197-201, 2008.
DOI : 10.1093/nar/gkn238

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.
DOI : 10.1093/bioinformatics/btp187

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.