P. Abad, J. Gouzy, J. M. Aury, P. Castagnone-sereno, E. G. Danchin et al., Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita, Nature Biotechnology, vol.14, issue.8, pp.909-915, 2008.
DOI : 10.1101/gr.3729105
URL : https://hal.archives-ouvertes.fr/hal-01189285

A. Azzi, C. Cosseau, and C. Grunau, Schistosoma mansoni: Developmental arrest of miracidia treated with histone deacetylase inhibitors, Experimental Parasitology, vol.121, issue.3, 2009.
DOI : 10.1016/j.exppara.2008.11.010
URL : https://hal.archives-ouvertes.fr/halsde-00371695

E. Bártová, J. Pacherník, A. Harnicarová, A. Kovarík, M. Kovaríková et al., Nuclear levels and patterns of histone H3 modification and HP1 proteins after inhibition of histone deacetylases, Journal of Cell Science, vol.118, issue.21, pp.5035-5046, 2005.
DOI : 10.1242/jcs.02621

A. Bird, DNA methylation and the frequency of CpG in animal DNA, Nucleic Acids Research, vol.8, issue.7, pp.1499-1504, 1980.
DOI : 10.1093/nar/8.7.1499

S. Caby, P. , and R. J. , Quantitative chromatin immunoprecipitation (Q-ChIP) applied to Schistosoma mansoni, Molecular and Biochemical Parasitology, vol.166, issue.1, 2009.
DOI : 10.1016/j.molbiopara.2009.02.014

M. C. Caillaud, G. Dubreuil, M. Quentin, L. Perfus-barbeoch, P. Lecomte et al., Root-knot nematodes manipulate plant cell functions during a compatible interaction, Journal of Plant Physiology, vol.165, issue.1, pp.104-113, 2008.
DOI : 10.1016/j.jplph.2007.05.007

P. Castagnone-sereno, Genetic variability and adaptive evolution in parthenogenetic root-knot nematodes, Heredity, vol.11, issue.4, 2006.
DOI : 10.1038/sj.hdy.6800794

P. Castagnone-sereno, E. Wajnberg, M. Bongiovanni, F. Leroy, and A. Dalmasso, Genetic variation inMeloidogyne incognita virulence against the tomatoMi resistance gene: evidence from isofemale line selection studies, Theoretical and Applied Genetics, vol.50, issue.6-7, pp.749-753, 1007.
DOI : 10.1007/BF01253980

T. Chookajorn, R. Dzikowski, M. Frank, F. Li, A. Z. Jiwani et al., Epigenetic memory at malaria virulence genes, Proceedings of the National Academy of Sciences, vol.104, issue.3, pp.899-902, 2007.
DOI : 10.1073/pnas.0609084103

C. Cosseau, A. Azzi, K. Smith, M. Freitag, G. Mitta et al., Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma mansoni: Critical experimental parameters, Molecular and Biochemical Parasitology, vol.166, issue.1, pp.70-76, 2009.
DOI : 10.1016/j.molbiopara.2009.02.015
URL : https://hal.archives-ouvertes.fr/halsde-00459175

E. G. Danchin, M. N. Rosso, P. Vieira, J. De-almeida-engler, P. M. Coutinho et al., Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes, Proceedings of the National Academy of Sciences, vol.107, issue.41, pp.17651-17656, 2010.
DOI : 10.1073/pnas.1008486107

A. F. Dernburg, Z. Du, H. Li, Q. Wei, X. Zhao et al., Here, there, and everywhere: kinetochore function on holocentric chromosomes Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera, Proc. Natl. Acad. Sci. U.S.A. 106, pp.33-38, 2001.

S. Fneich, N. Dheilly, C. Adema, A. Rognon, M. Reichelt et al., 5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria glabrata, a snail intermediate host of Schistosoma mansoni, Parasites & Vectors, vol.6, issue.1, pp.167-177, 2013.
DOI : 10.1073/pnas.0900301106
URL : https://hal.archives-ouvertes.fr/halsde-00839033

L. H. Freitas-junior, R. Hernandez-rivas, S. A. Ralph, D. Montiel-condado, O. K. Ruvalcaba-salazar et al., Telomeric Heterochromatin Propagation and Histone Acetylation Control Mutually Exclusive Expression of Antigenic Variation Genes in Malaria Parasites, Cell, vol.121, issue.1, pp.25-36, 2005.
DOI : 10.1016/j.cell.2005.01.037

F. Gao, X. Liu, X. P. Wu, X. L. Wang, D. Gong et al., Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis, Genome Biology, vol.13, issue.10, 2012.
DOI : 10.1016/j.jchromb.2011.04.002

F. Gao, R. Wang, and M. Liu, Trichinella spiralis, potential model nematode for epigenetics and its implication in metazoan parasitism, Frontiers in Physiology, vol.4, 2014.
DOI : 10.3389/fphys.2013.00410

M. G. Goll and T. H. Bestor, EUKARYOTIC CYTOSINE METHYLTRANSFERASES, Annual Review of Biochemistry, vol.74, issue.1, pp.481-514, 2005.
DOI : 10.1146/annurev.biochem.74.010904.153721

E. Gómez-díaz, M. Jordà, M. A. Peinado, and A. Rivero, Epigenetics of Host-Pathogen Interactions, PLoS Pathog, 2012.
DOI : 10.1201/b16304-2

A. Gutierrez, R. J. Sommer, and S. Tweedie, Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae, Nucleic Acids Research, vol.32, issue.21, pp.6388-6396, 2003.
DOI : 10.1093/nar/gkh982

K. Jabbari and G. Bernardi, Cytosine methylation and CpG, TpG (CpA) and TpA frequencies, Gene, vol.333, 2004.
DOI : 10.1016/j.gene.2004.02.043

E. Jablonka and M. J. Lamb, The Changing Concept of Epigenetics, Annals of the New York Academy of Sciences, vol.401, issue.Suppl. 1, pp.82-96, 2002.
DOI : 10.1111/j.1749-6632.2002.tb04913.x

A. P. Jack, S. Bussemer, M. Hahn, S. Pünzeler, M. Snyder et al., H3K56me3 Is a Novel, Conserved Heterochromatic Mark That Largely but Not Completely Overlaps with H3K9me3 in Both Regulation and Localization, PLoS ONE, vol.453, issue.2, 2013.
DOI : 10.1371/journal.pone.0051765.s003

M. Jaouannet, L. Perfus-barbeoch, E. Deleury, M. Magliano, G. Engler et al., A root-knot nematode-secreted protein is injected into giant cells and targeted to the nuclei, New Phytologist, vol.8, issue.4, pp.924-931, 2012.
DOI : 10.1111/j.1469-8137.2012.04164.x

T. Jenuwein, A. , and C. D. , Translating the Histone Code, Science, vol.293, issue.5532, 2001.
DOI : 10.1126/science.1063127

L. Jiang, J. Mu, Q. Zhang, T. Ni, P. Srinivasan et al., PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum, Nature, vol.56, issue.7457, pp.223-227, 1974.
DOI : 10.1038/nature12361
URL : https://hal.archives-ouvertes.fr/pasteur-00842612

S. Kumar, X. Cheng, S. Klimasauskas, S. Mi, J. Posfai et al., The DNA (cytosine-5) methyltransferases, Nucleic Acids Research, vol.22, issue.1, pp.1-10, 1994.
DOI : 10.1093/nar/22.1.1

N. Kunert, J. Marhold, J. Stanke, D. Stach, and F. Lyko, A Dnmt2-like protein mediates DNA methylation in Drosophila, Development, vol.130, issue.21, pp.5083-5090, 2003.
DOI : 10.1242/dev.00716

J. Lancelot, S. Caby, F. Dubois-abdesselem, M. Vanderstraete, J. Trolet et al., Schistosoma mansoni Sirtuins: Characterization and Potential as Chemotherapeutic Targets, PLoS Neglected Tropical Diseases, vol.26, issue.9, 2013.
DOI : 10.1371/journal.pntd.0002428.s003

J. M. Lepesant, C. Cosseau, J. Boissier, M. Freitag, J. Portela et al., Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence Towards an understanding of the epigenetics of schistosomes: a comparative epigenomic study, Genome Biol, vol.13, 2011.

B. Li, M. Carey, and J. L. Workman, The Role of Chromatin during Transcription, Cell, vol.128, issue.4, pp.707-719, 2007.
DOI : 10.1016/j.cell.2007.01.015

K. Luger, M. L. Dechassa, D. J. Tremethick, A. W. Mäder, R. K. Richmond et al., New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?, Nature Reviews Molecular Cell Biology, vol.21, issue.7, pp.436-447, 1038.
DOI : 10.1038/nrm3382

F. Lyko, B. H. Ramsahoye, and R. Jaenisch, DNA methylation in Drosophila melanogaster, Nature, vol.408, pp.538-540, 2000.

N. A. Malmquist, T. A. Moss, S. Mecheri, A. Scherf, and M. J. Fuchter, Small-molecule histone methyltransferase inhibitors display rapid antimalarial activity against all blood stage forms in Plasmodium falciparum, Proc. Natl, 2012.
DOI : 10.1073/pnas.1205414109
URL : https://hal.archives-ouvertes.fr/pasteur-01103641

M. Marek, S. Kannan, A. T. Hauser, M. Mourão, M. Caby et al., Structural Basis for the Inhibition of Histone Deacetylase 8 (HDAC8), a Key Epigenetic Player in the Blood Fluke Schistosoma mansoni, PLoS Pathogens, vol.7, issue.9, 2013.
DOI : 10.1371/journal.ppat.1003645.s007

L. Mariño-ramírez, I. K. Jordan, and D. Landsman, Multiple independent evolutionary solutions to core histone gene regulation, Genome Biol, vol.7, pp.10-1186, 2006.

D. P. Melters, L. V. Paliulis, I. F. Korf, C. , and S. W. , Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis, Chromosome Research, vol.7, issue.1, pp.579-593, 2012.
DOI : 10.1007/s10577-012-9292-1
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.458.5972

M. M. Mourão, C. Grunau, P. T. Loverde, M. K. Jones, and G. Oliveira, Recent advances in Schistosoma genomics, Parasite Immunology, vol.1, issue.Suppl. 1, 2012.
DOI : 10.1111/j.1365-3024.2011.01349.x

W. Niu, Z. J. Lu, M. Zhong, M. Sarov, J. I. Murray et al., Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans, Genome Research, vol.21, issue.2, pp.245-254, 2011.
DOI : 10.1101/gr.114587.110

C. Perrin, J. M. Lepesant, E. Roger, D. Duval, S. Fneich et al., Schistosoma mansoni Mucin Gene (SmPoMuc) Expression: Epigenetic Control to Shape Adaptation to a New Host, PLoS Pathogens, vol.29, issue.(13), 2013.
DOI : 10.1371/journal.ppat.1003571.s006

R. J. Pierce, F. Dubois-abdesselem, J. Lancelot, L. Andrade, and G. Oliveira, Targeting Schistosome Histone Modifying Enzymes for Drug Development, Current Pharmaceutical Design, vol.18, pp.3567-3578, 2012.
DOI : 10.2174/138161212801327248

O. J. Rando, M. N. Rosso, B. Favery, C. Piotte, L. Arthaud et al., Genome-wide measurement of histone H3 replacement dynamics in yeast Isolation of a cDNA encoding a beta-1,4-endoglucanase in the root-knot nematode Meloidogyne incognita and expression analysis during plant parasitism, Methods Mol. Biol. Mol. Plant-Microbe Interact, vol.759, issue.12, pp.41-60, 1999.

J. P. Semblat, M. Bongiovanni, E. Wajnberg, A. Dalmasso, P. Abad et al., Virulence and molecular diversity of parthenogenetic root-knot nematodes, Meloidogyne spp., Heredity, vol.91, issue.1, pp.81-89, 2000.
DOI : 10.1046/j.1365-294x.1998.00326.x

V. J. Simpson, T. E. Johnson, and R. F. Hammen, Caenorhabditis elegans DNA does not contain 5-methylcytosine at any time during development or aging, Nucleic Acids Res, vol.1416, pp.6711-6719, 1986.

B. D. Strahl, A. , and C. D. , The language of covalent histone modifications, Nature, vol.96, issue.6765, pp.41-45, 2000.
DOI : 10.1038/47412

J. A. Subirana and X. Messeguer, A Satellite Explosion in the Genome of Holocentric Nematodes, PLoS ONE, vol.19, issue.4, 2013.
DOI : 10.1371/journal.pone.0062221.s002

M. M. Suzuki and A. A. Bird, DNA methylation landscapes: provocative insights from epigenomics, Nature Reviews Genetics, vol.16, issue.6, pp.465-476, 1981.
DOI : 10.1038/nrg2341

A. C. Triantaphyllou, Cytogenetic aspects of nematode evolution, Concepts in Nematode Systematics, pp.55-71, 1983.

P. Trojer, R. , and D. , Facultative Heterochromatin: Is There a Distinctive Molecular Signature?, Molecular Cell, vol.28, issue.1, 2007.
DOI : 10.1016/j.molcel.2007.09.011

B. M. Turner, Decoding the nucleosome, Cell, vol.75, issue.1, pp.5-8, 1993.
DOI : 10.1016/S0092-8674(05)80078-9

B. M. Turner, Reading signals on the nucleosome with a new nomenclature for modified histones, Nature Structural & Molecular Biology, vol.7, issue.2, pp.110-112, 2005.
DOI : 10.1038/sj.embor.7400139

B. M. Turner, The adjustable nucleosome: an epigenetic signaling module, Trends in Genetics, vol.28, issue.9, pp.436-444, 2012.
DOI : 10.1016/j.tig.2012.04.003

S. Urieli-shoval, Y. Gruenbaum, J. Sedat, and A. Razin, The absence of detectable methylated bases in Drosophila melanogaster DNA, FEBS Lett, vol.14682, pp.148-152, 1982.

K. J. Verhoeven and V. Preite, EPIGENETIC VARIATION IN ASEXUALLY REPRODUCING ORGANISMS, Evolution, vol.19, issue.103, 2014.
DOI : 10.1111/evo.12320

D. Wenzel, F. Palladino, and M. Jedrusik-bode, Epigenetics in C. elegans: Facts and challenges, genesis, vol.4, issue.8, pp.647-661, 2011.
DOI : 10.1002/dvg.20762
URL : https://hal.archives-ouvertes.fr/ensl-00814756

B. Winnepenninckx, T. Backeljau, D. Wachter, R. Youngson, N. A. Whitelaw et al., Extraction of high molecular weight DNA from molluscs Transgenerational epigenetic effects, Trends Genet Annu. Rev. Genomics Hum. Genet, vol.9, pp.233-257, 1993.