J. C. Hatcher, P. D. Greenberg, J. Antique, and V. E. Jimenez-lucho, Severe Babesiosis in Long Island: Review of 34 Cases and Their Complications, Clinical Infectious Diseases, vol.32, issue.8, pp.1117-1125, 2001.
DOI : 10.1086/319742

P. J. Krause, B. E. Gewurz, D. Hill, F. M. Marty, E. Vannier et al., Persistent and Relapsing Babesiosis in Immunocompromised Patients, Clinical Infectious Diseases, vol.46, issue.3, pp.370-376, 2008.
DOI : 10.1086/525852

D. A. Leiby, Transfusion-Transmitted Babesia spp.: Bull's-Eye on Babesia microti, Clinical Microbiology Reviews, vol.24, issue.1, pp.14-28, 2011.
DOI : 10.1128/CMR.00022-10
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3021205

M. Institut, Committee on Lyme Disease and Other Tick-borne Diseases: The State of the Science. (2011) Prevention. In: Institute of Medicine of the National Academy of Sciences. Critical Needs and Gaps in Understanding Prevention, Amelioration, and Resolution of Lyme and Other Tick-Borne Diseases: The Short-Term and Long-Term Outcomes: Workshop Report, pp.155-176

R. M. Hemmer, D. A. Ferrick, and P. A. Conrad, Role of T cells and cytokines in fatal and resolving experimental babesiosis: protection in TNFRp55-/-mice infected with the human Babesia WA1 parasite, J. Parasitol, vol.86, pp.736-742, 2000.

P. J. Krause, J. Daily, S. R. Telford, E. Vannier, P. Lantos et al., Shared features in the pathobiology of babesiosis and malaria, Trends in Parasitology, vol.23, issue.12, pp.605-610, 2007.
DOI : 10.1016/j.pt.2007.09.005

D. Vallenet, P. Nordmann, V. Barbe, L. Poirel, S. Mangenot et al., Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles, PLoS ONE, vol.20, issue.3, p.1805, 2008.
DOI : 10.1371/journal.pone.0001805.s003

J. Brugere, E. Cornillot, G. Metenier, and C. P. Vivares, In-gel DNA radiolabelling and two-dimensional pulsed field gel electrophoresis procedures suitable for fingerprinting and mapping small eukaryotic genomes, Nucleic Acids Research, vol.28, issue.10, p.48, 2000.
DOI : 10.1093/nar/28.10.e48

. French-italian-public and . Consortium-for, The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Grapevine Genome Characterization. Nature, vol.449, pp.463-467, 2007.

M. D. Katinka, S. Duprat, E. Cornillot, G. Me´te´nierme´te´me´te´nier, F. Thomarat et al., Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi, Nature, vol.487, issue.6862, pp.450-453, 2001.
DOI : 10.1038/35106579
URL : https://hal.archives-ouvertes.fr/hal-00427201

W. J. Kent, BLAT?The BLAST-like alignment tool, 2002.

R. Mott, EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA, Bioinformatics, vol.13, issue.4, pp.477-478, 1997.
DOI : 10.1093/bioinformatics/13.4.477

I. Korf, Gene finding in novel genomes, BMC Bioinformatics, vol.5, issue.1, p.59, 2004.
DOI : 10.1186/1471-2105-5-59

K. L. Howe, T. Chothia, and R. Durbin, GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming, Genome Research, vol.12, issue.9, pp.1418-1427, 2002.
DOI : 10.1101/gr.149502

U. Consortium, The Universal Protein Resource (UniProt) in 2010, Nucleic Acids Research, vol.38, issue.Database, pp.142-148, 2010.
DOI : 10.1093/nar/gkp846

E. Birney, M. Clamp, R. Durbin, and G. Genewise, GeneWise and Genomewise, Genome Research, vol.14, issue.5, pp.988-995, 2004.
DOI : 10.1101/gr.1865504
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479130

M. Tarailo-graovac and N. Chen, UNIT 4.10 Using RepeatMasker to identify repetitive elements in genomic sequences, Current Protoc Bioinform, vol.25, pp.4-10, 2009.

G. Benson, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Research, vol.27, issue.2, pp.573-580, 1999.
DOI : 10.1093/nar/27.2.573

A. L. Price, N. C. Jones, and P. A. Pevzner, De novo identification of repeat families in large genomes, Bioinformatics, vol.21, issue.Suppl 1, pp.351-358, 2005.
DOI : 10.1093/bioinformatics/bti1018

W. H. Majoros, M. Pertea, and S. L. Salzberg, TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders, Bioinformatics, vol.20, issue.16, pp.2878-2879, 2004.
DOI : 10.1093/bioinformatics/bth315
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.150.4492

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice et al., Artemis: sequence visualization and annotation, Bioinformatics, vol.16, issue.10, pp.944-945, 2000.
DOI : 10.1093/bioinformatics/16.10.944
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/16/10/944

M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, and M. Tanabe, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Research, vol.40, issue.D1, pp.109-114, 2012.
DOI : 10.1093/nar/gkr988

C. Aurrecoechea, J. Brestelli, B. P. Brunk, J. Dommer, S. Fischer et al., PlasmoDB: a functional genomic database for malaria parasites, Nucleic Acids Research, vol.37, issue.Database, pp.37-539, 2009.
DOI : 10.1093/nar/gkn814

C. H. Kuo, J. P. Wares, and J. C. Kissinger, The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees, Molecular Biology and Evolution, vol.25, issue.12, pp.2689-2698, 2008.
DOI : 10.1093/molbev/msn213

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

S. Capella-gutierrez, J. M. Silla-martinez, and T. Gabaldon, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, pp.1972-1973, 2009.
DOI : 10.1093/bioinformatics/btp348

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446

S. Whelan and N. Goldman, A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach, Molecular Biology and Evolution, vol.18, issue.5, pp.691-699, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003851

B. R. Baum and M. A. Ragan, The MRP Method, Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Kluwer Academic, pp.17-34, 2004.
DOI : 10.1007/978-1-4020-2330-9_2

V. Ranwez, A. Criscuolo, and E. J. Douzery, SUPERTRIPLETS: a triplet-based supertree approach to phylogenomics, Bioinformatics, vol.26, issue.12, pp.115-123, 2010.
DOI : 10.1093/bioinformatics/btq196

D. L. Swofford, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4, 2002.

C. Scornavacca, V. Berry, V. Lefort, E. J. Douzery, and V. Ranwez, PhySIC_IST: cleaning source trees to infer more informative supertrees, BMC Bioinformatics, vol.9, issue.1, p.413, 2008.
DOI : 10.1186/1471-2105-9-413
URL : https://hal.archives-ouvertes.fr/lirmm-00324069

D. Depoix, B. Carcy, E. Jumas-bilak, M. Pages, E. Precigout et al., Chromosome number, genome size and polymorphism of European and South African isolates of large Babesia parasites that infect dogs, Parasitology, vol.125, issue.04, pp.313-321, 2002.
DOI : 10.1017/S0031182002002202

A. Pain, H. Renauld, M. Berriman, L. Murphy, C. A. Yeats et al., Genome of the Host-Cell Transforming Parasite Theileria annulata Compared with T. parva, Science, vol.309, issue.5731, pp.131-133, 2005.
DOI : 10.1126/science.1110418

K. A. Brayton, A. O. Lau, D. R. Herndon, L. Hannick, L. S. Kappmeyer et al., Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa, PLoS Pathogens, vol.31, issue.10, pp.1401-1413, 2007.
DOI : 10.1371/journal.ppat.0030148.st008

K. P. Hunfeld, A. Hildebrandt, and J. S. Gray, Babesiosis: Recent insights into an ancient disease, International Journal for Parasitology, vol.38, issue.11, pp.1219-1237, 2008.
DOI : 10.1016/j.ijpara.2008.03.001

G. Uilenberg, Babesia???A historical overview, Veterinary Parasitology, vol.138, issue.1-2, pp.3-10, 2006.
DOI : 10.1016/j.vetpar.2006.01.035

M. J. Homer, E. S. Bruinsma, M. J. Lodes, M. H. Moro, S. R. Telford et al., A polymorphic multigene family encoding an immunodominant protein from Babesia microti, J. Clin. Microbiol, vol.38, pp.362-368, 2000.

M. J. Lodes, R. L. Houghton, E. S. Bruinsma, R. Mohamath, L. D. Reynolds et al., Serological Expression Cloning of Novel Immunoreactive Antigens of Babesia microti, Infection and Immunity, vol.68, issue.5, pp.2783-2790, 2000.
DOI : 10.1128/IAI.68.5.2783-2790.2000

J. D. Barry, M. L. Ginger, P. Burton, and R. Mcculloch, Why are parasite contingency genes often associated with telomeres?, International Journal for Parasitology, vol.33, issue.1, pp.29-45, 2003.
DOI : 10.1016/S0020-7519(02)00247-3

J. J. Lopez-rubio, L. Riviere, and A. Scherf, Shared epigenetic mechanisms control virulence factors in protozoan parasites, Current Opinion in Microbiology, vol.10, issue.6, pp.560-568, 2007.
DOI : 10.1016/j.mib.2007.10.003

K. Hikosaka, Y. Watanabe, N. Tsuji, K. Kita, H. Kishine et al., Divergence of the Mitochondrial Genome Structure in the Apicomplexan Parasites, Babesia and Theileria, Molecular Biology and Evolution, vol.27, issue.5, pp.1107-1116, 2010.
DOI : 10.1093/molbev/msp320

M. A. Rudzinska, with Emphasis on the Feeding Mechanism*, The Journal of Protozoology, vol.42, issue.2, pp.224-233, 1976.
DOI : 10.1111/j.1550-7408.1976.tb03759.x

H. K. Goethert and S. R. Telford, What is Babesia microti? Parasitology, pp.301-309, 2003.

R. Nakajima, M. Tsuji, K. Oda, A. Zamoto-niikura, Q. Wei et al., Babesia microti-Group Parasites Compared Phylogenetically by Complete Sequencing of the CCT.ETA. Gene in 36 Isolates, Journal of Veterinary Medical Science, vol.71, issue.1, pp.55-68, 2009.
DOI : 10.1292/jvms.71.55

J. B. Lack, M. V. Reichard, and R. A. Van-den-bussche, Phylogeny and evolution of the Piroplasmida as inferred from 18S rRNA sequences, International Journal for Parasitology, vol.42, issue.4, pp.353-363, 2012.
DOI : 10.1016/j.ijpara.2012.02.005

H. Jomaa, J. Wiesner, S. Sanderbrand, B. Altincicek, C. Weidemeyer et al., Inhibitors of the Nonmevalonate Pathway of Isoprenoid Biosynthesis as Antimalarial Drugs, Science, vol.285, issue.5433, pp.1573-1576, 1999.
DOI : 10.1126/science.285.5433.1573

E. Yeh and J. L. Derisi, Chemical Rescue of Malaria Parasites Lacking an Apicoplast Defines Organelle Function in Blood-Stage Plasmodium falciparum, PLoS Biology, vol.29, issue.Pt. 3, p.1001138, 2011.
DOI : 10.1371/journal.pbio.1001138.s009

D. Madern, Molecular Evolution Within the L-Malate and L-Lactate Dehydrogenase Super-Family, Journal of Molecular Evolution, vol.54, issue.6, pp.825-840, 2002.
DOI : 10.1007/s00239-001-0088-8

G. Zhu and J. S. Keithly, alpha-Proteobacterial Relationship of Apicomplexan Lactate and Malate Dehydrogenases, The Journal of Eukaryotic Microbiology, vol.50, issue.3, pp.255-261, 2002.
DOI : 10.1016/S0378-1119(96)00566-5

D. Madern, X. Cai, M. S. Abrahamsen, and G. Zhu, Evolution of Cryptosporidium parvum Lactate Dehydrogenase from Malate Dehydrogenase by a Very Recent Event of Gene Duplication, Molecular Biology and Evolution, vol.21, issue.3, pp.489-497, 2004.
DOI : 10.1093/molbev/msh042

F. Seeber, J. Limenitakis, and D. Soldati-favre, Apicomplexan mitochondrial metabolism: a story of gains, losses and retentions, Trends in Parasitology, vol.24, issue.10, pp.468-478, 2008.
DOI : 10.1016/j.pt.2008.07.004

K. L. Olszewski, M. W. Mather, J. M. Morrisey, B. A. Garcia, A. B. Vaidya et al., Branched tricarboxylic acid metabolism in Plasmodium falciparum, Nature, vol.6, issue.7307, pp.774-778, 2010.
DOI : 10.1038/nature09301

E. Pays, Genetics of antigenic variation in African trypanosomes, Research in Microbiology, vol.142, issue.6, pp.731-735, 1991.
DOI : 10.1016/0923-2508(91)90088-R

B. Carcy, E. Pre´cigoutpre´cigout, T. Schetters, and A. Gorenflot, Genetic basis for GPI-anchor merozoite surface antigen polymorphism of Babesia and resulting antigenic diversity, Veterinary Parasitology, vol.138, issue.1-2, pp.33-49, 2006.
DOI : 10.1016/j.vetpar.2006.01.038

P. R. Gilson, T. Nebl, D. Vukcevic, R. L. Moritz, T. Sargeant et al., Identification and Stoichiometry of Glycosylphosphatidylinositol-anchored Membrane Proteins of the Human Malaria Parasite Plasmodium falciparum, Molecular & Cellular Proteomics, vol.5, issue.7, pp.1286-1299, 2006.
DOI : 10.1074/mcp.M600035-MCP200

J. Iyer, A. C. Gru¨nergru¨ner, L. Re´niare´nia, G. Snounou, and P. R. Preiser, Invasion of host cells by malaria parasites: a tale of two protein families, Molecular Microbiology, vol.91, issue.2, pp.231-249, 2007.
DOI : 10.1046/j.1537-2995.2000.40080949.x

T. Naderer, J. E. Vince, and M. J. Mcconville, Surface Determinants of Leishmania Parasites and their Role in Infectivity in the Mammalian Host, Current Molecular Medicine, vol.4, issue.6, pp.649-665, 2004.
DOI : 10.2174/1566524043360069

L. Schofield and F. Hackett, Signal transduction in host cells by a glycosylphosphatidylinositol toxin of malaria parasites, Journal of Experimental Medicine, vol.177, issue.1, 1993.
DOI : 10.1084/jem.177.1.145

S. D. Tachado, P. Gerold, R. T. Schwarz, S. Novakovic, M. Mcconville et al., Signal transduction in macrophages by glycosylphosphatidylinositols of Plasmodium, Trypanosoma, and Leishmania: Activation of protein tyrosine kinases and protein kinase C by inositolglycan and diacylglycerol moieties, Proc. Natl Acad. Sci. USA, pp.4022-4027, 1997.
DOI : 10.1073/pnas.94.8.4022

F. Debierre-grockiego and R. T. Schwarz, Immunological reactions in response to apicomplexan glycosylphosphatidylinositols, Glycobiology, vol.20, issue.7, pp.801-811, 2010.
DOI : 10.1093/glycob/cwq038

B. Striepen, C. F. Zinecker, J. B. Damm, P. A. Melgers, G. J. Gerwig et al., Molecular structure of the ???low molecular weight antigen??? of Toxoplasma gondii: a glucose ??1-4 N-acetylgalactosamine makes free glycosyl-phosphatidylinositols highly immunogenic, Journal of Molecular Biology, vol.266, issue.4, pp.797-813, 1997.
DOI : 10.1006/jmbi.1996.0806

P. Gerold, N. Jung, N. Azzouz, N. Freiberg, S. Kobe et al., Biosynthesis of glycosylphosphatidylinositols of Plasmodium falciparum in a cell-free incubation system: inositol acylation is needed for mannosylation of glycosylphosphatidylinositols, Biochemical Journal, vol.344, issue.3, pp.731-738, 1999.
DOI : 10.1042/bj3440731

F. Debierre-grockiego, C. Desaint, V. Fuentes, M. Poussin, G. Socie et al., Evidence for glycosylphosphatidylinositol (GPI)-anchored eosinophil-derived neurotoxin (EDN) on human granulocytes, FEBS Letters, vol.125, issue.1-3, pp.111-116, 2003.
DOI : 10.1016/S0014-5793(03)00106-6

V. L. Stevens, Biosynthesis of glycosylphosphatidylinositol membrane anchors, Biochemical Journal, vol.310, issue.2, pp.361-370, 1995.
DOI : 10.1042/bj3100361

M. Wittner, K. S. Rowin, H. B. Tanowitz, J. F. Hobbs, S. Saltzman et al., Successful Chemotherapy of Transfusion Babesiosis, Annals of Internal Medicine, vol.96, issue.5, pp.601-604, 1982.
DOI : 10.7326/0003-4819-96-5-601

P. J. Krause, T. Lepore, V. K. Sikand, J. Gadbaw, . Jr et al., Atovaquone and Azithromycin for the Treatment of Babesiosis, New England Journal of Medicine, vol.343, issue.20, pp.1454-1458, 2000.
DOI : 10.1056/NEJM200011163432004

G. P. Wormser, R. J. Dattwyler, E. D. Shapiro, J. J. Halperin, A. C. Steere et al., The Clinical Assessment, Treatment, and Prevention of Lyme Disease, Human Granulocytic Anaplasmosis, and Babesiosis: Clinical Practice Guidelines by the Infectious Diseases Society of America, Clinical Infectious Diseases, vol.43, issue.9, pp.1089-1134, 2006.
DOI : 10.1086/508667

G. P. Wormser, A. Prasad, E. Neuhaus, S. Joshi, J. Nowakowski et al., Infection, Clinical Infectious Diseases, vol.50, issue.3, pp.381-386, 2010.
DOI : 10.1086/649859

M. Clastre, A. Goubard, A. Prel, Z. Mincheva, M. C. Viaud-massuart et al., The methylerythritol phosphate pathway for isoprenoid biosynthesis in coccidia: Presence and sensitivity to fosmidomycin, Experimental Parasitology, vol.116, issue.4, pp.375-384, 2007.
DOI : 10.1016/j.exppara.2007.02.002

R. Lizundia, D. Werling, G. Langsley, and S. A. Ralph, Theileria Apicoplast as a Target for Chemotherapy, Antimicrobial Agents and Chemotherapy, vol.53, issue.3, pp.1213-1217, 2009.
DOI : 10.1128/AAC.00126-08

F. Seeber and D. Soldati-favre, Metabolic Pathways in the Apicoplast of Apicomplexa, Int. Rev. Cell Mol. Biol, vol.281, pp.161-228, 2010.
DOI : 10.1016/S1937-6448(10)81005-6

S. Baumeister, J. Wiesner, A. Reichenberg, M. Hintz, S. Bietz et al., Fosmidomycin Uptake into Plasmodium and Babesia-Infected Erythrocytes Is Facilitated by Parasite-Induced New Permeability Pathways, PLoS ONE, vol.25, issue.Suppl 1, p.19334, 2011.
DOI : 10.1371/journal.pone.0019334.s013
URL : http://doi.org/10.1371/journal.pone.0019334

D. Raoult, L. Soulayrol, B. Toga, H. Dumon, and P. Casanova, Babesiosis, Pentamidine, and Cotrimoxazole, Annals of Internal Medicine, vol.107, issue.6, p.944, 1987.
DOI : 10.7326/0003-4819-107-6-944_2

A. S. Olmeda, P. M. Armstrong, B. M. Rosenthal, B. Valladares, A. Del-castillo et al., A subtropical case of human babesiosis, Acta Tropica, vol.67, issue.3, pp.229-234, 1997.
DOI : 10.1016/S0001-706X(97)00045-4