W. Mulla, J. Zhu, and R. Li, Yeast: a simple model system to study complex phenomena of aneuploidy, FEMS Microbiol Rev, vol.38, pp.201-212, 2014.

S. I. Nagaoka, T. J. Hassold, and P. A. Hunt, Human aneuploidy: mechanisms and new insights into an age-old problem, Nat Rev Genet, vol.13, pp.493-504, 2012.

A. Selmecki, A. Forche, and J. Berman, Aneuploidy and isochromosome formation in drug-resistant Candida albicans, Science, vol.313, pp.367-370, 2006.

J. Hose, C. M. Yong, M. Sardi, Z. Wang, M. A. Newton et al., Dosage compensation can buffer copy-number variation in wild yeast, Elife, vol.4, p.5462, 2015.

E. Sionov, H. Lee, Y. C. Chang, and K. J. Kwon-chung, Cryptococcus neoformans overcomes stress of azole drugs by formation of disomy in specific multiple chromosomes, PLoS Pathog, vol.6, 2010.

C. A. Anderson, S. Roberts, H. Zhang, C. M. Kelly, A. Kendall et al., Ploidy variation in multinucleate cells changes under stress, Mol Biol Cell, vol.26, pp.1129-1140, 2015.

J. Berman, Ploidy plasticity: a rapid and reversible strategy for adaptation to stress, FEMS Yeast Res, vol.16, issue.020, 2016.

J. M. Refsnider, T. J. Poorten, P. F. Langhammer, P. A. Burrowes, and E. B. Rosenblum, Genomic correlates of virulence attenuation in the deadly amphibian chytrid fungus, vol.5, pp.2291-2298, 2015.

C. B. Ford, J. M. Funt, D. Abbey, L. Issi, C. Guiducci et al., The evolution of drug resistance in clinical isolates of Candida albicans, Elife, vol.4, p.662, 2015.

K. Ersfeld, Nuclear architecture, genome and chromatin organisation in Trypanosoma brucei, Res Microbiol, vol.162, pp.626-636, 2011.

M. B. Rogers, J. D. Hilley, N. J. Dickens, J. Wilkes, P. A. Bates et al., Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania, Genome Res, vol.21, pp.2129-2142, 2011.

H. Imamura, T. Downing, F. Van-den-broeck, M. J. Sanders, S. Rijal et al., Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent, Elife, vol.5, pp.1-39, 2016.

Y. Sterkers, L. Lachaud, L. Crobu, P. Bastien, and M. Pagès, FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major, Cell Microbiol, vol.13, pp.274-283, 2011.

J. M. Ubeda, D. Légaré, F. Raymond, A. A. Ouameur, S. Boisvert et al., Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy, Genome Biol, vol.9, 2008.

C. D. Shaw, J. Lonchamp, T. Downing, H. Imamura, T. M. Freeman et al., In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization, Mol Microbiol, vol.99, pp.1134-1148, 2016.

Y. Sterkers, L. Crobu, L. Lachaud, M. Pagès, and P. Bastien, Parasexuality and mosaic aneuploidy in Leishmania: alternative genetics, Trends Parasitol, vol.30, pp.429-435, 2014.

P. Leprohon, D. Légaré, F. Raymond, E. Madore, G. Hardiman et al., Gene expression modulation is associated with gene amplification, supernumerary chromosomes and chromosome loss in antimony-resistant Leishmania infantum, Nucleic Acids Res, vol.37, pp.1387-1399, 2009.

D. Gaudenzi, J. G. Noé, G. Campo, V. A. Frasch, A. C. Cassola et al., Gene expression regulation in trypanosomatids, Essays Biochem, vol.51, pp.31-46, 2011.

T. Downing, H. Imamura, S. Decuypere, T. G. Clark, G. H. Coombs et al., Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance, Genome Res, vol.21, pp.2143-2156, 2011.

S. Kramer, Developmental regulation of gene expression in the absence of transcriptional control: the case of kinetoplastids, Mol Biochem Parasitol, vol.181, pp.61-72, 2012.

S. M. Gossage, M. E. Rogers, and P. A. Bates, Two separate growth phases during the development of Leishmania in sand flies: implications for understanding the life cycle, Int J Parasitol, vol.33, pp.1027-1034, 2003.

J. Kloehn, E. C. Saunders, S. O'callaghan, M. J. Dagley, and M. J. Mcconville, Characterization of metabolically quiescent Leishmania parasites in murine lesions using heavy water labeling, PLOS Pathog, vol.11, 2015.

A. M. Selmecki, K. Dulmage, L. E. Cowen, J. B. Anderson, and J. Berman, Acquisition of aneuploidy provides increased fitness during the evolution of antifungal drug resistance, PLoS Genet, vol.5, p.1000705, 2009.

T. Kasuga, M. Bui, E. Bernhardt, T. Swiecki, A. K. Cano et al., Hostinduced aneuploidy and phenotypic diversification in the sudden Oak death pathogen Phytophthora ramorum, BMC Genomics, vol.17, p.385, 2016.

A. P. Jackson, The evolution of amastin surface glycoproteins in trypanosomatid parasites, Mol Biol Evol, vol.27, pp.33-45, 2010.

R. De-paiva, V. Grazielle-silva, M. S. Cardoso, B. N. Nakagaki, R. P. Mendonçaneto et al., Amastin knockdown in Leishmania braziliensis affects parasite-macrophage interaction and results in impaired viability of intracellular amastigotes, PLoS Pathog, vol.11, 2015.

J. Sádlová, P. Volf, K. Victoir, J. C. Dujardin, and J. Votýpka, Virulent and attenuated lines of Leishmania major: DNA karyotypes and differences in metalloproteinase GP63, Folia Parasitol (Praha), vol.53, pp.81-90, 2006.

D. Q. Chen, B. K. Kolli, N. Yadava, H. G. Lu, A. Gilman-sachs et al., Episomal expression of specific sense and antisense mRNAs in Leishmania amazonensis: modulation of gp63 level in promastigotes and their infection of macrophages in vitro, Infect Immun, vol.68, pp.80-86, 2000.

K. V. Bulazel, G. C. Ferreri, M. Eldridge, and R. J. O'neill, Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages, Genome Biol, vol.8, 2007.

M. Fiebig, S. Kelly, and E. Gluenz, Comparative life cycle transcriptomics revises Leishmania mexicana genome annotation and links a chromosome duplication with parasitism of vertebrates, PLoS Pathog, vol.11, pp.1-28, 2015.

P. J. Alcolea, A. Alonso, M. Domínguez, V. Parro, M. Jiménez et al., Influence of the microenvironment in the transcriptome of Leishmania infantum promastigotes: sand fly versus culture, PLOS Negl Trop Dis, vol.10, 2016.

G. F. Späth, S. Drini, and N. Rachidi, A touch of zen: post-translational regulation of the Leishmania stress response, Cell Microbiol, vol.17, pp.632-638, 2015.

M. A. Mandell and S. M. Beverley, Continual renewal and replication of persistent Leishmania major parasites in concomitantly immune hosts, Proc Natl Acad Sci U S A, vol.114, pp.801-810, 2017.

S. Rijal, Y. V. Chappuis, F. Decuypere, S. Khanal, B. Singh et al., Antimonial treatment of visceral leishmaniasis: are current in vitro susceptibility assays adequate for prognosis of in vivo therapy outcome?, Microbes Infect, vol.9, pp.529-535, 2007.

H. W. Murray, Susceptibility of Leishmania to oxygen intermediates and killing by normal macrophages, J Exp Med, vol.153, pp.1302-1315, 1981.

J. S. Keithly, Infectivity of Leishmania donovani amastigotes and promastigotes for golden hamsters, J Protozool, vol.23, pp.244-245, 1976.

P. Pescher, T. Blisnick, P. Bastin, and G. F. Späth, Quantitative proteome profiling informs on phenotypic traits that adapt Leishmania donovani for axenic and intracellular proliferation, Cell Microbiol, vol.13, pp.978-991, 2011.
DOI : 10.1111/j.1462-5822.2011.01593.x

URL : https://hal.archives-ouvertes.fr/pasteur-01433560

J. Sadlova, V. Seblova, J. Votypka, A. Warburg, and P. Volf, Xenodiagnosis of Leishmania donovani in BALB/c mice using Phlebotomus orientalis: a new laboratory model, Parasit Vectors, vol.8, p.158, 2015.

I. F. Bronner, M. A. Quail, D. J. Turner, and H. Swerdlow, Improved protocols for Illumina sequencing, Curr Protoc Hum Genet, vol.80, 2014.
DOI : 10.1002/0471142905.hg1802s80

URL : http://europepmc.org/articles/pmc3849550?pdf=render

S. Zhao, Y. Guo, Q. Sheng, and Y. Shyr, Heatmap3: an improved heatmap package with more powerful and convenient features, BMC Bioinformatics, vol.15, p.16, 2014.
DOI : 10.1186/1471-2105-15-s10-p16

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-15-S10-P16

J. D. Hunter, Matplotlib: a 2D graphics environment, Comput Sci Eng, vol.9, pp.90-95, 2007.

S. Van-der-walt, S. C. Colbert, and G. Varoquaux, The NumPy array: a structure for efficient numerical computation, Comput Sci Eng, vol.13, pp.22-30, 2011.
URL : https://hal.archives-ouvertes.fr/inria-00564007

S. Anders, W. Huber, U. Nagalakshmi, Z. Wang, K. Waern et al., Differential expression analysis for sequence count data, Genome Biol, vol.11, 2010.

. Dumetz,