S. M. Adl, A. G. Simpson, C. E. Lane, J. Luke?, D. Bass et al., The revised classification of eukaryotes, J Eukaryot Microbiol, vol.59, pp.429-493, 2012.

M. S. Atkins, A. P. Teske, and O. R. Anderson, A survey of flagellate diversity at four deep-sea hydrothermal vents in the eastern Pacific Ocean using structural and molecular approaches, J Eukaryot Microbiol, vol.47, pp.400-411, 2000.

A. C. Aufderheide, W. Salo, M. Madden, J. Streitz, J. Buikstra et al., 000-year record of Chagas disease, Proc Natl Acad Sci, vol.9, pp.2034-2039, 2004.

E. Aylagas, A. Borja, and N. Rodríguez-ezpeleta, Environmental status assessment using DNA metabarcoding: towards a genetics based marine biotic index (gAMBI), PLoS ONE, vol.9, p.90529, 2014.

C. Bachy, J. R. Dolan, P. López-garcía, P. Deschamps, and D. Moreira, Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study, ISME J, vol.7, pp.244-255, 2013.

S. T. Bates, J. C. Clemente, G. E. Flores, W. A. Walters, L. W. Parfrey et al., Global biogeography of highly diverse protistan communities in soil, ISME J, vol.7, pp.652-659, 2013.

D. Begerow, H. Nilsson, M. Unterseher, and W. Maier, Current state and perspectives of fungal DNA barcoding and rapid identification procedures, Appl Microbiol Biotechnol, vol.87, pp.99-108, 2010.

C. Berney, J. Fahrni, and J. Pawlowski, How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys, BMC Biol, vol.2, p.13, 2004.

M. Berriman, E. Ghedin, C. Hertz-fowler, G. Blandin, H. Renauld et al., Science, vol.5733, pp.416-422

T. C. Borghesan, R. C. Ferreira, C. S. Takata, M. Campaner, C. C. Borda et al., Molecular phylogenetic redefinition of Herpetomonas (Kinetoplastea, Trypanosomatidae), a genus of insect parasites associated with flies, Protist, vol.164, pp.129-152, 2013.

P. Bouchet, V. Héros, P. Lozouet, and P. Maestrati, A quarter-century of deep-sea malacological exploration in the South and West Pacific: where do we stand? How far to go?, Tropical deep-sea Benthos 25, Muséum National d'Histoire Naturelle, pp.9-40, 2008.

P. B. Brown and G. V. Wolfe, Protist genetic diversity in the acidic hydrothermal environments of Lassen Volcanic National Park, USA, J Eukaryot Microbiol, vol.53, pp.420-431, 2006.

E. P. Camargo, Phytomonas and other trypanosomatid parasites of plants and fruit, Adv Parasitol, vol.42, pp.29-112, 1999.

J. Carnes, A. Anupama, O. Balmer, A. Jackson, M. Lewis et al., Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty, PLoS Negl Trop Dis, vol.9, p.3404, 2015.

T. Cavalier-smith, Eukaryote kingdoms: seven or nine?, Biosystems, vol.14, pp.461-481, 1981.

T. Cavalier-smith, Only six kingdoms of life, Proc Biol Sci, vol.271, pp.1251-1262, 2004.

C. Chantangsi, D. H. Lynn, M. T. Brandl, J. C. Cole, N. Hetrick et al., Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena, Int J Syst Evol Microbiol, vol.57, pp.2412-2425, 2007.

D. G. Croan, D. A. Morrison, and J. T. Ellis, Evolution of the genus Leishmania revealed by comparison of DNA and RNA polymerase gene sequences, Mol Biochem Parasitol, vol.89, pp.149-159, 1997.

P. López-garcía, P. H. Gail, F. Moreira, and D. , Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge, Proc Natl Acad Sci, vol.100, pp.697-702, 2003.

P. López-garcía, F. Rodríguez-valera, C. Pedrós-alió, and D. Moreira, Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton, Nature, vol.409, pp.603-607, 2001.

A. Losev, A. Grybchuk-ieremenko, A. Y. Kostygov, J. Luke?, and V. Yurchenko, Host specificity, pathogenicity, and mixed infections of trypanoplasms from freshwater fishes, Parasitol Res, vol.114, pp.1071-1078, 2015.

J. Luke?, O. Flegontova, and A. Horák, Diplonemids. Curr Biol, vol.25, pp.1-3, 2015.

J. Luke?, D. L. Guilbride, J. Votýpka, A. Zíková, R. Benne et al., Kinetoplast DNA network: evolution of an improbable structure, Eukaryot Cell, vol.1, pp.495-502, 2002.

J. Luke?, M. Jirk?, D. Dole?el, I. Král'ová, L. Hollar et al., Analysis of ribosomal RNA genes suggests that trypanosomes are monophyletic, J Mol Evol, vol.44, pp.521-527, 1997.

J. Luke?, T. Skalický, J. Tý?, J. Votýpka, and V. Yurchenko, Evolution of parasitism in kinetoplastid flagellates, Mol Biochem Parasitol, vol.195, pp.115-122, 2014.

D. A. Maslov, L. Luke?, M. Jirku, and L. Simpson, Phylogeny of trypanosomes as inferred from the small and large subunit rRNAs: implications for the evolution of parasitism in the trypanosomatid protozoa, Mol Biochem Parasitol, vol.75, pp.197-205, 1996.

D. A. Maslov, S. J. Westenberger, X. Xu, D. A. Campbell, and N. R. Sturm, Discovery and barcoding by analysis of spliced leader RNA gene sequences of new isolates of Trypanosomatidae from Heteroptera in Costa Rica and Ecuador, J Eukaryot Microbiol, vol.54, pp.57-65, 2007.

D. A. Maslov, V. Y. Yurchenko, M. Jirk?, and J. Luke?, Two new species of trypanosomatid parasites isolated from Heteroptera in Costa Rica, J Eukaryot Microbiol, vol.57, pp.177-188, 2010.

C. B. Mccarthy, L. A. Diambra, and R. Pomar, Metagenomic analysis of taxa associated with Lutzomyia longipalpis, vector of visceral leishmaniasis using an unbiased high-throughput approach, PLoS Negl Trop Dis, vol.5, p.1304, 2011.

R. Mcghee and W. B. Cosgrove, Biology and physiology of the lower Trypanosomatidae, Microbiol Rev, vol.44, pp.140-173, 1980.

R. Medinger, V. Nolte, R. V. Pandey, S. Jost, B. Ottenwälder et al., Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms, Mol Ecol, vol.19, pp.32-40, 2010.

M. Mendoza, T. Sicheritz-pontén, and M. Gilbert, Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses, Brief Bioinform, vol.16, pp.745-758, 2015.

E. Merzlyak, V. Yurchenko, A. A. Kolesnikov, K. Alexandrov, S. A. Podlipaev et al., Diversity and phylogeny of insect trypanosomatids based on small subunit rRNA genes: polyphyly of Leptomonas and Blastocrithidia, J Eukaryot Microbiol, vol.48, pp.161-169, 2001.

D. Moreira, P. López-garcía, and K. Vickerman, An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea, Int J Syst Evol Microbiol, vol.54, pp.1861-1875, 2004.

E. Nassonova, A. Smirnov, J. Fahrni, and J. Pawlowski, Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae, Protist, vol.161, pp.102-115, 2010.

N. Pace, A molecular view of microbial diversity and the biosphere, Science, vol.276, pp.734-740, 1997.

N. Pace, Mapping the tree of life: progress and prospects. Microbiol, Mol Biol Rev, vol.73, pp.565-576, 2009.

H. Pawar, A. Kulkarni, T. Dixit, D. Chaphekar, and M. S. Patole, A bioinformatics approach to reanalyze the genome annotation of kinetoplastid protozoan parasite Leishmania donovani, Genomics, vol.104, pp.554-561, 2014.

J. Pawlowski, S. Audic, S. Adl, D. Bass, L. Belbahri et al., CBOL Protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms, vol.10, p.1001419, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01258240

J. Pawlowski, R. Christen, B. Lecroq, D. Bachar, H. R. Shahbazkia et al., Eukaryotic richness in the abyss: insights from pyrotag sequencing, PLoS ONE, vol.6, p.18169, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00604768

S. A. Podlipaev, Catalogue of world fauna of Trypanosomatidae (Protozoa), Proc Zool Inst Leningrad, vol.144, pp.1-178, 1990.

S. A. Podlipaev, N. R. Sturm, I. Fiala, O. Fernandes, S. J. Westenberger et al., Diversity of insect trypanosomatids assessed from the spliced leader RNA and 5S rRNA genes and intergenic regions, J Eukaryot Microbiol, vol.51, pp.283-290, 2004.

F. Pompanon, E. Coissac, and P. Taberlet, Metabarcoding, une nouvelle façon d'analyser la biodiversité, Biofutur, vol.319, pp.30-32, 2011.

F. Pompanon and S. Samadi, Next generation sequencing for characterizing diversity: promises and challenges, Genetica, vol.143, pp.133-138, 2015.

E. Pruesse, C. Quast, K. Knittel, B. M. Fuchs, W. Ludwig et al., SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res, vol.35, pp.7188-7196, 2007.

F. S. Salani, H. Arndt, K. Hausmann, F. Nitsche, and F. Scheckenbach, Analysis of the community structure of abyssal kinetoplastids revealed similar communities at larger spatial scales, ISME J, vol.6, pp.713-723, 2012.

A. L. Sauvadet, A. Gobet, and . Guillou, Comparative analysis between protist communities from the deep-sea pelagic ecosystem and specific deep hydrothermal habitats, Environ Microbiol, vol.12, pp.2946-2964, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01254021

F. Scheckenbach, K. Hausmann, C. Wylezich, M. Weitere, and H. Arndt, Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor, Proc Natl Acad Sci, vol.107, pp.115-120, 2010.

A. G. Simpson, J. R. Stevens, and J. Lukes, The evolution and diversity of kinetoplastid flagellates, Trends Parasitol, vol.4, pp.168-174, 2006.

L. Simpson, Behavior of the kinetoplast of Leishmania tarentolae upon cell rupture, J Protozool, vol.15, pp.132-136, 1986.

I. ?kodová-sveráková, Z. Verner, T. Skalický, J. Votýpka, A. Horváth et al., Lineage-specific activities of a multipotent mitochondrion of trypanosomatid flagellates, Mol Microbiol, vol.96, pp.55-67, 2015.

J. ?lapeta, D. Moreira, and P. Lopez-garcia, The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes, Proc Biol Sci, vol.272, pp.2073-2081, 2005.

R. F. Stern, A. Horak, R. L. Andrew, M. A. Coffroth, R. A. Andersen et al., Environmental barcoding reveals massive dinoflagellate diversity in marine environments, PLoS ONE, vol.5, p.13991, 2010.

P. H. Stoco, G. Wagner, C. Talavera-lopez, A. Gerber, A. Zaha et al., Genome of the avirulent human-infective Trypanosome-Trypanosoma rangeli, vol.8, p.3176, 2014.

T. Stoeck, M. V. Schwarz, J. Boenigk, M. Schweikert, V. Der-heyden et al., Cellular identity of an 18S rRNA gene sequence clade within the class Kinetoplastea: the novel genus Actuariola gen. nov. (Neobodonida) with description of the type species Actuariola framvarensis sp. nov, Int J Syst Evol Microbiol, vol.55, pp.2623-2635, 2005.

K. Stuart, R. Brun, S. Croft, A. Fairlamb, R. E. Gurtler et al., Kinetoplastids: related protozoan pathogens, different diseases, J Clin Invest, vol.118, pp.1301-1310, 2008.

N. R. Sturm, L. Martinez, and S. Thomas, Kinetoplastid genomics: the thin end of the wedge, Infect Genet Evol, vol.8, pp.901-906, 2008.

A. K. Suarez and N. D. Tsutsui, The value of museum collections for research and society, Bioscience, vol.54, pp.66-73, 2004.

P. Taberlet, E. Coissac, F. Pompanon, C. Brochmann, and E. Willerslev, Towards next-generation biodiversity assessment using DNA metabarcoding, Mol Ecol, vol.21, pp.2045-2050, 2012.

N. Taib, J. F. Mangot, I. Domaizon, G. Bronner, and D. Debroas, Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity, PLoS ONE, vol.8, p.58950, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00840867

M. M. Teixeira, T. C. Borghesan, R. C. Ferreira, M. A. Santos, C. S. Takata et al., Phylogenetic validation of the genera Angomonas and Strigomonas of trypanosomatids harboring bacterial endosymbionts with the description of new species of trypanosomatids and of proteobacterial symbionts, Protist, vol.162, pp.503-524, 2011.

S. Thomas, S. J. Westenberger, D. A. Campbell, and N. R. Sturm, Intragenomic spliced leader RNA array analysis of kinetoplastids reveals unexpected transcribed region diversity in Trypanosoma cruzi, Gene, vol.352, pp.100-108, 2005.

P. Truc, P. Büscher, G. Cuny, M. I. Gonzatti, J. Jannin et al., Atypical human infections by animal trypanosomes, PLoS Negl Trop Dis, vol.7, p.2256, 2013.

J. Tý?, J. Votýpka, H. Klepetková, H. ?uláková, M. Jirk? et al., Growing diversity of trypanosomatid parasites of flies (Diptera: Brachycera): frequent cosmopolitism and moderate host specificity, Mol Phylogenet Evol, vol.69, pp.255-264, 2013.

M. J. Vaerewijck, K. Sabbe, J. Baré, and K. Houf, Microscopic and molecular studies of the diversity of free-living protozoa in meatcutting plants, Appl Environ Microbiol, vol.74, pp.5741-5749, 2008.

E. J. Van-hannen, G. Zwart, M. P. Van-agterveld, H. J. Gons, J. Ebert et al., Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses, Appl Environ Microbiol, vol.65, pp.795-801, 1999.

K. Vickerman, The diversity of the kinetoplastid flagellates, Biology of the Kinetoplastida, pp.1-34, 1976.

K. Vickerman, The evolutionary expansion of the trypanosomatid flagellates, Int J Parasitol, vol.24, pp.1317-1331, 1994.

K. Vickerman and T. M. Preston, Comparative cell biology of the kinetoplastid flagellates, Biology of the Kinetoplastida, pp.35-130, 1976.

L. B. Viola, R. S. Almeida, R. C. Ferreira, M. Campaner, C. Takata et al., Evolutionary history of trypanosomes from South American Caiman (Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes, Int J Parasitol, vol.40, pp.345-355, 2009.

S. Von-der-heyden and T. Cavalier-smith, Culturing and environmental DNA sequencing uncover hidden kinetoplastid diversity and a major marine clade within ancestrally freshwater Bodo designis, Int J Syst Evol Microbiol, vol.55, pp.2605-2621, 2005.

J. Votýpka, C. M. Avila-levy, P. Grellier, D. Maslov, J. Luke? et al., Systematics of Trypanosomatidae: criteria for taxonomic (re-) description, Trends Parasitol, vol.31, pp.460-469, 2015.

J. Votýpka, H. Klepetková, M. Jirk?, P. Kment, and J. Luke?, Phylogenetic relationships of trypanosomatids parasitising true bugs (Insecta: Heteroptera) in sub-Saharan Africa, Int J Parasitol, vol.42, pp.489-500, 2012.

J. Votýpka, A. Y. Kostygov, N. Kraeva, A. Grybchuk-ieremenko, M. Tesa?ová et al., Kentomonas gen. n., a new genus of endosymbiont-containing trypanosomatids of Strigomonadinae subfam, n. Protist, vol.165, pp.825-838, 2014.

J. Votýpka, D. A. Maslov, V. Yurchenko, M. Jirk?, P. Kment et al., Probing into the diversity of trypanosomatid flagellates parasitizing insect hosts in South-West China reveals both endemism and global dispersal, Mol Phylogenet Evol, vol.54, pp.243-253, 2010.

J. Votýpka, J. Rádrová, T. Skalický, M. Jirk?, D. Jirsová et al., A tsetse and tabanid fly survey of African great apes habitats reveals the presence of a novel trypanosome lineage but the absence of Trypanosoma brucei, Int J Parasitol, 2015.

J. Votýpka, E. Suková, N. Kraeva, A. Ishemgulova, I. Du?í et al., Diversity of trypanosomatids (Kinetoplastea: Trypanosomatidae) parasitizing fleas (Insecta: Siphonaptera) and description of a new genus Blechomonas gen, n. Protist, vol.164, pp.763-781, 2013.

G. M. Weinstock, Genomic approaches to studying the human microbiota, Nature, vol.489, pp.250-256, 2013.

S. J. Westenberger, N. R. Sturm, D. Yanega, S. A. Podlipaev, R. Zeledón et al., Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene, Parasitology, vol.129, pp.537-547, 2004.

L. Wilfert, B. Longdon, A. G. Ferreira, F. Bayer, and F. M. Jiggins, Trypanosomatids are common and diverse parasites of Drosophila, Parasitology, vol.138, pp.858-865, 2011.

K. B. Wyatt, P. F. Campos, M. T. Gilbert, S. O. Kolokotronis, W. H. Hynes et al., Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease, PLoS ONE, vol.3, p.3602, 2008.

V. Y. Yurchenko, A. A. Kolesnikov, and J. Luke?, Phylogenetic analysis of Trypanosomatina (Protozoa: Kinetoplastida) based on minicircle conserved regions, Folia Parasitol, vol.47, pp.1-5, 2000.

V. Y. Yurchenko, J. Luke?, M. Jirk?, and D. A. Maslov, Selective recovery of the cultivation-prone components from mixed trypanosomatid infections: a case of several novel species isolated from Neotropical Heteroptera, Int J Syst Evol Microbiol, vol.59, pp.893-909, 2009.

V. Y. Yurchenko, J. Luke?, M. Tesa?ová, M. Jirk?, and D. A. Maslov, Morphological discordance of the new trypanosomatid species phylogenetically associated with the genus Crithidia, Protist, vol.159, pp.99-114, 2008.

L. Zídková, I. Cepicka, J. Szabová, and M. Svobodová, Biodiversity of avian trypanosomes, Infect Genet Evol, vol.12, pp.102-112, 2012.