Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania

English version

Autoři: Megan A. Sloan ^aff001; Karen Brooks ^aff002; Thomas D. Otto ^aff002; Mandy J. Sanders ^aff002; James A. Cotton ^aff002; Petros Ligoxygakis ^aff001
Působiště autorů: Department of Biochemistry, University of Oxford, Oxford, United Kingdom ^aff001; The Wellcome Sanger Institute, Wellcome Genome Campus, Hixton, Cambridgeshire, United Kingdom ^aff002
Vyšlo v časopise: Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania. PLoS Genet 15(11): e32767. doi:10.1371/journal.pgen.1008452
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1008452

Souhrn

Trypanosomatid parasites are causative agents of important human and animal diseases such as sleeping sickness and leishmaniasis. Most trypanosomatids are transmitted to their mammalian hosts by insects, often belonging to Diptera (or true flies). These are called dixenous trypanosomatids since they infect two different hosts, in contrast to those that infect just insects (monoxenous). However, it is still unclear whether dixenous and monoxenous trypanosomatids interact similarly with their insect host, as fly-monoxenous trypanosomatid interaction systems are rarely reported and under-studied–despite being common in nature. Here we present the genome of monoxenous trypanosomatid Herpetomonas muscarum and discuss its transcriptome during in vitro culture and during infection of its natural insect host Drosophila melanogaster. The H. muscarum genome is broadly syntenic with that of human parasite Leishmania major. We also found strong similarities between the H. muscarum transcriptome during fruit fly infection, and those of Leishmania during sand fly infections. Overall this suggests Drosophila-Herpetomonas is a suitable model for less accessible insect-trypanosomatid host-parasite systems such as sand fly-Leishmania.

Klíčová slova:

Drosophila melanogaster – Protein domains – Transcriptome analysis – Ingestion – Leishmania – Invertebrate genomics – Trypanosoma brucei gambiense – Trypanosoma

Zdroje

1. Pacheco, Raquel S, Marzochi, Mauro CA, Pires, Marize Q, Brito, Célia MM, Madeira, de Fátima Maria, & Barbosa-Santos, Elizabeth GO. (1998). Parasite Genotypically Related to a Monoxenous Trypanosomatid of Dog's Flea Causing Opportunistic Infection in an HIV Positive Patient. Memórias do Instituto Oswaldo Cruz, 93(4), 531–537. doi: 10.1590/s0074-02761998000400021 9711346

2. Zídková L., Cepicka I., Votypka J., Svobodová M. 2010. Herpetomonas trimorpha sp. nov. (Trypanosomatidae, Kinetoplastida), a parasite of the biting midge Culicoides truncorum (Ceratopogonidae, Diptera). International Journal of Systematic and Evolutionary Microbiology. 60(9): pp. 2236–2246.

3. Rowton E. D. and Barclay McGhee R. (1978) ‘Population Dynamics of Herpetomonasampelophilae, with a Note on the Systematics of Herpetomonas from Drosophila spp.’, The Journal of Protozoology. John Wiley & Sons, Ltd (10.1111), 25(2), pp. 232–235. doi: 10.1111/j.1550-7408.1978.tb04402.x

4. Lange C. E., and Lord J. (2012). “Protistan entomopathogens,” in Insect Pathology, 2nd Edn., eds Vega B. and Kaya H.(Amsterdam: Elsevier), 367–394. doi: 10.1016/B978-0-12-384984-7.00010–5

5. Vega F. E. and Kaya H. K. 2012. Insect Pathology. Second Edition. Academic Press. Amsterdam (The Netherlands) and Boston (Massachusetts). Elsevier. ISBN: 978-0-12-384984-7.

6. Erwin T. L. 1983. Tropical forest canopies: the last biotic frontier. Bulletin of the Entomological Society of America, Volume 29: 14–19.

7. Hallmann CA, Sorg M, Jongejans E, Siepel H, Hofland N, et al. (2017) More than 75 percent decline over 27 years in total flying insect biomass in protected areas. PLOS ONE 12(10): e0185809. doi: 10.1371/journal.pone.0185809 29045418

8. Motta M. C. M., Martins A. C., de Souza S. S., Catta-Preta C. M., Silva R., Klein C. C., de Almeida L. G., de Lima Cunha O., Ciapina L. P., Brocchi M. 2013. Predicting the Proteins of Angomonas deanei, Strigomonas culicis and Their Respective Endosymbionts Reveals New Aspects of the Trypanosomatidae Family. PLoS ONE. 8(4): e60209. doi: 10.1371/journal.pone.0060209 23560078

9. Schmid-Hempel P. et al. (2018) ‘The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees’, PLoS ONE, 13(1). doi: 10.1371/journal.pone.0189738 29304093

10. Runckel C., DeRisi J., Flenniken M. L. 2014. A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae. PLoS ONE, 9(4).

11. Flegontov P., Butenko A., Firsov S., Kraeva N., Eliáš M., Field M. C., Filatov D., Flegontova O., Gerasimov E. S., Hlaváčová J. et al., 2016. Genome of Leptomonas pyrrhocoris: A high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Scientific Reports, 6.

12. Teixeira S. M., de Paiva R. M., Kangussu-Marcolino M. M., Darocha W. D. 2012. Trypanosomatid comparative genomics: Contributions to the study of parasite biology and different parasitic diseases. Genetics and Molecular Biology, 35(1): pp. 1–17. 22481868

13. Zoltner M, Krienitz N, Field MC, Kramer S (2018) Comparative proteomics of the two T. brucei PABPs suggests that PABP2 controls bulk mRNA. PLOS Neglected Tropical Diseases 12(7): e0006679. doi: 10.1371/journal.pntd.0006679 30040867

14. Stuart K., Allen T. E., Heidmann S., Seiwert S. D. 1997. RNA editing in kinetoplastid protozoa. Microbiology and Molecular Biology Reviews, 61(1): pp. 105–120. 9106367

15. Liang X. Haritan, A., Uliel, S., Michaeli, S. 2003. trans and cis Splicing in Trypanosomatids: Mechanism, Factors, and Regulation. Eukaryotic Cell, 2(5): pp. 830–840. doi: 10.1128/EC.2.5.830-840.2003 14555465

16. Chen J., Rauch C. A., White J. H., Englund P. T., Cozzarelli N. R. 1995. The topology of the kinetoplast DNA network. Cell, 80(1): pp. 61–69. doi: 10.1016/0092-8674(95)90451-4 7813018

17. Lukeš J., Guilbride D. L., Votýpka J., Zíková A., Benne R., Englund P. T. 2002. Kinetoplast DNA Network: Evolution of an Improbable Structure. Eukaryotic Cell, 1(4): pp. 495–502. doi: 10.1128/EC.1.4.495-502.2002 12455998

18. Borghesan T. C., Ferreira R. C., Takata C. S., Campaner M., Borda C. C., Paiva F., Milder R. V., Teixeira M. M., Camargo E. P. 2013. Molecular Phylogenetic Redefinition of Herpetomonas (Kinetoplastea, Trypanosomatidae), a Genus of Insect Parasites Associated with Flies. Protist. Urban & Fischer, 164(1): pp. 129–152.

19. Simpson L. and Thiemann O. H. 1995. Sense from nonsense: RNA editing in mitochondria of kinetoplastid protozoa and slime molds. Cell, 81: pp. 837–840. doi: 10.1016/0092-8674(95)90003-9 7781060

20. Wang L., Sloan M., Ligoxygakis P. 2018. Intestinal NF-κB and STAT signalling is important for uptake and clearance in a Drosophila-Herpetomonas interaction model. PLoS Genetics.

21. Van Den Abbeele J., & Rotureau B. (2013). New insights in the interactions between African trypanosomes and tsetse flies. Frontiers in cellular and infection microbiology, 3, 63. doi: 10.3389/fcimb.2013.00063 24137569

22. Vurture G. W., Sedlazeck F. J., Nattestad M., Underwood C. J., Fang H., Gurtowski J., Schatz M. C. 2017. GenomeScope: fast reference-free genome profiling from short reads, Bioinformatics, 33(14): pp. 2202–2204. doi: 10.1093/bioinformatics/btx153 28369201

23. Steinbiss S., Silva-Franco F., Brunk B., Foth B., Hertz-Fowler C., Berriman M., Otto T. D. 2016. Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Research, 44: pp. W29–W34. doi: 10.1093/nar/gkw292 27105845

24. Berriman M., Ghedin E., Hertz-Fowler C., Blandin G., Renauld H., Bartholomeu D. C., Lennard N. J., Caler E., Hamlin N. E., Haas B., et al. 2005. The Genome of the African Trypanosome Trypanosoma brucei. Science 309(5733): 416 LP–422.

25. Thomas S., Green A., Sturm N. R., Campbell D. A., & Myler P. J. (2009). Histone acetylations mark origins of polycistronic transcription in Leishmania major. BMC genomics, 10, 152. doi: 10.1186/1471-2164-10-152 19356248

26. Daniels J. P., Gull K., & Wickstead B. 2010. Cell biology of the trypanosome genome. Microbiology and molecular biology reviews: MMBR, 74(4): pp. 552–569. doi: 10.1128/MMBR.00024-10 21119017

27. El-Sayed N. M., Myler P. J., Blandin G., et al. (2005) ‘Comparative Genomics of Trypanosomatid Parasitic Protozoa’, Science, 309(5733), p. 404 LP-409. doi: 10.1126/science.1112181 16020724

28. Yurchenko V., Kostygov A., Havlová J., Grybchuk-Ieremenko A., Ševčíková T., Lukeš J., Ševčík J., Votýpka J. 2016. Diversity of Trypanosomatids in Cockroaches and the Description of Herpetomonas tarakana sp. n.’, Journal of Eukaryotic Microbiology. 63(2): pp. 198–209. doi: 10.1111/jeu.12268 26352484

29. Jackson A. P., Vaughan S. and Gull K. (2006) ‘Evolution of Tubulin Gene Arrays in Trypanosomatid parasites: genomic restructuring in Leishmania’, BMC Genomics. London: BioMed Central, 7, p. 261. doi: 10.1186/1471-2164-7-261 17044946

30. Emms D. and Kelly S. 2015. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology. 16(157).

31. Sutterwala S. S., Hsu F., Sevova E. S., Schwartz K. J., Zhang K., Key P., Turk J., Beverley S. M., Bangs J. D. 2008. Developmentally regulated sphingolipid synthesis in African trypanosomes. Molecular Microbiology, 70: pp. 281–296. doi: 10.1111/j.1365-2958.2008.06393.x 18699867

32. Zhang K., Showalter M., Revollo J., Hsu F. F., Turk J., Beverley S. M. 2003. Sphingolipids are essential for differentiation but not growth in Leishmania. EMBO J., 22: pp. 6016–6026. doi: 10.1093/emboj/cdg584 14609948

33. Vanlerberghe G. C. and McIntosh L. (1997) ‘Alternative Oxidase: From Gene to Function’, Annual Review of Plant Physiology and Plant Molecular Biology. Annual Reviews, 48(1), pp. 703–734. doi: 10.1146/annurev.arplant.48.1.703 15012279

34. Jackson A. P. 2007. Origins of amino acid transporter loci in trypanosomatid parasites. BMC evolutionary biology, 7, 26. doi: 10.1186/1471-2148-7-26 17319943

35. Shaked‐Mishan P., Suter‐Grotemeyer M., Yoel‐Almagor T., Holland N., Zilberstein D. and Rentsch D. 2006. A novel high‐affinity arginine transporter from the human parasitic protozoan Leishmania donovani. Molecular Microbiology, 60: pp. 30–38. doi: 10.1111/j.1365-2958.2006.05060.x 16556218

36. Martin J. L. et al. (2014) ‘Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani’, PLoS pathogens. Public Library of Science, 10(2), p. e1003938. doi: 10.1371/journal.ppat.1003938 24586154

37. Inbar E., Hughitt V. K., Dillon L. A. L., Ghosh K., El-Sayed N. M. and Sacks D. L. 2017. The Transcriptome of Leishmania major Developmental Stages in Their Natural Sand Fly Vector, mBio, 8(2). doi: 10.1128/mBio.00029-17 28377524

38. Kolev N. G., Ullu E. and Tschudi C. (2014) The emerging role of RNA-binding proteins in the life cycle of Trypanosoma brucei. Cellular microbiology 16(4): 482–489. doi: 10.1111/cmi.12268 24438230

39. Naguleswaran A., Gunasekera K., Schimanski B., Heller M., Hemphill A., Ochsenreiter T. and Roditi I. (2015) Trypanosoma brucei RRM1 Is a Nuclear RNA-Binding Protein and Modulator of Chromatin Structure. mBio 6(2): e00114–15. doi: 10.1128/mBio.00114-15 25784696

40. Wippel H. H., Malgarin J. S., Martins S. de T., Vidal N. M., Marcon B. H., Miot H. T., Marchini F. K., Goldenberg S. and Alves. (2019) The Nuclear RNA-binding Protein RBSR1 Interactome in Trypanosoma cruzi. Journal of Eukaryotic Microbiology. John Wiley & Sons, Ltd

41. Wurst M., Seliger B., Jha B. A., Klein C., Queiroz R., Clayton C. Expression of the RNA recognition motif protein RBP10 promotes a bloodstream-form transcript pattern in Trypanosoma brucei. Mol Microbiol. 2012; 83:1048–1063.1111) 66(2): 244–253. doi: 10.1111/j.1365-2958.2012.07988.x 22296558

42. Jones N. G. et al. (2014) ‘Regulators of Trypanosoma brucei cell cycle progression and differentiation identified using a kinome-wide RNAi screen’, PLoS pathogens. Public Library of Science, 10(1), pp. e1003886–e1003886. doi: 10.1371/journal.ppat.1003886 24453978

43. Acosta-Serrano A. et al. (2001) ‘The surface coat of procyclic Trypanosoma brucei: Programmed expression and proteolytic cleavage of procyclin in the tsetse fly’, Proceedings of the National Academy of Sciences. National Academy of Sciences, 98(4), pp. 1513–1518. doi: 10.1073/pnas.041611698 11171982

44. Haines L. R. et al. (2010) ‘Tsetse EP protein protects the fly midgut from trypanosome establishment’, PLoS pathogens. Public Library of Science, 6(3), pp. e1000793–e1000793. doi: 10.1371/journal.ppat.1000793 20221444

45. Pimenta P. F. et al. (1992) ‘Stage-specific adhesion of Leishmania promastigotes to the sandfly midgut’, Science, 256(5065), pp. 1812 LP–1815. doi: 10.1126/science.1615326 1615326

46. Kamhawi S. et al. (2004) ‘A role for insect galectins in parasite survival.’, Cell. United States, 119(3), pp. 329–341.

47. Urwyler S., Studler E., Renggli C. K., Roditi I. 2007. A family of stage-specific alanine-rich proteins on the surface of epimastigote forms of Trypanosoma brucei. Mol Microbiol., 63: pp. 218–228 doi: 10.1111/j.1365-2958.2006.05492.x 17229212

48. Fragoso C. M., Schumann Burkard G., Oberle M., Renggli C. K., Hilzinger K., Roditi I. 2009. PSSA-2, a Membrane-Spanning Phosphoprotein of Trypanosoma brucei, Is Required for Efficient Maturation of Infection. PLoS ONE, 4(9):e7074 doi: 10.1371/journal.pone.0007074 19759911

49. Casas-Sánchez A. and Acosta-Serrano Á. (2016) Skin deep. eLife. eLife Sciences Publications, Ltd 5: e21506. doi: 10.7554/eLife.21506 27740910

50. Pereira F., Santos-Mallet J. R., Branquinha M. H., d'Avila-Levy C. M., Santos A. L. 2010. Influence of leishmanolysin-like molecules of Herpetomonas samuelpessoai on the interaction with macrophages. Microbes and infection, doi: 10.1016/j.micinf.2010.07.010 20670690

51. D’Archivio S. and Wickstead B. (2017) ‘Trypanosome outer kinetochore proteins suggest conservation of chromosome segregation machinery across eukaryotes’, The Journal of Cell Biology, 216(2), p. 379 LP–391. doi: 10.1083/jcb.201608043 28034897

52. Robinson K.A. and Beverley S.M., 2003. Improvements in transfection efficiency and tests of RNA interference (RNAi) approaches in the protozoan parasite Leishmania. Molecular and biochemical parasitology, 128(2), pp.217–228. doi: 10.1016/s0166-6851(03)00079-3 12742588

53. DaRocha W.D., Otsu K. and Teixeira S.M., 2004. Tests of cytoplasmic RNA interference (RNAi) and construction of a tetracyclineinducible T7 promoter system in Trypanosome cruzi. Mol Biochem Parasitol, 133(2): pp.175–186 doi: 10.1016/j.molbiopara.2003.10.005 14698430

54. Beverley S.M., 2003. Protozomics: trypanosomatid parasite genetics comes of age. Nature Reviews Genetics, 4(1): pp.11 doi: 10.1038/nrg980 12509749

55. Lye L. F., Owens K., Shi H., Murta S. M. F., Vieira A. C., Turco S. J., Tschudi C., Ullu E., Beverley. 2010. Retention and Loss of RNA Interference Pathways in Trypanosomatid Protozoans. PLOS Pathogens, 6(10): e1001161. doi: 10.1371/journal.ppat.1001161 21060810

56. Peacock C. S., Seeger K., Harris D., Murphy L., Ruiz J. C., Quail M. A., Peters N., Adlem E., Tivey A., Aslett M., Kerhornou A., et al. 2007. Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat. Genet. 39(7): pp. 839–47. doi: 10.1038/ng2053 17572675

57. Vingron M. et al. (2007) ‘Improved detection of overrepresentation of Gene-Ontology annotations with parent–child analysis’, Bioinformatics, 23(22), pp. 3024–3031. doi: 10.1093/bioinformatics/btm440 17848398

58. Tu X. and Wang C. C. (2004) ‘The Involvement of Two cdc2-related Kinases (CRKs) in Trypanosoma brucei Cell Cycle Regulation and the Distinctive Stage-specific Phenotypes Caused by CRK3 Depletion’, Journal of Biological Chemistry, 279(19), pp. 20519–20528. doi: 10.1074/jbc.M312862200 15010459

59. Hammarton T. C., Engstler M. and Mottram J. C. (2004) ‘The Trypanosoma brucei Cyclin, CYC2, Is Required for Cell Cycle Progression through G1 Phase and for Maintenance of Procyclic Form Cell Morphology’, Journal of Biological Chemistry, 279(23), pp. 24757–24764. doi: 10.1074/jbc.M401276200 15039435

60. Liu Y., Hu H. and Li Z. (2013) ‘The cooperative roles of PHO80-like cyclins in regulating the G1/S transition and posterior cytoskeletal morphogenesis in Trypanosoma brucei’, Molecular Microbiology. John Wiley & Sons, Ltd (10.1111), 90(1), pp. 130–146. doi: 10.1111/mmi.12352 23909752

61. Monnerat S. et al. (2013) ‘Identification and Functional Characterisation of CRK12:CYC9, a Novel Cyclin-Dependent Kinase (CDK)-Cyclin Complex in Trypanosoma brucei’, PloS one. Public Library of Science, 8(6), pp. e67327–e67327. doi: 10.1371/journal.pone.0067327 23805309

62. Lee S. H., Stephens J. L., Paul K. S., Englund P. T. 2006. Fatty Acid Synthesis by Elongases in Trypanosomes. Cell, 126(4): pp. 691–699. doi: 10.1016/j.cell.2006.06.045 16923389

63. Svärd S. G. et al. (1998) ‘Differentiation-associated surface antigen variation in the ancient eukaryote Giardia lamblia’, Molecular Microbiology. John Wiley & Sons, Ltd (10.1111), 30(5), pp. 979–989. doi: 10.1046/j.1365-2958.1998.01125.x 9988475

64. Adam R. D. (2001) ‘Biology of Giardia lamblia’, Clinical Microbiology Reviews, 14(3), p. 447 LP–475. doi: 10.1128/CMR.14.3.447–475.2001

65. Nash T. E. et al. (1988) ‘Antigenic variation in Giardia lamblia.’, The Journal of Immunology, 141(2), p. 636 LP–641.

66. Aitcheson N. et al. (2005) ‘VSG switching in Trypanosoma brucei: antigenic variation analysed using RNAi in the absence of immune selection’, Molecular microbiology, 57(6), pp. 1608–1622. doi: 10.1111/j.1365-2958.2005.04795.x 16135228

67. Käll L., Krogh A., Sonnhammer E. L. L. 2004. A Combined Transmembrane Topology and Signal Peptide Prediction Method. Journal of Molecular Biology, 338(5): pp. 1027–1036. doi: 10.1016/j.jmb.2004.03.016 15111065

68. Van Damme E. and Van Loock M. (2014) ‘Functional annotation of human cytomegalovirus gene products: an update’, Frontiers in microbiology. Frontiers Media S.A., 5, p. 218. doi: 10.3389/fmicb.2014.00218 24904534

69. Matthews K. R. (2005) ‘The developmental cell biology of Trypanosoma brucei’, Journal of cell science, 118(Pt 2), pp. 283–290. doi: 10.1242/jcs.01649 15654017

70. Savage A. F. et al. (2016) ‘Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans’, PloS one. Public Library of Science, 11(12), pp. e0168877–e0168877. doi: 10.1371/journal.pone.0168877 28002435

71. Krogh A., Larsson B., von Heijne G., and Sonnhammer E. L. L. 2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology, 305(3): pp. 567–580. doi: 10.1006/jmbi.2000.4315 11152613

72. de Paiva RMC, Grazielle-Silva V, Cardoso MS, Nakagaki BN, Mendonça-Neto RP, et al. (2015) Amastin Knockdown in Leishmania braziliensis Affects Parasite-Macrophage Interaction and Results in Impaired Viability of Intracellular Amastigotes. PLOS Pathogens 11(12): e1005296. doi: 10.1371/journal.ppat.1005296 26641088

73. Kangussu-Marcolino M. M., de Paiva R. M. C., Araújo P. R., de Mendonça-Neto R. P., Lemos L., Bartholomeu D. C., Mortara R. A., da Rocha W. D., Teixeira S. M. R. 2013. Distinct genomic organization, mRNA expression and cellular localization of members of two amastin sub-families present in Trypanosoma cruzi. BMC Microbiology, 13(1): pp. 10.

74. Fankhauser N. and Mäser P. (2005) Identification of GPI anchor attachment signals by a Kohonen self-organizing map. Bioinformatics. 21(9), pp. 1846–1852. doi: 10.1093/bioinformatics/bti299 15691858

75. Darlyuk I. et al. (2009) ‘Arginine Homeostasis and Transport in the Human Pathogen Leishmania donovani’, Journal of Biological Chemistry, 284(30), pp. 19800–19807. doi: 10.1074/jbc.M901066200 19439418

76. Marchese L. et al. (2018) ‘The Uptake and Metabolism of Amino Acids, and Their Unique Role in the Biology of Pathogenic Trypanosomatids’, Pathogens. doi: 10.3390/pathogens7020036 29614775

77. Cunningham M. L. and Beverley S. M. 2001. ‘Pteridine salvage throughout the Leishmania infectious cycle: implications for antifolate chemotherapy. Molecular and Biochemical Parasitology. Elsevier, 113(2): pp. 199–213. doi: 10.1016/s0166-6851(01)00213-4 11295174

78. Gourguechon S. and Wang C. C. (2009) ‘CRK9 contributes to regulation of mitosis and cytokinesis in the procyclic form of Trypanosoma brucei’, BMC cell biology. BioMed Central, 10, p. 68. doi: 10.1186/1471-2121-10-68 19772588

79. Gupta S. K., Kosti I., Plaut G., Pivko A., Tkacz I. D., Cohen-Chalamish S., et al. (2013) The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability. Nucleic Acids Res. 41:6577–6594 doi: 10.1093/nar/gkt369 23666624

80. Smith T. K. et al. (2017) ‘Metabolic reprogramming during the Trypanosoma brucei lifecycle’, F1000Research. F1000Research, 6, p. F1000 Faculty Rev-683. doi: 10.12688/f1000research.10342.2 28620452

81. Benz C., Mulindwa J., Ouna B., Clayton C. (2011) The Trypanosoma brucei zinc finger protein ZC3H18 is involved in differentiation. Mol Biochem Parasitol. 177:148–151. doi: 10.1016/j.molbiopara.2011.02.007 21354218

82. Droll D., Minia I., Fadda A., Singh A., Stewart M., Queiroz R., Clayton C. (2013) Post-transcriptional regulation of the trypanosome heat shock response by a zinc finger protein. PLoS Pathog. 9:e1003286. doi: 10.1371/journal.ppat.1003286 23592996

83. Subota I., Rotureau B., Blisnick T., Ngwabyt S., Durand-Dubief M., Engstler M., Bastin P. (2011) ALBA proteins are stage regulated during trypanosome development in the tsetse fly and participate in differentiation. Mol Biol Cell. 22:4205–4219. doi: 10.1091/mbc.E11-06-0511 21965287

84. Dang H. Q. and Li Z. (2011) ‘The Cdc45·Mcm2-7·GINS protein complex in trypanosomes regulates DNA replication and interacts with two Orc1-like proteins in the origin recognition complex’, The Journal of biological chemistry. 2011/07/28. American Society for Biochemistry and Molecular Biology, 286(37), pp. 32424–32435. doi: 10.1074/jbc.M111.240143 21799014

85. DeBrot A., Lancaster C. and Bjornsti M.A. (2016) ‘Function of Cdc45 in DNA Replication and in Response to Genotoxic Stress’, The FASEB Journal. Federation of American Societies for Experimental Biology, 30(1_supplement), p. 798.2 798.2. doi: 10.1096/fj.15-275990

86. Kawale A. S. and Povirk L. F. (2018) ‘Tyrosyl-DNA phosphodiesterases: rescuing the genome from the risks of relaxation’, Nucleic acids research. 2017/12/04. Oxford University Press, 46(2), pp. 520–537. doi: 10.1093/nar/gkx1219 29216365

87. Capul A. A. et al. (2007) ‘Two Functionally Divergent UDP-Gal Nucleotide Sugar Transporters Participate in Phosphoglycan Synthesis in Leishmania major’, Journal of Biological Chemistry, 282(19), pp. 14006–14017. doi: 10.1074/jbc.M610869200 17347153

88. Pita S. et al. (2019) ‘The Tritryps Comparative Repeatome: Insights on Repetitive Element Evolution in Trypanosomatid Pathogens’, Genome biology and evolution. Oxford University Press, 11(2), pp. 546–551. doi: 10.1093/gbe/evz017 30715360

89. Jackson A. P. 2016. Gene family phylogeny and the evolution of parasite cell surfaces. Molecular and Biochemical Parasitology, 209(1): pp. 64–75.

90. Kozarewa I., Ning Z., Quail M. A., Sanders M. J., Berriman M., Turner D. J. 2009. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods, 6: pp. 291–295. doi: 10.1038/nmeth.1311 19287394

91. Iraad F., Bronner M. A., Quail D. J., Turner H. S. 2014. Improved Protocols for Illumina Sequencing. Curr. Protoc. Hum. Genet., 80:18(2): pp. 1–42.

92. Eid J. L., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P., Bettman B., Bibillo A., et al. 2009. Real-time DNA sequencing from single polymerase molecules. Science, 323: pp. 133–138 doi: 10.1126/science.1162986 19023044

93. Chin C. S., Alexander D. H., Marks P., Klammer A. A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., Eichler E. E., Turner S. W., Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569 doi: 10.1038/nmeth.2474 23644548

94. Otto T. D., Sanders M., Berriman M., Newbold C. 2010. Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinforma. Oxf. Engl. 26: pp. 1704–1707.

95. Hunt M., Kikuchi T., Sanders M., Newbold C., Berriman M., Otto T. D. 2013. REAPR: a universal tool for genome assembly evaluation. Genome Biol, 14: R47 doi: 10.1186/gb-2013-14-5-r47 23710727

96. Marçais G. and Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27(6): pp. 764–770. doi: 10.1093/bioinformatics/btr011 21217122

97. Kim D., Langmead B. and Salzberg S. L. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12, pp. 357. doi: 10.1038/nmeth.3317 25751142

98. Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D. R., Pimentel H., Salzberg S. L., Rinn J. L., Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7: pp. 562. doi: 10.1038/nprot.2012.016 22383036

99. Jackson A. P., Sanders M., Berry A., McQuillan J., Aslett M. A., Quail M. A., Chukualim B., Capewell P., MacLeod A., Melville S. E., Gibson W., Barry J. D., Berriman M., Hertz-Fowler C. 2010. The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human African trypanosomiasis. PLoS Negl. Trop. Dis., 13(4):e658.

100. Jackson A. P., Berry A., Aslett M., Allison H. C., Burton P., Vavrova-Anderson J., Brown R., Browne H., Corton N., Hauser H. et al. 2012. Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species. PNAS, 109: pp. 3416–3421. doi: 10.1073/pnas.1117313109 22331916

101. Carnes J., Anupama A., Balmer O., Jackson A., Lewis M., Brown R., Cestari I., Desquesnes M., Gendrin C., Hertz-Fowler C. 2015. Genome and Phylogenetic Analyses of Trypanosoma evansi Reveal Extensive Similarity to T. brucei and Multiple Independent Origins for Dyskinetoplasty. PLOS Neglected Tropical Diseases. Public Library of Science 9(1): e3404. doi: 10.1371/journal.pntd.0003404 25568942

102. Kelly S., Ivens A., Manna P. T., Gibson W., Field M. C. 2014. A draft genome for the African crocodilian trypanosome Trypanosoma grayi. Sci Data. 5(1):140024.

103. Stoco P. H., Wagner G., Talavera-Lopez C., Gerber A., Zaha A., et al. 2014. Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli. PLOS Neglected Tropical Diseases, 8(9): e3176. doi: 10.1371/journal.pntd.0003176 25233456

104. Kelly S., Ivens A., Mott G. A., O'Neill E., Emms D., Macleod O., Voorheis P., Tyler K., Clark M., Matthews J., Matthews K., Carrington M. 2017. An Alternative Strategy for Trypanosome Survival in the Mammalian Bloodstream Revealed through Genome and Transcriptome Analysis of the Ubiquitous Bovine Parasite Trypanosoma (Megatrypanum) theileri. Genome Biol Evol., 9(8): pp. 2093–2109. doi: 10.1093/gbe/evx152 28903536

105. Downing T., Imamura H., Decuypere S., Clark T. G., Coombs G. H., Cotton J. A., Hilley J. D., de Doncker S., Maes I., Mottram J. C., et al. 2011. Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res, 21(12): pp. 2143–56. doi: 10.1101/gr.123430.111 22038251

106. Ivens A. C., Peacock C. S., Worthey E. A., Murphy L., Aggarwal G., Berriman M., Sisk E., Rajandream M. A., Adlem E., Aert R., et al. 2005. The genome of the kinetoplastid parasite, Leishmania major. Science, 309(5733): pp. 436–42. doi: 10.1126/science.1112680 16020728

107. Kraeva N., Butenko A., Hlaváčová J., Kostygov A., Myškova J., Grybchuk D., Leštinová T., Votýpka J., Volf P., Opperdoes F., Flegontov P., Lukeš J., Yurchenko V. 2015. Leptomonas seymouri: Adaptations to the Dixenous Life Cycle Analyzed by Genome Sequencing, Transcriptome Profiling and Co-infection with Leishmania donovani. PLoS Pathog., 11(8):e1005127. doi: 10.1371/journal.ppat.1005127 26317207

108. Runckel C., DeRisi J., & Flenniken M. L. (2014). A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae. PloS one, 9(4), e95057. doi: 10.1371/journal.pone.0095057 24743507

109. Porcel B. M., Denoeud F., Opperdoes F., Noel B., Madoui M-A., Hammarton T. C., Field M. C., Da Silva, Couloux A., Poulain J., et al. 2014. The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants. PLoS genetics. e1004007. doi: 10.1371/journal.pgen.1004007 24516393

110. Jackson A. P., Quail M. A., Berriman M. 2008. Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa). BMC Genomics. 9(9):594.

111. Aslett M., Aurrecoechea C., Berriman M., Brestelli J., Brunk B. P., Carrington M., Depledge D. P., Fischer S., Garjria B., Gao X., et al., 2010. TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Research. 38(37): D457–D462

112. Anders S., Pyl P. T. and Huber W. 2015. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics, 31(2): pp. 166–169. doi: 10.1093/bioinformatics/btu638 25260700

113. Love M. I., Huber W., Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15: pp. 550. doi: 10.1186/s13059-014-0550-8 25516281