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Trypanosoma cruzi Genome Assemblies: Challenges and Milestones of Assembling a Highly Repetitive and Complex Genome

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T. cruzi Infection

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1955))

Abstract

Trypanosoma cruzi present one of the most complex parasite genomes sequenced to date. Among its features are 600-kb-long repetitive multigene families’ clusters, hybrid strains, and aneuploidies, which hampered genome assembly completeness and contiguity. Several approaches, such as Sanger sequencing in 2005, next-generation sequencing in 2011 and third-generation sequencing in 2018, were used to improve draft assemblies of different strains of this parasite. Hence, the study of T. cruzi genome assemblies’ history is an excellent way to describe the evolution of genome sequencing methodologies and compare their efficiency and limitations to assembly complex genomes. In this book chapter, we summarize the principal findings and methodologies of T. cruzi genome assembly projects to date, highlighting the improvements and limitations of each approach.

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References

  1. El-Sayed NM (2005) The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309:409–415

    Article  CAS  Google Scholar 

  2. Berriman M, Ghedin E, Hertz-Fowler C (2005) The genome of the African trypanosome, Trypanosoma brucei. Science 309(5733):416–422

    Article  CAS  Google Scholar 

  3. Ivens AC (2005) The genome of the kinetoplastid parasite, Leishmania major. Science 309:436–442

    Article  Google Scholar 

  4. El-Sayed NM (2005) Comparative genomics of trypanosomatid parasitic protozoa. Science 309:404–409

    Article  CAS  Google Scholar 

  5. Zingales B et al (2009) A new consensus for Trypanosoma cruzi intraspecific nomenclature: second revision meeting recommends TcI to TcVI. Mem Inst Oswaldo Cruz 104:1051–1054

    Article  CAS  Google Scholar 

  6. Zingales B et al (2012) The revised Trypanosoma cruzi subspecific nomenclature: rationale, epidemiological relevance and research applications. Infect Genet Evol 12:240–253

    Article  Google Scholar 

  7. Berná L et al (2018) Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi. Microb Genom:279174. https://doi.org/10.1101/279174

  8. Bartholomeu D, El-Sayed NM (2004) Sequencing strategies for parasite genomes. Methods Mol Biol 270:1–16

    CAS  PubMed  Google Scholar 

  9. Venter JC, Smith HO, Hood L (1996) A new strategy for genome sequencing. Nature 381:364–366

    Article  CAS  Google Scholar 

  10. El-Sayed NMA et al (2003) The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Res 31:4856–4863

    Article  CAS  Google Scholar 

  11. Souza RT et al (2011) Genome size, karyotype polymorphism and chromosomal evolution in Trypanosoma cruzi. PLoS One 6:e23042

    Article  CAS  Google Scholar 

  12. Henriksson J et al (2002) Chromosomal size variation in Trypanosoma cruzi is mainly progressive and is evolutionarily informative. Parasitology 124:277–286

    Article  CAS  Google Scholar 

  13. Miller JR et al (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24:2818–2824

    Article  CAS  Google Scholar 

  14. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    Article  CAS  Google Scholar 

  15. Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM (2016) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. bioRxiv:71282. https://doi.org/10.1101/071282

  16. Bartholomeu DC et al (2009) Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi. Nucleic Acids Res 37:3407–3417

    Article  CAS  Google Scholar 

  17. De Pablos LM et al (2011) Differential expression and characterization of a member of the mucin-associated surface protein family secreted by Trypanosoma cruzi. Infect Immun 79:3993–4001

    Article  Google Scholar 

  18. dos Santos SL et al (2012) The MASP family of Trypanosoma cruzi: changes in gene expression and antigenic profile during the acute phase of experimental infection. PLoS Negl Trop Dis 6:e1779

    Article  Google Scholar 

  19. Seco-Hidalgo V, De Pablos LM, Osuna A (2015) Transcriptional and phenotypical heterogeneity of Trypanosoma cruzi cell populations. Open Biol 5:150190

    Article  Google Scholar 

  20. Weatherly DB, Boehlke C, Tarleton RL (2009) Chromosome level assembly of the hybrid Trypanosoma cruzi genome. BMC Genomics 10:255

    Article  Google Scholar 

  21. Aslett M et al (2009) TriTrypDB: a functional genomic resource for the trypanosomatidae. Nucleic Acids Res 38:457–462

    Article  Google Scholar 

  22. Stein LD et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12:1599–1610. https://doi.org/10.1101/gr.403602.12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Stein LD (2013) Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief Bioinform 14:162–171

    Article  CAS  Google Scholar 

  24. Zhang J, Chiodini R, Badr A, Zhang G (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38:95–109

    Article  Google Scholar 

  25. Heather JM, Chain B (2016) The sequence of sequencers: the history of sequencing DNA. Genomics 107:1–8

    Article  CAS  Google Scholar 

  26. Franzén O et al (2011) Shotgun sequencing analysis of Trypanosoma cruzi i Sylvio X10/1 and comparison with T. cruzi VI CL Brener. PLoS Negl Trop Dis 5:1–9

    Google Scholar 

  27. Franzén O et al (2012) Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei. BMC Genomics 13:531

    Article  Google Scholar 

  28. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579

    Article  CAS  Google Scholar 

  29. Tsai IJ, Otto TD, Berriman M (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol 11:R41

    Article  Google Scholar 

  30. Grisard EC et al (2014) Trypanosoma cruzi clone Dm28c draft genome sequence. Genome Announc 2:2–3

    Article  Google Scholar 

  31. Stoco PH et al (2014) Genome of the avirulent human-infective trypanosome – Trypanosoma rangeli. PLoS Negl Trop Dis 8:e3176

    Article  Google Scholar 

  32. Boetzer M et al (2012) Toward almost closed genomes with GapFiller. Genome Biol 13:R56

    Article  Google Scholar 

  33. Baptista RP et al (2018) Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231. Microb Genom 4:e000156. https://doi.org/10.1099/mgen.0.000156

    Article  PubMed Central  Google Scholar 

  34. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  Google Scholar 

  35. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv Prepr. arXiv 0, 3

    Google Scholar 

  36. Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  Google Scholar 

  37. Otto TD, Sanders M, Berriman M, Newbold C (2010) Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 26:1704–1707

    Article  CAS  Google Scholar 

  38. Otto TD, Dillon GP, Degrave WS, Berriman M (2011) RATT: rapid annotation transfer tool. Nucleic Acids Res 39:1–7

    Article  Google Scholar 

  39. Dumetz F et al (2017) Modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments and its impact on gene expression. MBio 8:1–14

    Article  Google Scholar 

  40. Barja PP et al (2017) Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani. Nat Ecol Evol 1:1961–1969

    Article  Google Scholar 

  41. Ubeda J-M et al (2008) Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biol 9:R115

    Article  Google Scholar 

  42. Torres EM, Williams BR, Amon A (2008) Aneuploidy: cells losing their balance. Genetics 179:737–746

    Article  CAS  Google Scholar 

  43. Hassold T, Hunt P (2001) To err (meiotically) is human: the genesis of human aneuploidy. Nat Rev Genet 2:280–291

    Article  CAS  Google Scholar 

  44. Lv L et al (2012) Tetraploid cells from cytokinesis failure induce aneuploidy and spontaneous transformation of mouse ovarian surface epithelial cells. Cell Cycle 11:2864–2875

    Article  CAS  Google Scholar 

  45. Selmecki A, Forche A, Berman J (2010) Genomic plasticity of the human fungal pathogen Candida albicans. Eukaryot Cell 9:991–1008

    Article  CAS  Google Scholar 

  46. Sheltzer JMJ et al (2011) Aneuploidy drives genomic instability in yeast. Science 333:1026–1030

    Article  CAS  Google Scholar 

  47. Sterkers Y, Lachaud L, Crobu L, Bastien P, Pagès M (2011) FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major. Cell Microbiol 13:274–283

    Article  CAS  Google Scholar 

  48. Rogers MB et al (2011) Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res 21:2129–2142

    Article  CAS  Google Scholar 

  49. Downing T et al (2011) Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res 21:2143–2156

    Article  CAS  Google Scholar 

  50. Sterkers Y, Crobu L, Lachaud L, Pagès M, Bastien P (2014) Parasexuality and mosaic aneuploidy in Leishmania: alternative genetics. Trends Parasitol 30:429–435

    Article  Google Scholar 

  51. Reis-Cunha JL et al (2015) Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains. BMC Genomics 16:499

    Article  Google Scholar 

  52. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  Google Scholar 

  53. Chaisson MJ, Tesler G (2012) Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13:238

    Article  CAS  Google Scholar 

  54. McKenna A et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Aaron. Genome Res 20:1297–1303

    Article  CAS  Google Scholar 

  55. Depristo MA et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–501

    Article  CAS  Google Scholar 

  56. Garrison E, Marth G (2012) Haplotype-based variant detection from short-read sequencing. 1–9 . arXiv:1207.3907 [q-bio.GN]

    Google Scholar 

  57. Mannaert A, Downing T, Imamura H, Dujardin JC (2012) Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania. Trends Parasitol 28:370–376

    Article  CAS  Google Scholar 

  58. Dujardin JC, Mannaert A, Durrant C, Cotton JA (2014) Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing. Trends Parasitol 30:554–555

    Article  CAS  Google Scholar 

  59. Iantorno SA et al (2017) Gene expression in Leishmania is regulated predominantly by gene dosage. MBio 8:e01393-17

    Article  Google Scholar 

  60. Buscaglia CA, Campo VA, Frasch ACC, Di Noia JM (2006) Trypanosoma cruzi surface mucins: host-dependent coat diversity. Nat Rev Microbiol 4:229–236

    Article  CAS  Google Scholar 

  61. Quail MA et al (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:1–13

    Article  Google Scholar 

  62. Walker BJ et al (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963

    Article  Google Scholar 

  63. Hackl T, Hedrich R, Schultz J, Förster F (2014) Proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics 30:3004–3011

    Article  CAS  Google Scholar 

  64. Callejas-Hernández F, Gironès N, Fresno M (2018) Genome sequence of Trypanosoma cruzi strain Bug2148. Genome Announc 6:e01497–e01417

    Article  Google Scholar 

  65. Chin C-S et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569

    Article  CAS  Google Scholar 

  66. Andersson B (2011) The Trypanosoma cruzi genome; conserved core genes and extremely variable surface molecule families. Res Microbiol 162:619–625

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

    João Luís Reis-Cunha & Daniella C. Bartholomeu

Authors
  1. João Luís Reis-Cunha
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  2. Daniella C. Bartholomeu
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Corresponding author

Correspondence to Daniella C. Bartholomeu .

Editor information

Editors and Affiliations

  1. INGEBI-CONICET, Buenos Aires, Argentina

    Karina Andrea Gómez

  2. UNSAM-CONICET, IIB-INTECH, San Martin, Buenos Aires, Argentina

    Carlos Andrés Buscaglia

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Reis-Cunha, J.L., Bartholomeu, D.C. (2019). Trypanosoma cruzi Genome Assemblies: Challenges and Milestones of Assembling a Highly Repetitive and Complex Genome. In: Gómez, K., Buscaglia, C. (eds) T. cruzi Infection. Methods in Molecular Biology, vol 1955. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9148-8_1

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  • DOI: https://doi.org/10.1007/978-1-4939-9148-8_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9147-1

  • Online ISBN: 978-1-4939-9148-8

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