Genome size, karyotype polymorphism and chromosomal evolution in Trypanosoma cruzi

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Souza, Renata T ^a   Lima, Fábio M ^a   Barros, Roberto Moraes ^a   Cortez, Danielle R ^a   Santos, Michele F ^a   Cordero, Esteban M ^a,e   Ruiz, Jeronimo Conceiçao ^b   Goldenberg, Samuel ^c   Teixeira, Marta M G ^d   da Silveira, José Franco ^a  

^a FEDERAL UNIVERSITY OF SÃO PAULO   (Brazil)

^b INSTITUTO OSWALDO CRUZ   (Brazil)

^c INSTITUTO CARLOS CHAGAS   (Brazil)

^d UNIVERSITY OF SÃO PAULO   (Brazil)

^e UNIVERSITY OF TEXAS AT EL PASO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTOZOAL DNA; SATELLITE DNA;

ARTICLE; CHROMOSOMAL EVOLUTION; CHROMOSOME BAND; CHROMOSOME DUPLICATION; CHROMOSOME NUMBER; CHROMOSOME POLYMORPHISM; CHROMOSOME SIZE; CHROMOSOME STRUCTURE; CONTROLLED STUDY; DNA CONTENT; DNA DETERMINATION; GENE AMPLIFICATION; GENE DOSAGE; GENE LOCUS; GENE REARRANGEMENT; GENETIC CONSERVATION; GENETIC POLYMORPHISM; GENOME ANALYSIS; GENOME SIZE; KARYOTYPE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PROTOZOAL GENETICS; RETROPOSON; SPECIES COMPARISON; STRAIN DIFFERENCE; SYNTENY; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI; CHROMOSOME; CHROMOSOME MAP; CLASSIFICATION; COPY NUMBER VARIATION; GENETICS; GENOME; PULSED FIELD GEL ELECTROPHORESIS; SPECIES DIFFERENCE;

TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI;

CHROMOSOME MAPPING; CHROMOSOMES; DNA COPY NUMBER VARIATIONS; DNA, PROTOZOAN; DNA, SATELLITE; ELECTROPHORESIS, GEL, PULSED-FIELD; EVOLUTION, MOLECULAR; GENOME SIZE; GENOME, PROTOZOAN; KARYOTYPE; POLYMORPHISM, GENETIC; SPECIES SPECIFICITY; SYNTENY; TRYPANOSOMA BRUCEI BRUCEI; TRYPANOSOMA CRUZI;

EID: 80051621434     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023042     Document Type: Article

References (61)

1. Rassi A Jr, Rassi A, Marin-Neto JA, (2010) Chagas disease. Lancet 375: 1388-1402.
2. Schmunis GA, Yadon ZE, (2010) Chagas disease: a Latin American health problem becoming a world health problem. Acta Trop 115: 14-21.
3. Bern C, Montgomery SP, Herwaldt BL, Rassi A Jr, Marin-Neto JA, et al. (2007) Evaluation and treatment of chagas disease in the United States: a systematic review. JAMA 298: 2171-2181.
4. Tibayrenc M, (2003) Genetic subdivisions within Trypanosoma cruzi (Discrete Typing Units) and their relevance for molecular epidemiology and experimental evolution. Kinetoplastid Biol Dis 2: 12.
5. Tibayrenc M, (1998) Genetic epidemiology of parasitic protozoa and other infectious agents: the need for an integrated approach. Int J Parasitol 28: 85-104.
6. Tibayrenc M, Ward P, Moya A, Ayala FJ, (1986) Natural populations of Trypanosoma cruzi, the agent of Chagas disease, have a complex multiclonal structure. Proc Natl Acad Sci U S A 83: 115-119.
7. Tomazi L, Kawashita SY, Pereira PM, Zingales B, Briones MR, (2009) Haplotype distribution of five nuclear genes based on network genealogies and Bayesian inference indicates that Trypanosoma cruzi hybrid strains are polyphyletic. Genet Mol Res 8: 458-476.
8. Westenberger SJ, Barnabe C, Campbell DA, Sturm NR, (2005) Two hybridization events define the population structure of Trypanosoma cruzi. Genetics 171: 527-543.
9. Gaunt MW, Yeo M, Frame IA, Stothard JR, Carrasco HJ, et al. (2003) Mechanism of genetic exchange in American trypanosomes. Nature 421: 936-939.
10. de Freitas JM, Augusto-Pinto L, Pimenta JR, Bastos-Rodrigues L, Goncalves VF, et al. (2006) Ancestral genomes, sex, and the population structure of Trypanosoma cruzi. PLoS Pathog 2: e24.
11. Zingales B, Andrade SG, Briones MR, Campbell DA, Chiari E, 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.
12. Henriksson J, Pettersson U, Solari A, (1993) Trypanosoma cruzi: correlation between karyotype variability and isoenzyme classification. Exp Parasitol 77: 334-348.
13. Henriksson J, Aslund L, Pettersson U, (1996) Karyotype variability in Trypanosoma cruzi. Parasitol Today 12: 108-114.
14. Henriksson J, Dujardin JC, Barnabe C, Brisse S, Timperman G, et al. (2002) Chromosomal size variation in Trypanosoma cruzi is mainly progressive and is evolutionarily informative. Parasitology 124: 277-286.
15. Henriksson J, Aslund L, Macina RA, Franke de Cazzulo BM, Cazzulo JJ, et al. (1990) Chromosomal localization of seven cloned antigen genes provides evidence of diploidy and further demonstration of karyotype variability in Trypanosoma cruzi. Mol Biochem Parasitol 42: 213-223.
16. Pedroso A, Cupolillo E, Zingales B, (2003) Evaluation of Trypanosoma cruzi hybrid stocks based on chromosomal size variation. Mol Biochem Parasitol 129: 79-90.
17. Vargas N, Pedroso A, Zingales B, (2004) Chromosomal polymorphism, gene synteny and genome size in T. cruzi I and T. cruzi II groups. Mol Biochem Parasitol 138: 131-141.
18. Cano MI, Gruber A, Vazquez M, Cortes A, Levin MJ, et al. (1995) Molecular karyotype of clone CL Brener chosen for the Trypanosoma cruzi genome project. Mol Biochem Parasitol 71: 273-278.
19. Henriksson J, Porcel B, Rydaker M, Ruiz A, Sabaj V, et al. (1995) Chromosome specific markers reveal conserved linkage groups in spite of extensive chromosomal size variation in Trypanosoma cruzi. Mol Biochem Parasitol 73: 63-74.
20. Santos MR, Cano MI, Schijman A, Lorenzi H, Vazquez M, et al. (1997) The Trypanosoma cruzi genome project: nuclear karyotype and gene mapping of clone CL Brener. Mem Inst Oswaldo Cruz 92: 821-828.
21. Lewis MD, Llewellyn MS, Gaunt MW, Yeo M, Carrasco HJ, et al. (2009) Flow cytometric analysis and microsatellite genotyping reveal extensive DNA content variation in Trypanosoma cruzi populations and expose contrasts between natural and experimental hybrids. Int J Parasitol 39: 1305-1317.
22. McDaniel JP, Dvorak JA, (1993) Identification, isolation, and characterization of naturally-occurring Trypanosoma cruzi variants. Mol Biochem Parasitol 57: 213-222.
23. Thompson CT, Dvorak JA, (1989) Quantitation of total DNA per cell in an exponentially growing population using the diphenylamine reaction and flow cytometry. Anal Biochem 177: 353-357.
24. Castro C, Craig SP, Castaneda M, (1981) Genome organization and ploidy number in Trypanosoma cruzi. Mol Biochem Parasitol 4: 273-282.
25. Lanar DE, Levy LS, Manning JE, (1981) Complexity and content of the DNA and RNA in Trypanosoma cruzi. Mol Biochem Parasitol 3: 327-341.
26. Dvorak JA, Hall TE, Crane MS, Engel JC, McDaniel JP, et al. (1982) Trypanosoma cruzi: flow cytometric analysis. I. Analysis of total DNA/organism by means of mithramycin-induced fluorescence. J Protozool 29: 430-437.
27. Kooy RF, Ashall F, Van der Ploeg M, Overdulve JP, (1989) On the DNA content of Trypanosoma cruzi. Mol Biochem Parasitol 36: 73-76.
28. El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, et al. (2005) The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309: 409-415.
29. Machado CA, Ayala FJ, (2001) Nucleotide sequences provide evidence of genetic exchange among distantly related lineages of Trypanosoma cruzi. Proc Natl Acad Sci U S A 98: 7396-7401.
30. Araya J, Cano MI, Gomes HB, Novak EM, Requena JM, et al. (1997) Characterization of an interspersed repetitive DNA element in the genome of Trypanosoma cruzi. Parasitology 115 (Pt6): 563-570.
31. Cornillot E, Keller B, Cushion MT, Metenier G, Vivares CP, (2002) Fine analysis of the Pneumocystis carinii f. sp. carinii genome by two-dimensional pulsed-field gel electrophoresis. Gene 293: 87-95.
32. Weatherly DB, Boehlke C, Tarleton RL, (2009) Chromosome level assembly of the hybrid Trypanosoma cruzi genome. BMC Genomics 10: 255.
33. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
34. Pearson WR, Lipman DJ, (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85: 2444-2448.
35. Pearson WR, Miller W, (1992) Dynamic programming algorithms for biological sequence comparison. Methods Enzymol 210: 575-601.
36. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, et al. (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21: 3422-3423.
37. Brisse S, Dujardin JC, Tibayrenc M, (2000) Identification of six Trypanosoma cruzi lineages by sequence-characterised amplified region markers. Mol Biochem Parasitol 111: 95-105.
38. Campbell DA, Westenberger SJ, Sturm NR, (2004) The determinants of Chagas disease: connecting parasite and host genetics. Curr Mol Med 4: 549-562.
39. Llewellyn MS, Miles MA, Carrasco HJ, Lewis MD, Yeo M, et al. (2009) Genome-scale multilocus microsatellite typing of Trypanosoma cruzi discrete typing unit I reveals phylogeographic structure and specific genotypes linked to human infection. PLoS Pathog 5: e1000410.
40. Miles MA, Llewellyn MS, Lewis MD, Yeo M, Baleela R, et al. (2009) The molecular epidemiology and phylogeography of Trypanosoma cruzi and parallel research on Leishmania: looking back and to the future. Parasitology 136: 1509-1528.
41. Cura CI, Mejia-Jaramillo AM, Duffy T, Burgos JM, Rodriguero M, et al. (2010) Trypanosoma cruzi I genotypes in different geographical regions and transmission cycles based on a microsatellite motif of the intergenic spacer of spliced-leader genes. Int J Parasitol 40: 1599-1607.
42. Ocana-Mayorga S, Llewellyn MS, Costales JA, Miles MA, Grijalva MJ, (2010) Sex, subdivision, and domestic dispersal of Trypanosoma cruzi lineage I in southern Ecuador. PLoS Negl Trop Dis 4: e915.
43. Elias MC, Faria M, Mortara RA, Motta MC, de Souza W, et al. (2002) Chromosome localization changes in the Trypanosoma cruzi nucleus. Eukaryot Cell 1: 944-953.
44. Teixeira MM, da Silva FM, Marcili A, Umezawa ES, Shikanai-Yasuda MA, et al. (2006) Short communication: Trypanosoma cruzi lineage I in endomyocardial biopsy from a north-eastern Brazilian patient at end-stage chronic Chagasic cardiomyopathy. Trop Med Int Health 11: 294-298.
45. Degrave W, Fragoso SP, Britto C, van Heuverswyn H, Kidane GZ, et al. (1988) Peculiar sequence organization of kinetoplast DNA minicircles from Trypanosoma cruzi. Mol Biochem Parasitol 27: 63-70.
46. Martins C, Baptista CS, Ienne S, Cerqueira GC, Bartholomeu DC, et al. (2008) Genomic organization and transcription analysis of the 195-bp satellite DNA in Trypanosoma cruzi. Mol Biochem Parasitol 160: 60-64.
47. Souza RT, Santos MR, Lima FM, El-Sayed NM, Myler PJ, et al. (2007) New Trypanosoma cruzi Repeated Element That Shows Site Specificity for Insertion. Eukaryot Cell 6: 1228-1238.
48. Franzen O, Ochaya S, Sherwood E, Lewis MD, Llewellyn MS, 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: e984.
49. Santos MR, Lorenzi H, Porcile P, Carmo MS, Schijman A, et al. (1999) Physical mapping of a 670-kb region of chromosomes XVI and XVII from the human protozoan parasite Trypanosoma cruzi encompassing the genes for two immunodominant antigens. Genome Res 9: 1268-1276.
50. Porcile PE, Santos MR, Souza RT, Verbisck NV, Brandao A, et al. (2003) A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers. Gene 308: 53-65.
51. El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, et al. (2005) Comparative genomics of trypanosomatid parasitic protozoa. Science 309: 404-409.
52. Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, et al. (2004) Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol 134: 183-191.
53. Telleria J, Lafay B, Virreira M, Barnabe C, Tibayrenc M, et al. (2006) Trypanosoma cruzi: sequence analysis of the variable region of kinetoplast minicircles. Exp Parasitol 114: 279-288.
54. Westenberger SJ, Cerqueira GC, El-Sayed NM, Zingales B, Campbell DA, et al. (2006) Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region. BMC Genomics 7: 60.
55. Branche C, Ochaya S, Aslund L, Andersson B, (2006) Comparative karyotyping as a tool for genome structure analysis of Trypanosoma cruzi. Mol Biochem Parasitol 147: 30-38.
56. Nozaki T, Dvorak JA, (1991) Trypanosoma cruzi: flow cytometric analysis of developmental stage differences in DNA. J Protozool 38: 234-243.
57. Barnabe C, Yaeger R, Pung O, Tibayrenc M, (2001) Trypanosoma cruzi: a considerable phylogenetic divergence indicates that the agent of Chagas disease is indigenous to the native fauna of the United States. Exp Parasitol 99: 73-79.
58. Gibson WC, Miles MA, (1986) The karyotype and ploidy of Trypanosoma cruzi. Embo J 5: 1299-1305.
59. Minning TA, Weatherly DB, Flibotte S, Tarleton RL, (2011) Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization. BMC Genomics 12: 139.
60. Sterkers Y, Lachaud L, Crobu L, Bastien P, Pages M, (2011) FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major. Cell Microbiol 13: 274-283.
61. Briones MR, Souto RP, Stolf BS, Zingales B, (1999) The evolution of two Trypanosoma cruzi subgroups inferred from rRNA genes can be correlated with the interchange of American mammalian faunas in the Cenozoic and has implications to pathogenicity and host specificity. Mol Biochem Parasitol 104: 219-232.