Hotez PJ, Bottazzi ME, Franco-Paredes C, Ault SK, Periago MR. The neglected tropical diseases of Latin America and the Caribbean: a review of disease burden and distribution and a roadmap for control and elimination. PLoS Negl Trop Dis. 2008;2.
Article
PubMed
PubMed Central
Google Scholar
Coura JR, Borges-Pereira J. Chagas disease: what is known and what should be improved: a systemic review. Rev Soc Bras Med Trop. 2012;45:286–96.
Article
PubMed
Google Scholar
WHO. Research priorities for Chagas disease, human African trypanosomiasis and leishmaniasis. World Health Organ Tech Rep Ser. 2012;v–xii, 1–100. Available from: http://www.ncbi.nlm.nih.gov/pubmed/23484340
Zingales B, Andrade SG, Briones MRS, Campbell DA, Chiari E, Fernandes O, et al. A new consensus for Trypanosoma cruzi intraspecific nomenclature: second revision meeting recommends TcI to TcVI. Mem Inst Oswaldo Cruz. 2009;104:1051–4.
Article
CAS
PubMed
Google Scholar
Zingales B, Miles MA, Campbell DA, Tibayrenc M, Macedo AM, Teixeira MMG, et al. The revised Trypanosoma cruzi subspecific nomenclature: Rationale, epidemiological relevance and research applications. Infect Genet Evol. 2012;12:240–53 Available from: https://doi.org/10.1016/j.meegid.2011.12.009.
Article
PubMed
Google Scholar
Pinto CM, Kalko EKV, Cottontail I, Wellinghausen N, Cottontail VM. TcBat a bat-exclusive lineage of Trypanosoma cruzi in the Panama Canal zone, with comments on its classification and the use of the 18S rRNA gene for lineage identification. Infect Genet Evol. 2012;12:1328–32.
Article
CAS
PubMed
Google Scholar
Barnabé C, De Meeûs T, Noireau F, Bosseno MF, Monje EM, Renaud F, et al. Trypanosoma cruzi discrete typing units (DTUs): microsatellite loci and population genetics of DTUs TcV and TcI in Bolivia and Peru. Infect Genet Evol. 2011;11:1752–60.
Article
PubMed
Google Scholar
del P Fernández M, Cecere MC, Lanati LA, Lauricella MA, Schijman AG, Gürtler RE, et al. Geographic variation of Trypanosoma cruzi discrete typing units from Triatoma infestans at different spatial scales. Acta Trop. 2014;140:10–8 Available from: https://doi.org/10.1016/j.actatropica.2014.07.014.
Article
Google Scholar
Lima VDS, Xavier S, das Cristina C, Maldonado I, Fabiola R, Rodrigues RAL, Vicente A, Carolina P, Maria JA. Expanding the knowledge of the geographic distribution of Trypanosoma cruzi TcII and TcV/TcVI genotypes in the Brazilian Amazon. PLoS One. 2014;9:e116137.
Article
PubMed Central
CAS
Google Scholar
Messenger LA, Ramirez JD, Llewellyn MS, Guhl F, Miles MA. Importation of hybrid human-associated Trypanosoma cruzi strains of southern south American origin. Colombia Emerg Infect Dis. 2016;22:1452–5.
Article
PubMed
Google Scholar
De Freitas JM, Augusto-Pinto L, Pimenta JR, Bastos-Rodrigues L, Gonçalves VF, Teixeira SMR, et al. Ancestral genomes, sex, and the population structure of Trypanosoma cruzi. PLoS Pathog. 2006;2:0226–35.
Article
CAS
Google Scholar
Westenberger SJ, Barnabé C, Campbell DA, Sturm NR. Two hybridization events define the population structure of Trypanosoma cruzi. Genetics. 2005;171:527–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Burgos JM, Risso MG, Brenière SF, Barnabé C, Campetella O, Leguizamón MS. Differential distribution of genes encoding the virulence factor trans-Sialidase along Trypanosoma cruzi discrete typing units. PLoS One. 2013;8:9–11.
Google Scholar
Tomasini N, Diosque P. Evolution of Trypanosoma cruzi: clarifying hybridisations, mitochondrial introgressions and phylogenetic relationships between major lineages. Mem Inst Oswaldo Cruz. 2015;110:403–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Machado CA, Flores-lo CA. Analyses of 32 loci clarify phylogenetic relationships among Trypanosoma cruzi lineages and support a single hybridization prior to human. Contact Dermatitis. 2011;5.
Lewis MD, Llewellyn MS, Yeo M, Acosta N, Gaunt MW, Miles MA. Recent, independent and anthropogenic origins of Trypanosoma cruzi hybrids. PLoS Negl Trop Dis. 2011;5.
Article
PubMed
PubMed Central
Google Scholar
Messenger LA, Miles MA. Evidence and importance of genetic exchange among field populations of Trypanosoma cruzi. Acta Trop. 2015;151:150–5.
Article
PubMed
PubMed Central
Google Scholar
Tibayrenc M, Kjellberg F. A clonal theory of parasitic protozoa : The population structures of Trichomonas, and Trypanosoma and their medical and taxonomical consequences. Proc Natl Acad Sci U S A. 1990;87:2414–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tibayrenc M, Ayala FJ. Is predominant clonal evolution a common evolutionary adaptation to parasitism in pathogenic parasitic Protozoa, Fungi, Bacteria, and viruses? [internet]. Adv Parasitol. Elsevier Ltd; 2016. Available from: https://doi.org/10.1016/bs.apar.2016.08.007
Google Scholar
Tibayrenc M, Ayala FJ. How clonal are Trypanosoma and Leishmania. Trends Parasitol. [Internet]. Elsevier Ltd. 2012:1–6 Available from: https://doi.org/10.1016/j.pt.2013.03.007.
Article
CAS
PubMed
Google Scholar
Baptista R de P, D’Avila DA, Segatto M, Valle ÍF do, Franco GR, Valadares HMS, et al. Evidence of substantial recombination among Trypanosoma cruzi II strains from Minas Gerais. Infect Genet Evol. [Internet]. Elsevier B.V.; 2014;22:183–191. Available from: https://doi.org/10.1016/j.meegid.2013.11.021
Article
CAS
Google Scholar
Ramírez JD, Guhl F, Messenger LA, Lewis MD, Montilla M, Cucunuba Z, et al. Contemporary cryptic sexuality in Trypanosoma cruzi. Mol Ecol. 2012;21:4216–26.
Article
PubMed
Google Scholar
Ramírez JD, Llewellyn MS. Reproductive clonality in protozoan pathogens-truth or artefact? Mol Ecol. [internet]. 2014;23:4195–4202. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25060834.
Article
PubMed
Google Scholar
Messenger LA, Miles MA, Bern C. Between a bug and a hard place: Trypanosoma cruzi genetic diversity and the clinical outcomes of Chagas disease. Expert Rev Anti Infect Ther. 2015;13:995–1029 Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4784490&tool=pmcentrez&rendertype=abstract.
Article
CAS
PubMed
PubMed Central
Google Scholar
Machado C a, Ayala FJ. Nucleotide sequences provide evidence of genetic exchange among distantly related lineages of Trypanosoma cruzi. Proc Natl Acad Sci USA. 2001;98:7396–401.
Article
CAS
PubMed
PubMed Central
Google Scholar
Messenger LA, Llewellyn MS, Bhattacharyya T, Franzén O, Lewis MD, Ramírez JD, et al. Multiple mitochondrial introgression events and heteroplasmy in Trypanosoma cruzi revealed by maxicircle MLST and next generation sequencing. PLoS Negl Trop Dis. 2012;6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Minning T a, Weatherly DB, Flibotte S, Tarleton RL. Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization. BMC Genomics. 2011;12:139 Available from: http://www.biomedcentral.com/1471-2164/12/139.
Article
PubMed
PubMed Central
Google Scholar
Reis-Cunha JL, Rodrigues-Luiz GF, Valdivia HO, Baptista RP, Mendes TAO, de Morais GL, et al. Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains. BMC Genomics. 2015;16:499 Available from: http://www.biomedcentral.com/1471-2164/16/499.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bennett RJ. The parasexual lifestyle of Candida albicans. Curr Opin Microbiol. 2015;28:10–7 Available from: https://doi.org/10.1016/j.mib.2015.06.017.
Article
PubMed
PubMed Central
Google Scholar
Gaunt MW, Yeo M, Frame IA, Stothard JR, Carrasco HJHJ, Taylor MC, et al. Mechanism of genetic exchange in American trypanosomes. Nature. 2003;421:936–9.
Article
CAS
PubMed
Google Scholar
Heitman J. Sexual Reproduction and the Evolution of Microbial Pathogens Review. Curr Biol. 2006;16:711–25.
Article
CAS
Google Scholar
Sturm NR, Campbell DA. Alternative lifestyles: The population structure of Trypanosoma cruzi. Acta Trop. 2010;115:35–43 Available from: https://doi.org/10.1016/j.actatropica.2009.08.018.
Article
PubMed
Google Scholar
Lewis MD, Llewellyn MS, Gaunt MW, Yeo M, Carrasco HJ, Miles MA. 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 ; 2009;39:1305–1317. Available from: https://doi.org/10.1016/j.ijpara.2009.04.001
Article
CAS
PubMed
Google Scholar
Souza RT, Lima FM, Barros RM, Cortez DR, Santos MF, Cordero EM, et al. Genome size, karyotype polymorphism and chromosomal evolution in Trypanosoma cruzi. PLoS One. 2011;6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lukes J, Guilbride DL, Voty J, Zíkova A, Benne R, Englund PT. MINIREVIEW Kinetoplast DNA Network : Evolution of an Improbable Structure. Eukaryot Cell. 2002;1:495–502.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aphasizheva I, Aphasizhev R. U-insertion/deletion mRNA-editing holoenzyme: definition in sight. Trends Parasitol. 2016;32:144–56 Available from: https://doi.org/10.1016/j.pt.2015.10.004.
Article
CAS
PubMed
Google Scholar
Feagin JE. RNA editing in kinetoplastid mitochondria. J Biol Chem. 1990;265:19373–6.
CAS
PubMed
Google Scholar
Landweber LF. The evolution of RNA editing in kinetoplastid protozoa. Biosystems. 1992;28:41–5.
Article
CAS
PubMed
Google Scholar
Stuart K. RNA editing in kinetoplastid protozoa. Curr Opin Genet Dev. 1991;1:412–6.
Article
CAS
PubMed
Google Scholar
Telleria J, Lafay B, Virreira M, Barnabé C, Tibayrenc M, Svoboda M. Trypanosoma cruzi : Sequence analysis of the variable region of kinetoplast minicircles. Exp Parasitol. 2006;114:279–88.
Article
CAS
PubMed
Google Scholar
Carranza JC, Valadares HMS, D’Ávila DA, Baptista RP, Moreno M, Galvão LMC, et al. Trypanosoma cruzi maxicircle heterogeneity in Chagas disease patients from Brazil. Int J Parasitol 2009;39:963–973. Available from: https://doi.org/10.1016/j.ijpara.2009.01.009
Article
CAS
PubMed
Google Scholar
Miles MA, Llewellyn MS, Lewis MD, Yeo M, Baleela R, Fitzpatrick S, et al. The molecular epidemiology and phylogeography of Trypanosoma cruzi and parallel research on Leishmania: looking back and to the future. Parasitology. 2009;136:1509–1528. Available from: http://www.ncbi.nlm.nih.gov/pubmed/19691868.
Article
CAS
PubMed
Google Scholar
Llewellyn MS, Miles MA, Carrasco HJ, Lewis MD, Yeo M, Vargas J, et al. Genome-scale multilocus microsatellite typing of Trypanosoma cruzi discrete typing unit I reveals phylogeographic structure and specific genotypes linked to human infection. PLoS Pathog. 2009;5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lima VS, Jansen AM, Messenger L a, Miles M a, Llewellyn MS. Wild Trypanosoma cruzi I genetic diversity in Brazil suggests admixture and disturbance in parasite populations from the Atlantic Forest region. Parasit Vectors [Internet]. 2014;7:263. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4062772&tool=pmcentrez&rendertype=abstract
Messenger LA, Garcia L, Vanhove M, Huaranca C, Bustamante M, Torrico M, et al. Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal. Mol Ecol. 2015;24:2406–22.
Article
PubMed
PubMed Central
Google Scholar
Barnabe C, Buitrago R, Bremond P, Aliaga C, Salas R, Vidaurre P, et al. Putative panmixia in restricted populations of Trypanosoma cruzi isolated from wild triatoma infestans in Bolivia. PLoS One. 2013;8.
Article
PubMed
PubMed Central
CAS
Google Scholar
D’Ávila DA, Macedo AM, Valadares HMS, Gontijo ED, De Castro AM, Machado CR, et al. Probing population dynamics of Trypanosoma cruzi during progression of the chronic phase in chagasic patients. J Clin Microbiol. 2009;47:1718–25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Da Câmara ACJ, Lages-Silva E, Sampaio GHF, D’Ávila DA, Chiari E, Da Cunha Galvão LM. Homogeneity of Trypanosoma cruzi I, II, and III populations and the overlap of wild and domestic transmission cycles by Triatoma brasiliensis in northeastern Brazil. Parasitol Res. 2013;112:1543–50.
Article
PubMed
Google Scholar
Luquetti AO, Miles MA, Rassi A, de Rezende JM, de Souza AA, Povoa MM, et al. Trypanosoma cruzi: zymodemes associated with acute and chronic Chagas’ disease in central Brazil. Trans R Soc Trop Med Hyg [Internet]. 1986;80:462–470. Available from: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3099437
Weatherly DB, Boehlke C, Tarleton RL. Chromosome level assembly of the hybrid Trypanosoma cruzi genome. BMC Genomics. 2009;10:255.
Article
PubMed
PubMed Central
CAS
Google Scholar
El-Sayed NM. The genome sequence of Trypanosoma cruzi, etiologic agent of chagas disease. Science [Internet]. 2005;309:409–15. Available from: http://www.sciencemag.org/cgi/doi/10.1126/science.1112631
Article
CAS
PubMed
Google Scholar
Peacock L, Ferris V, Sharma R, Sunter J, Bailey M, Carrington M, et al. Identification of the meiotic life cycle stage of Trypanosoma brucei in the tsetse fly. Proc Natl Acad Sci USA. [Internet]. 2011;108:3671–3676. Available from: http://www.pnas.org/content/108/9/3671.abstract
Article
CAS
Google Scholar
Peacock L, Bailey M, Carrington M, Gibson W. Meiosis and haploid gametes in the pathogen Trypanosoma brucei. Curr Biol. 2014;24:181–6 Available from: https://doi.org/10.1016/j.cub.2013.11.044.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rogers MB, Downing T, Smith BA, Imamura H, Sanders M, Svobodova M, et al. Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. PLoS Genet. 2014;10.
Article
PubMed
PubMed Central
CAS
Google Scholar
Downing T, Imamura H, Decuypere S, Clark TG, Coombs GH, Cotton J a., et al. Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res. [Internet]. 2011;21:2143–2156. Available from: https://doi.org/10.1101/gr.123430.111
Article
CAS
PubMed
PubMed Central
Google Scholar
Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates P a, Depledge DP, et al. Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res. 2011;21:2129–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sterkers Y, Lachaud L, Crobu L, Bastien P, Pagès M. FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major. Cell Microbiol. 2011;13:274–83.
Article
CAS
PubMed
Google Scholar
Sterkers Y, Crobu L, Lachaud L, Pagès M, Bastien P. Parasexuality and mosaic aneuploidy in Leishmania: alternative genetics. Trends Parasitol. 2014;30:429–35.
Article
PubMed
Google Scholar
Valdivia HO, Reis-Cunha JL, Rodrigues-Luiz GF, Baptista RP, Baldeviano GC, Gerbasi R V., et al. Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis. BMC Genomics [Internet]. 2015;16:715. Available from: http://www.biomedcentral.com/1471-2164/16/715
Reis-Cunha JL, Valdivia HO, Bartholomeu DC. Trypanosomatid Genome Organization and Ploidy. In: Silva MS, Cano MI, editors. Mol. Cell. Biol. Pathog. Trypanos. 1st ed Frontiers in Parasitology; 2017. p. 61–103.
Chapter
Google Scholar
Dumetz F, Imamura H, Sanders M, Seblova V, Myskova J, Pescher P. Modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments and its impact on gene expression. MBio. 2017;8:1–14.
Article
Google Scholar
Vargas N, Pedroso A, Zingales B. Chromosomal polymorphism, gene synteny and genome size in T. cruzi I and T. cruzi II groups. Mol Biochem Parasitol. 2004;138:131–41.
Article
CAS
PubMed
Google Scholar
Pedroso A, Cupolillo E, Zingales B. Evaluation of Trypanosoma cruzi hybrid stocks based on chromosomal size variation. Mol Biochem Parasitol. 2003;129:79–90.
Article
CAS
PubMed
Google Scholar
Triana O, Ortiz S, Dujardin JC, Solari A. Trypanosoma cruzi: variability of stocks from Colombia determined by molecular karyotype and minicircle southern blot analysis. Exp Parasitol. 2006;113:62–6.
Article
CAS
PubMed
Google Scholar
Branche C, Ochaya S, Åslund L, Andersson B. Comparative karyotyping as a tool for genome structure analysis of Trypanosoma cruzi. Mol Biochem Parasitol. 2006;147:30–8.
Article
CAS
PubMed
Google Scholar
Franzén O, Ochaya S, Sherwood E, Lewis MD, Llewellyn MS, Miles MA, et al. Shotgun sequencing analysis of Trypanosoma cruzi i Sylvio X10/1 and comparison with T. cruzi VI CL Brener. PLoS Negl Trop Dis. 2011;5:1–9.
Google Scholar
El-Sayed NM. Comparative genomics of Trypanosomatid parasitic Protozoa. Science 2005;309:404–9. Available from: http://www.sciencemag.org/cgi/doi/10.1126/science.1112181
Article
CAS
PubMed
Google Scholar
Baptista RP, Reis-Cunha JL, DeBarry JD, Chiari E, Kissinger JC, Bartholomeu DC, et al. Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231. Microb Genomics [Internet]. 2018; Available from: http://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000156.v1
Dujardin JC, Mannaert A, Durrant C, Cotton JA. Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing. Trends Parasitol. 2014;30:554–5 Available from: https://doi.org/10.1016/j.pt.2014.09.004.
Article
CAS
PubMed
Google Scholar
Lachaud L, Bourgeois N, Kuk N, Morelle C, Crobu L, Merlin G, et al. Constitutive mosaic aneuploidy is a unique genetic feature widespread in the Leishmania genus. Microbes Infect. 2014;16:61–6.
Article
PubMed
Google Scholar
Lima FM, Souza RT, Santori FR, Santos MF, Cortez DR, Barros RM, et al. Interclonal variations in the molecular karyotype of Trypanosoma cruzi: chromosome rearrangements in a single cell-derived clone of the G strain. PLoS One. 2013;8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mannaert A, Downing T, Imamura H, Dujardin JC. Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania. Trends Parasitol. 2012;28:370–6.
Article
CAS
PubMed
Google Scholar
Selmecki A, Forche A, Berman J. Genomic plasticity of the human fungal pathogen Candida albicans. Eukaryot Cell. 2010;9:991–1008.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hassold T, Hunt P. To err (meiotically) is human: the genesis of human aneuploidy. Nat Rev Genet [Internet] 2001;2:280–291. Available from: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11283700
Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med [Internet] 2010;61:437–455. Available from: http://www.annualreviews.org/doi/10.1146/annurev-med-100708-204735
Article
CAS
PubMed
Google Scholar
Lv L, Zhang T, Yi Q, Huang Y, Wang Z, Hou H, et al. Tetraploid cells from cytokinesis failure induce aneuploidy and spontaneous transformation of mouse ovarian surface epithelial cells. Cell Cycle. 2012;11:2864–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Doubre H, Césari D, Mairovitz A, Bénac C, Chantot-Bastaraud S, Dagnon K, et al. Multidrug resistance-associated protein (MRP1) is overexpressed in DNA aneuploid carcinomatous cells in non-small cell lung cancer (NSCLC). Int J Cancer. 2005;113:568–74.
Article
CAS
PubMed
Google Scholar
Abbey D, Hickman M, Gresham D, Berman J. High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains. G3 (Bethesda). [Internet]. 2011;1:523–530. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3276171&tool=pmcentrez&rendertype=abstract
Leprohon P, Légaré D, Raymond F, Madore É, Hardiman G, Corbeil J, et al. Gene expression modulation is associated with gene amplification, supernumerary chromosomes and chromosome loss in antimony-resistant Leishmania infantum. Nucleic Acids Res. 2009;37:1387–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weir W, Capewell P, Foth B, Clucas C, Pountain A, Steketee P, et al. Population genomics reveals the origin and asexual evolution of human infective trypanosomes. elife. 2016;5:1–14.
Article
Google Scholar
Berriman M, Ghedin E, Hertz-fowler C. The genome of the African trypanosome, Trypanosoma brucei. Science. 2005;309(5733):416–22.
Article
CAS
PubMed
Google Scholar
Ivens AC. The genome of the Kinetoplastid parasite, Leishmania major. Science [Internet] 2005;309:436–442. Available from: http://www.sciencemag.org/cgi/doi/10.1126/science.1112680%5Cnpapers3://publication/doi/10.1126/science.1112680
Article
PubMed
PubMed Central
Google Scholar
Clayton CE. Gene expression in Kinetoplastids. Curr Opin Microbiol. 2016;32:46–51 Available from: https://doi.org/10.1016/j.mib.2016.04.018.
Article
CAS
PubMed
Google Scholar
Günzl A, Bruderer T, Laufer G, Schimanski B, Tu LC, Chung HM, et al. RNA polymerase I transcribes procyclin genes and variant surface glycoprotein gene expression sites in Trypanosoma brucei. Eukaryot Cell. 2003;2:542–51.
Article
PubMed
PubMed Central
CAS
Google Scholar
Teixeira SM, de Paiva RMC, Kangussu-Marcolino MM, DaRocha WD. Trypanosomatid comparative genomics: contributions to the study of parasite biology and different parasitic diseases. Genet Mol Biol. 2012;35:1–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sheltzer JMJ, Blank HHM, Pfau SJS, Tange Y, George BM, Humpton TJ, et al. Aneuploidy drives genomic instability in yeast. Science [Internet]. 2011;333:1026–30. Available from: http://www.sciencemag.org/content/333/6045/1026.abstract
Article
CAS
PubMed
PubMed Central
Google Scholar
Ubeda J-M, Légaré D, Raymond F, Ouameur AA, Boisvert S, Rigault P, et al. Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biol [Internet]. 2008;9:R115. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2530873&tool=pmcentrez&rendertype=abstract
Cardoso MS, Junqueira C, Trigueiro RC, Shams-eldin H, Previato O, Mendonc L, et al. Identification and Functional Analysis of Trypanosoma cruzi Genes That Encode Proteins of the Glycosylphosphatidylinositol Biosynthetic Pathway. PLoS Negl Trop Dis. 2013;7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Buscaglia CA, Campo VA, ACC F, Di Noia JM. Trypanosoma cruzi surface mucins: host-dependent coat diversity. Nat Rev Microbiol. 2006;4:229–36.
Article
CAS
PubMed
Google Scholar
De Pablos LM, Osuna A. Multigene families in Trypanosoma cruzi and their role in infectivity. Infect Immun. 2012;80:2258–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, et al. TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res. 2009;38:457–62.
Article
CAS
Google Scholar
Souto RP, Fernandes O, Macedo AM, Campbell DA, Zingales B. DNA markers define two major phylogenetic lineages of Trypanosoma cruzi. Mol Biochem Parasitol. 1996;83:141–52.
Article
CAS
PubMed
Google Scholar
Burgos JM, Altcheh J, Bisio M, Duffy T, Valadares HMS, Seidenstein ME, et al. Direct molecular profiling of minicircle signatures and lineages of Trypanosoma cruzi bloodstream populations causing congenital Chagas disease. Int J Parasitol. 2007;37:1319–27.
Article
CAS
PubMed
Google Scholar
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zerbino DR. Technologies. Curr Protoc Bioinforma. [Internet]. 2011;1–13. Available from: http://doi.wiley.com/10.1002/0471250953.bi1105s31
Myers EW. A whole-genome assembly of drosophila. Science [Internet]. 2000;287:2196–204 Available from: http://www.sciencemag.org/cgi/doi/10.1126/science.287.5461.2196.
CAS
Google Scholar
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, et al. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics. 2008;24:2818–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv Prepr. arXiv [Internet]. 2013;0:3. Available from: http://arxiv.org/abs/1303.3997
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol [Internet] 1990;215:403–410. Available from: http://www.sciencedirect.com/science/article/pii/S0022283605803602
Article
CAS
PubMed
Google Scholar
Darzentas N. Circoletto: visualizing sequence similarity with Circos. Bioinformatics. 2010;26:2620–1.
Article
CAS
PubMed
Google Scholar
Zhang H, Meltzer P, Davis S. RCircos : an R package for Circos 2D track plots. BMC Bioinformatics [internet]. BMC Bioinformatics. 2013;14:1.
Article
CAS
Google Scholar
Kent WJ. BLAT — the BLAST -like alignment tool. Genome Res. 2002;12:656–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Castresana J. Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis. Mol Biol Evol. 2000;17:540–52.
Article
CAS
PubMed
Google Scholar
Posada D. jModelTest: Phylogenetic model averaging. Mol Biol Evol. 2008;25:1253–6.
Article
CAS
PubMed
Google Scholar
Guindon S, Delsuc F, Dufayard JF, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol. 2009;537:113–37.
Article
CAS
PubMed
Google Scholar
Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics [Internet]. 2007;8:460. Available from: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-460
Article
PubMed
PubMed Central
CAS
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics. 2006;22:1540–2.
Article
CAS
PubMed
Google Scholar
Shimodaira H. An Approximately Unbiased Test of Phylogenetic Tree Selection. Syst Biol. 2002;51:492–508.
Article
PubMed
Google Scholar