{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T23:30:18Z","timestamp":1783380618235,"version":"3.54.6"},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T00:00:00Z","timestamp":1595462400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T00:00:00Z","timestamp":1595462400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["#55479712006-2"],"award-info":[{"award-number":["#55479712006-2"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005279","name":"Universidade Federal do Piau\u00ed","doi-asserted-by":"publisher","award":["#23111.026931\/2915-71 (WD)"],"award-info":[{"award-number":["#23111.026931\/2915-71 (WD)"]}],"id":[{"id":"10.13039\/501100005279","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Visceral leishmaniasis (VL) is a life-threatening disease caused by the protozoa <jats:italic>Leishmania donovani<\/jats:italic> and <jats:italic>L. infantum<\/jats:italic>. Likely, <jats:italic>L. infantum<\/jats:italic> was introduced in the New World by the Iberic colonizers. Due to recent introduction, the genetic diversity is low. Access to genomic information through the sequencing of <jats:italic>Leishmania<\/jats:italic> isolates allows the characterization of populations through the identification and analysis of variations. Population structure information may reveal important data on disease dynamics. Aiming to describe the genetic diversity of <jats:italic>L. infantum<\/jats:italic> from the Middle-North, Brazil, next generation sequencing of 30 <jats:italic>Leishmania<\/jats:italic> isolates obtained in the city of Teresina, from where the disease dispersed, was performed. The variations were categorized accordingly to the genome region and impact and provided the basis for chromosomal ploidy and population structure analysis. The results showed low diversity between the isolates and the Iberic reference genome JPCM5. Most variations were seen in non-coding regions, with modifying impact. The ploidy number analysis showed aneuploid profile. The population structure analysis revealed the presence of two <jats:italic>L. infantum<\/jats:italic> populations identified in Teresina. Further population genetics studies with a larger number of isolates should be performed in order to identify the genetic background associated with virulence and parasite ecology.<\/jats:p>","DOI":"10.1038\/s41598-020-68953-9","type":"journal-article","created":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T10:05:06Z","timestamp":1595498706000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Application of next generation sequencing (NGS) for descriptive analysis of 30 genomes of Leishmania infantum isolates in Middle-North Brazil"],"prefix":"10.1038","volume":"10","author":[{"given":"K\u00e1tia Silene Sousa","family":"Carvalho","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wilson Jos\u00e9","family":"da Silva J\u00fanior","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcos","family":"da Silveira Regueira Neto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir Costa","family":"Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00e9rgio","family":"de S\u00e1 Leit\u00e3o Paiva J\u00fanior","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valdir Queiroz","family":"Balbino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorcas Lamounier","family":"Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos Henrique Nery","family":"Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,7,23]]},"reference":[{"key":"68953_CR1","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1016\/j.pt.2014.12.012","volume":"31","author":"C Cantacessi","year":"2015","unstructured":"Cantacessi, C., Dantas-Torres, F., Nolan, M. J. & Otranto, D. The past, present, and future of Leishmania genomics and transcriptomics. Trends Parasitol. 31, 100\u2013108 (2015).","journal-title":"Trends Parasitol."},{"key":"68953_CR2","unstructured":"World Health Organization. Leishmaniasis. https:\/\/www.who.int\/leishmaniasis\/en\/. Accessed 8 May 2020."},{"key":"68953_CR3","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1038\/nrmicro2608","volume":"9","author":"P Kaye","year":"2011","unstructured":"Kaye, P. & Scott, P. Leishmaniasis: Complexity at the host\u2013pathogen interface. Nat. Rev. Microbiol. 9, 604\u2013615 (2011).","journal-title":"Nat. Rev. Microbiol."},{"key":"68953_CR4","unstructured":"Pan American Health Organization. Leishmaniasis: Epidemiological Report of the Americas. Leishmaniasis Rep.7. www.paho.org\/leishmaniasis (2019). Accessed 8 May 2020."},{"key":"68953_CR5","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1590\/S0034-89101990000500003","volume":"24","author":"CHN Costa","year":"1990","unstructured":"Costa, C. H. N., Pereira, H. F. & Ara\u00fajo, M. V. Epidemia de leishmaniose visceral no estado do Piau\u00ed, Brasil, 1980\u20131986. Rev. Sa\u00fade P\u00fabl. 24, 361\u2013372 (1990).","journal-title":"Rev. Sa\u00fade P\u00fabl."},{"key":"68953_CR6","doi-asserted-by":"publisher","first-page":"e0006697","DOI":"10.1371\/journal.pntd.0006697","volume":"12","author":"JMT Bezerra","year":"2018","unstructured":"Bezerra, J. M. T. et al. Burden of leishmaniasis in Brazil and federated units, 1990\u20132016: Findings from global burden of disease study 2016. PLoS Neglect. Trop. D 12, e0006697. https:\/\/doi.org\/10.1371\/journal.pntd.0006697 (2018).","journal-title":"PLoS Neglect. Trop. D"},{"key":"68953_CR7","unstructured":"Brasil. Minist\u00e9rio da Sa\u00fade\/SVS. Leishmaniose visceral\u2014Casos confirmados notificados no sistema de informa\u00e7\u00e3o de agravos de notifica\u00e7\u00e3o\u2014Piau\u00ed. https:\/\/tabnet.datasus.gov.br\/cgi\/tabcgi.exe?sinannet\/cnv\/leishvpi.def (2017). Accessed 12 September 2019."},{"key":"68953_CR8","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1016\/j.ijpara.2007.05.015","volume":"37","author":"DF Smith","year":"2007","unstructured":"Smith, D. F., Peacock, C. S. & Cruz, A. K. Comparative genomics: From genotype to disease phenotype in the leishmaniases. Int. J. Parasitol. 37, 1173\u20131186 (2007).","journal-title":"Int. J. Parasitol."},{"key":"68953_CR9","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1016\/j.meegid.2008.11.007","volume":"9","author":"J-C Dujardin","year":"2009","unstructured":"Dujardin, J.-C. Structure, dynamics and function of Leishmania genome: Resolving the puzzle of infection, genetics and evolution?. Infect. Genet. Evol. 9, 290\u2013297 (2009).","journal-title":"Infect. Genet. Evol."},{"key":"68953_CR10","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1126\/science.1112680","volume":"15","author":"AC Ivens","year":"2005","unstructured":"Ivens, A. C. et al. The genome of the kinetoplastid parasite, Leishmania major. Science 15, 436\u2013442 (2005).","journal-title":"Science"},{"key":"68953_CR11","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1038\/ng2053","volume":"39","author":"CS Peacock","year":"2007","unstructured":"Peacock, C. S. et al. Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat. Genet. 39, 839\u2013847 (2007).","journal-title":"Nat. Genet."},{"key":"68953_CR12","doi-asserted-by":"publisher","first-page":"2129","DOI":"10.1101\/gr.122945.111","volume":"21","author":"MB Rogers","year":"2011","unstructured":"Rogers, M. B. et al. Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res. 21, 2129\u20132142 (2011).","journal-title":"Genome Res."},{"key":"68953_CR13","doi-asserted-by":"publisher","first-page":"2143","DOI":"10.1101\/gr.123430.111","volume":"21","author":"T Downing","year":"2011","unstructured":"Downing, T. et al. Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res. 21, 2143\u20132156 (2011).","journal-title":"Genome Res."},{"key":"68953_CR14","doi-asserted-by":"publisher","first-page":"18050","DOI":"10.1038\/s41598-017-18374-y","volume":"7","author":"S Gonz\u00e1lez-de la Fuente","year":"2017","unstructured":"Gonz\u00e1lez-de la Fuente, S. et al. Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs. Sci. Rep. 7, 18050. https:\/\/doi.org\/10.1038\/s41598-017-18374-y (2017).","journal-title":"Sci. Rep."},{"key":"68953_CR15","doi-asserted-by":"publisher","first-page":"172212","DOI":"10.1098\/rsos.172212","volume":"5","author":"S Coughlan","year":"2018","unstructured":"Coughlan, S. et al. Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus. R. Soc. Open Sci. 5, 172212. https:\/\/doi.org\/10.1098\/rsos.172212 (2018).","journal-title":"R. Soc. Open Sci."},{"key":"68953_CR16","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1186\/s12864-015-1928-z","volume":"16","author":"HO Valdivia","year":"2015","unstructured":"Valdivia, H. O. et al. Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis. BMC Genomics 16, 715. https:\/\/doi.org\/10.1186\/s12864-015-1928-z (2015).","journal-title":"BMC Genomics"},{"key":"68953_CR17","doi-asserted-by":"publisher","first-page":"e01524","DOI":"10.1128\/mra.01524-18","volume":"8","author":"W Lin","year":"2019","unstructured":"Lin, W. et al. First draft genome sequence of leishmania (Viannia) lainsoni strain 216\u201334, isolated from a peruvian clinical case. Microbiol. Resour. Announc. 8, e01524-e1618. https:\/\/doi.org\/10.1128\/mra.01524-18 (2019).","journal-title":"Microbiol. Resour. Announc."},{"key":"68953_CR18","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1093\/nar\/gkr834","volume":"40","author":"F Raymond","year":"2012","unstructured":"Raymond, F. et al. Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Nucleic Acids Res. 40, 1131\u20131147 (2012).","journal-title":"Nucleic Acids Res."},{"key":"68953_CR19","doi-asserted-by":"publisher","first-page":"43747","DOI":"10.1038\/srep43747","volume":"7","author":"S Coughlan","year":"2017","unstructured":"Coughlan, S. et al. The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania. Sci. Rep. 7, 43747. https:\/\/doi.org\/10.1038\/srep43747 (2017).","journal-title":"Sci. Rep."},{"key":"68953_CR20","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1186\/s12864-019-6126-y","volume":"20","author":"A Butenko","year":"2019","unstructured":"Butenko, A. et al. Comparative genomics of Leishmania (Mundinia). BMC Genomics 20, 726. https:\/\/doi.org\/10.1186\/s12864-019-6126-y (2019).","journal-title":"BMC Genomics"},{"key":"68953_CR21","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1242\/jeb.001370","volume":"210","author":"N Hall","year":"2007","unstructured":"Hall, N. Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210, 1518\u20131525 (2007).","journal-title":"J. Exp. Biol."},{"key":"68953_CR22","doi-asserted-by":"publisher","first-page":"17336","DOI":"10.1038\/s41598-018-35778-6","volume":"8","author":"DA Urrea","year":"2018","unstructured":"Urrea, D. A. et al. Genomic analysis of colombian Leishmania panamensis strains with different level of virulence. Sci. Rep. 8, 17336. https:\/\/doi.org\/10.1038\/s41598-018-35778-6 (2018).","journal-title":"Sci. Rep."},{"key":"68953_CR23","doi-asserted-by":"publisher","first-page":"e248","DOI":"10.1371\/journal.pntd.0000248","volume":"2","author":"W-W Zhang","year":"2008","unstructured":"Zhang, W.-W., Peacock, C. S. & Matlashewski, G. A Genomic-based approach combining in vivo selection in mice to identify a novel virulence gene in Leishmania. PLoS Neglect. Trop. D 2, e248. https:\/\/doi.org\/10.1371\/journal.pntd.0000248 (2008).","journal-title":"PLoS Neglect. Trop. D"},{"key":"68953_CR24","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1016\/j.jaad.2014.08.051","volume":"73","author":"MZ Handler","year":"2015","unstructured":"Handler, M. Z., Patel, P. A., Kapila, R., Al-Qubati, Y. & Schwartz, R. A. Cutaneous and mucocutaneous leishmaniasis. J. Am. Acad. Dermatol. 73, 897\u2013908 (2015).","journal-title":"J. Am. Acad. Dermatol."},{"key":"68953_CR25","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1016\/j.ijpara.2017.04.004","volume":"47","author":"DG Teixeira","year":"2017","unstructured":"Teixeira, D. G. et al. Comparative analyses of whole genome sequences of Leishmania infantum isolates from humans and dogs in northeastern Brazil. Int. J. Parasitol. 47, 655\u2013665 (2017).","journal-title":"Int. J. Parasitol."},{"key":"68953_CR26","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1186\/s12864-018-5271-z","volume":"19","author":"SR Samarasinghe","year":"2018","unstructured":"Samarasinghe, S. R. et al. Genomic insights into virulence mechanisms of Leishmania donovani: Evidence from an atypical strain. BMC Genomics 19, 843. https:\/\/doi.org\/10.1186\/s12864-018-5271-z (2018).","journal-title":"BMC Genomics"},{"key":"68953_CR27","doi-asserted-by":"publisher","first-page":"e1004092","DOI":"10.1371\/journal.pgen.1004092","volume":"10","author":"MB Rogers","year":"2014","unstructured":"Rogers, M. B. et al. Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. PLoS Genet. 10, e1004092. https:\/\/doi.org\/10.1371\/journal.pgen.1004092 (2014).","journal-title":"PLoS Genet."},{"key":"68953_CR28","doi-asserted-by":"publisher","first-page":"e889","DOI":"10.1371\/journal.pntd.0000889","volume":"4","author":"T Gelanew","year":"2010","unstructured":"Gelanew, T. et al. Inference of population structure of Leishmania donovani strains isolated from different ethiopian visceral leishmaniasis endemic areas. PLoS Neglect. Trop. D 4, e889. https:\/\/doi.org\/10.1371\/journal.pntd.0000889 (2010).","journal-title":"PLoS Neglect. Trop. D"},{"key":"68953_CR29","doi-asserted-by":"publisher","first-page":"e0007382","DOI":"10.1371\/journal.pntd.0007382","volume":"13","author":"SLFB de S\u00e1","year":"2019","unstructured":"de S\u00e1, S. L. F. B., Rezende, A. M., de Melo Neto, O. P., de Brito, M. E. F. & Brand\u00e3o Filho, S. P. Identification of divergent Leishmania (Viannia) braziliensis ecotypes derived from a geographically restricted area through whole genome analysis. PLoS Negletc. Trop. D 13, e0007382. https:\/\/doi.org\/10.1371\/journal.pntd.0007382 (2019).","journal-title":"PLoS Negletc. Trop. D"},{"key":"68953_CR30","doi-asserted-by":"publisher","first-page":"e51243","DOI":"10.7554\/eLife.51243","volume":"9","author":"SU Franssen","year":"2020","unstructured":"Franssen, S. U. et al. Global genome diversity of the Leishmania donovani complex. Elife 9, e51243. https:\/\/doi.org\/10.7554\/eLife.51243 (2020).","journal-title":"Elife"},{"key":"68953_CR31","doi-asserted-by":"publisher","first-page":"e1004244","DOI":"10.1371\/journal.ppat.1004244","volume":"10","author":"WW Zhang","year":"2014","unstructured":"Zhang, W. W. et al. Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain. PLoS Pathog. 10, e1004244. https:\/\/doi.org\/10.1371\/journal.ppat.1004244 (2014).","journal-title":"PLoS Pathog."},{"key":"68953_CR32","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1016\/j.meegid.2011.04.004","volume":"11","author":"R Leblois","year":"2011","unstructured":"Leblois, R., Kuhls, K., Fran\u00e7ois, O., Sch\u00f6nian, G. & Wirth, T. Guns, germs and dogs: On the origin of Leishmania chagasi. Infect. Genet. Evol. 11, 1091\u20131095 (2011).","journal-title":"Infect. Genet. Evol."},{"key":"68953_CR33","doi-asserted-by":"publisher","first-page":"9375","DOI":"10.1073\/pnas.0703678104","volume":"104","author":"J Lukes","year":"2007","unstructured":"Lukes, J. et al. Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy. Proc. Natl. Acad. Sci. U.S.A. 104, 9375\u20139380 (2007).","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"68953_CR34","doi-asserted-by":"publisher","first-page":"e1007133","DOI":"10.1371\/journal.pgen.1007133","volume":"14","author":"A Zackay","year":"2018","unstructured":"Zackay, A. et al. Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival. PLoS Genet. 14, e1007133. https:\/\/doi.org\/10.1371\/journal.pgen.1007133 (2018).","journal-title":"PLoS Genet."},{"key":"68953_CR35","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1007\/978-1-60327-411-1_2","volume-title":"Single Nucleotide Polymorphisms, Methods in Molecular Biology","author":"R Hunt","year":"2009","unstructured":"Hunt, R., Sauna, Z. E., Ambudkar, S. V., Gottesman, M. M. & Kimchi-Sarfaty, C. Silent (synonymous) SNPs: Should we care about them? In Single Nucleotide Polymorphisms, Methods in Molecular Biology (ed. Komar, A. A.) 23\u201339 (Humana Press, Totowa, 2009)."},{"key":"68953_CR36","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1016\/j.molbiopara.2017.11.001","volume":"219","author":"L Giordana","year":"2018","unstructured":"Giordana, L. et al. Molecular and functional characterization of two malic enzymes from Leishmania parasites. Mol. Biochem. Parasitol. 219, 67\u201376 (2018).","journal-title":"Mol. Biochem. Parasitol."},{"key":"68953_CR37","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1186\/s13071-018-3143-7","volume":"11","author":"M Ceccarelli","year":"2018","unstructured":"Ceccarelli, M. et al. Exploiting genetic polymorphisms in metabolic enzymes for rapid screening of Leishmania infantum genotypes. Parasit. Vectors 11, 572. https:\/\/doi.org\/10.1186\/s13071-018-3143-7 (2018).","journal-title":"Parasit. Vectors"},{"key":"68953_CR38","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80\u201392 (2012).","journal-title":"Fly"},{"key":"68953_CR39","volume-title":"Bioinformatics in Tropical Disease Research: A Practical and Case-Study Approach","author":"SRB Uliana","year":"2008","unstructured":"Uliana, S. R. B., Ruiz, J. C. & Cruz, A. K. Leishmania genomics: Where do we stand? In Bioinformatics in Tropical Disease Research: A Practical and Case-Study Approach (eds Gruber, A., Durham, A. M., Huynh, C. et al.) (National Center for Biotechnology Information, Bethesda, 2008)."},{"key":"68953_CR40","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1046\/j.1365-2958.2001.02286.x","volume":"39","author":"W-W Zhang","year":"2001","unstructured":"Zhang, W.-W. & Matlashewski, G. Characterization of the A2\u2013A2rel gene cluster in Leishmania donovani: Involvement of A2 in visceralization during infection. Mol. Microbiol. 39, 935\u2013948 (2001).","journal-title":"Mol. Microbiol."},{"key":"68953_CR41","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1111\/j.1365-2958.2012.08185.x","volume":"86","author":"Y Sterkers","year":"2012","unstructured":"Sterkers, Y. et al. Novel insights into genome plasticity in eukaryotes: mosaic aneuploidy in Leishmania. Mol. Microbiol. 86, 15\u201323 (2012).","journal-title":"Mol. Microbiol."},{"key":"68953_CR42","doi-asserted-by":"publisher","first-page":"e00599","DOI":"10.1128\/mBio.00599-17","volume":"8","author":"F Dumetz","year":"2017","unstructured":"Dumetz, F. et al. Modulation of Aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments and its impact on gene expression. MBio 8, e00599. https:\/\/doi.org\/10.1128\/mBio.00599-17 (2017).","journal-title":"MBio"},{"key":"68953_CR43","doi-asserted-by":"publisher","first-page":"e12613","DOI":"10.7554\/eLife.12613","volume":"5","author":"H Imamura","year":"2016","unstructured":"Imamura, H. et al. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. Elife 5, e12613. https:\/\/doi.org\/10.7554\/eLife.12613 (2016).","journal-title":"Elife"},{"key":"68953_CR44","doi-asserted-by":"publisher","first-page":"1688","DOI":"10.1093\/nar\/24.9.1688","volume":"24","author":"P Wincker","year":"1996","unstructured":"Wincker, P. et al. The Leishmania genome comprises 36 chromosomes conserved across widely divergent human pathogenic species. Nucleic Acids Res. 24, 1688\u20131694 (1996).","journal-title":"Nucleic Acids Res."},{"key":"68953_CR45","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1111\/j.1462-5822.2010.01534.x","volume":"13","author":"Y Sterkers","year":"2011","unstructured":"Sterkers, Y., Lachaud, L., Crobu, L., Bastien, P. & Pag\u00e8s, M. FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major. Cell. Microbiol. 13, 274\u2013283 (2011).","journal-title":"Cell. Microbiol."},{"key":"68953_CR46","doi-asserted-by":"publisher","first-page":"1881","DOI":"10.1093\/emboj\/21.8.1881","volume":"21","author":"CE Clayton","year":"2002","unstructured":"Clayton, C. E. Life without transcriptional control? From fly to man and back again. EMBO J. 21, 1881\u20131888 (2002).","journal-title":"EMBO J."},{"key":"68953_CR47","doi-asserted-by":"publisher","first-page":"9485","DOI":"10.1038\/s41598-019-45538-91","volume":"9","author":"LH Patino","year":"2019","unstructured":"Patino, L. H. et al. Major changes in chromosomal somy, gene expression and gene dosage driven by SbIII in Leishmania braziliensis and Leishmania panamensis. Sci. Rep. 9, 9485. https:\/\/doi.org\/10.1038\/s41598-019-45538-91 (2019).","journal-title":"Sci. Rep."},{"key":"68953_CR48","doi-asserted-by":"publisher","first-page":"e36242","DOI":"10.1371\/journal.pone.0036242","volume":"7","author":"GEM Ferreira","year":"2012","unstructured":"Ferreira, G. E. M. et al. The genetic structure of Leishmania infantum populations in Brazil and its possible association with the transmission cycle of visceral leishmaniasis. PLoS ONE 7, e36242. https:\/\/doi.org\/10.1371\/journal.pone.0036242 (2012).","journal-title":"PLoS ONE"},{"key":"68953_CR49","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1186\/1756-3305-6-342","volume":"6","author":"E Gouzelou","year":"2013","unstructured":"Gouzelou, E. et al. Genetic diversity and structure in Leishmania infantum populations from southeastern Europe revealed by microsatellite analysis. Parasit. Vectors 6, 342. https:\/\/doi.org\/10.1186\/1756-3305-6-342 (2013).","journal-title":"Parasit. Vectors"},{"key":"68953_CR50","doi-asserted-by":"publisher","first-page":"10224","DOI":"10.1073\/pnas.0904420106","volume":"106","author":"V Rougeron","year":"2009","unstructured":"Rougeron, V. et al. Extreme inbreeding in Leishmania braziliensis. Proc. Natl. Acad. Sci. U.S.A. 106, 10224\u201310229. https:\/\/doi.org\/10.1073\/pnas.0904420106 (2009).","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"68953_CR51","unstructured":"Andrews, S. Babraham Bioinformatics\u2014FastQC a quality control tool for high throughput sequence data. Babraham Inst. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/ (2015). Accessed 1 April 2019."},{"key":"68953_CR52","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/0888-7543(88)90007-9","volume":"2","author":"ES Lander","year":"1988","unstructured":"Lander, E. S. & Waterman, M. S. Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2, 231\u2013239 (1988).","journal-title":"Genomics"},{"key":"68953_CR53","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589\u2013595 (2010).","journal-title":"Bioinformatics"},{"key":"68953_CR54","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"68953_CR55","unstructured":"Broad Institute. Picard Tools. https:\/\/broadinstitute.github.io\/picard\/ (2019). Accessed 27 April 2019."},{"key":"68953_CR56","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna, A. et al. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297\u20131303 (2010).","journal-title":"Genome Res."},{"key":"68953_CR57","doi-asserted-by":"publisher","first-page":"1749","DOI":"10.1093\/bioinformatics\/btw044","volume":"32","author":"V Narasimhan","year":"2016","unstructured":"Narasimhan, V. et al. BCFtools\/RoH: A hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics 32, 1749\u20131751 (2016).","journal-title":"Bioinformatics"},{"key":"68953_CR58","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156\u20132158 (2011).","journal-title":"Bioinformatics"},{"key":"68953_CR59","doi-asserted-by":"publisher","first-page":"W187","DOI":"10.1093\/nar\/gku365","volume":"42","author":"F Ram\u00edrez","year":"2014","unstructured":"Ram\u00edrez, F., D\u00fcndar, F., Diehl, S., Gr\u00fcning, B. A. & Manke, T. deepTools: A flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187\u2013W191 (2014).","journal-title":"Nucleic Acids Res."},{"key":"68953_CR60","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4302-2956-8","volume-title":"Beginning Microsoft Excel 2010","author":"A Katz","year":"2010","unstructured":"Katz, A. Beginning Microsoft Excel 2010 (Apress, New York, 2010)."},{"key":"68953_CR61","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"L-T Nguyen","year":"2015","unstructured":"Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268\u2013274 (2015).","journal-title":"Mol. Biol. Evol."},{"key":"68953_CR62","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","volume":"155","author":"JK Pritchard","year":"2000","unstructured":"Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945\u2013959 (2000).","journal-title":"Genetics"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-68953-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-68953-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-68953-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,6]],"date-time":"2022-12-06T14:23:46Z","timestamp":1670336626000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-68953-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,23]]},"references-count":62,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["68953"],"URL":"https:\/\/doi.org\/10.1038\/s41598-020-68953-9","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,23]]},"assertion":[{"value":"18 November 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 May 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 July 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"12321"}}