Abstract
Purpose
Leishmania subgenus Leishmania causes leishmaniosis, which is a chronic systemic disease in humans and animals, in which the skin and visceral organs can be affected. The disease generally consists of three different clinical types in humans: visceral (kala-azar, VL), cutaneous (CL) and mucocutaneous leishmaniosis (MCL). According to the World Health Organization (WHO), leishmaniosis is still one of the world’s most neglected diseases. It has been nearly 13–14 years since the completion of the first complete genome sequence of a Leishmania parasite. However, much information about these parasites remains to be elucidated, such as the causes of differences in tissue tropism. The aim of this study is to perform the whole-genome sequencing of Leishmania infantum causing cutaneous leishmaniosis from a Turkish isolate with next-generation sequencing technology.
Methods
Genomic sequencing was performed on the Illumina HiSeq 2500 platform. The TruSeq Nano DNA Low Throughput Library Prep Kit, compatible with the Illumina HiSeq 2500 platform, was used to generate the library. Synthesis sequencing (SBS) was performed with a HiSeq Rapid SBS Kit v2 to generate single-fragment reads (2 × 150 bp; PE) with two fragment end-to-end assemblies. Bioinformatics analyses were performed on the Geneious 11.0.5. (www.genius.com) platform.
Results
In our study, a high-quality whole-genome sequence (WGS) of L. infantum was successfully generated, and a total of 32,009,137 base pairs of genomic DNA from 36 chromosomes were obtained. The resulting genomic DNA sequence was submitted to the US National Center for Biotechnology Information (NCBI) GenBank (www.ncbi.nlm.nih.gov) database and registered under the name Leishmania infantum_TR01 (Lin_TR01). The following accession numbers were assigned by NCBI to the 36 chromosomes of the Lin_TR01 genome: CP027807, CP027810, CP027808, CP027811, CP027809, CP027812, CP027813, CP027814, CP027817, CP027818, CP027819, CP027815, CP027821, CP027816, CP027823, CP027820, CP027822, CP027824, CP027825, CP027826, CP027827, CP027828, CP027829, CP027830, CP027831, CP027832, CP027833, CP027834, CP027835, CP027836, CP027837, CP027838, CP027839, CP027840, CP027841, CP027842. As a result of the annotation of the Lin_TR01 genome, 3153 polymorphisms, 8324 genes, 8199 CDSs, 8109 mRNAs, 67 tRNAs, 11 rRNAs and 58 ncRNA were identified. Among the 8199 CDS obtained, 5278 encode hypothetical proteins.
Conclusion
In this study, a high-quality WGS of Leishmania infantum was successfully obtained for the first time in Turkey. According to a review of WGS studies on this subject, the Lin_TR01 strain is the first strain to be isolated from cutaneous leishmaniosis. The reference genome of L. infantum JPCM5 (Peacock et al., 2007) was obtained from a visceral leishmaniosis case, in accordance with the classical tissue and organ tropism of the species. Lin_TR01 is the second whole-genome-sequenced strain in the world after the JPCM5 strain. The Lin_TR01 genome is the only L. infantum whole-genome sequence that is completed assembly level from 36 chromosomes among the genomes obtained thus far (https://www.ncbi.nlm.nih.gov/genome/genomes/249).
Similar content being viewed by others
References
Afgan E, Chapman B, Taylor J (2012) CloudMan as a platform for tool, data, and analysis distribution. BMC Bioinf 13(1):315. https://doi.org/10.1186/1471-2105-13-315
Andrews, S., 2010. FastQC: a quality control tool for high throughput sequence data. Available online at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc
Britto C, Ravel C, Bastien P, Blaineau C, Pages M, Dedet JP, Wincker P (1998) Conserved linkage groups associated with large-scale chromosomal rearrangements between OldWorld and NewWorld Leishmania genomes. Gene 222(1):107–117. https://doi.org/10.1016/s0378-1119(98)00472-7
Cantacessi C, Dantas-Torres F, Nolan MJ, Otranto D (2015) The past, present, and future of Leishmania genomics and transcriptomics. Trends Parasitol 31(3):100–108. https://doi.org/10.1016/j.pt.2014.12.012
Downing T, Imamura H, Decuypere S, Clark TG, Coombs GH, Cotton JA, Hilley JD, De Doncker S, Maes I, Mottram JC, Quail MA, Rijal S, Sanders M, Schönian G, Stark O, Sundar S, Vanaerschot M, Hertz-Fowler C, Dujardin JC, Berriman M (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. https://doi.org/10.1101/gr.123430.111
Galaxy (2018) https://usegalaxy.org/. Accessed: 14 Oct 2019
Geneious (2018) https://www.geneious.com/. Accessed: 14 Oct 2019
Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G et al (2005) The genome of the kinetoplastid parasite, Leishmania major. Science 309:436–442. https://doi.org/10.1126/science.1112680
JGI (Joint Genome Institute) (2018) https://jgi.doe.gov/. Accessed 14 Oct 2019
Karaer Z, Nalbantoglu S (2015) Trypanosomatidae. Veterinary Protozoology, Eds. Dumanli N, Karaer Z, Medisan Publishing, Ankara, 23–43.
Leprohon P, Fernandez-Prada C, Gazanion É, Monte-Neto R, Ouellette M (2014) Drug resistance analysis by next generation sequencing in Leishmania. Int J Parasitol Drugs Drug Resist. 22;5(1), 26–35. https://doi.org/10.1016/j.ijpddr.2014.09.005
Lye LF, Owens K, Shi H, Murta SM, Vieira AC, Turco SJ, Tschudi C, Ullu E, Beverley SM (2010) Retention and loss of RNA interference pathways in trypanosomatid protozoans. PLoS Pathog 6:e1001161. https://doi.org/10.1371/journal.ppat.1001161
NCBI (National Center For Biotechnology Information) (2018a) https://www.ncbi.nlm.nih.gov/. Accessed: 14 Oct 2019
NCBI (2018b) https://www.ncbi.nlm.nih.gov/genome/249?genome_assembly_id=368466. Accessed: 14 Oct 2019
NCBI (2018c) https://www.ncbi.nlm.nih.gov/genome/genomes/249. Accessed: 14 Oct 2019
Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC, Quail MA, Peters N, Adlem E, Tivey A, Aslett M, Kerhornou A, Ivens A, Fraser A, Rajandream MA, Carver T, Norbertczak H, Chillingworth T, Hance Z, Jagels K, Moule S, Ormond D, Rutter S, Squares R, Whitehead S, Rabbinowitsch E, Arrowsmith C, White B, Thurston S, Bringaud F, Baldauf SI, Faulconbridge A, Jeffares D, Depledge DP, Oyola SO, Hilley JD, Brito LO, Tosi LR, Barrell B, Cruz AK, Mottram JC, Smith DF, Berriman M (2007) Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat. Genet. 39:839–847. https://doi.org/10.1038/ng2053
Raymond F, Boisvert S, Roy G, Ritt JF, Legare D, Isnard A, Stanke M, Olivier M, Tremblay MJ, Papadopoulou B, Ouellette M, Corbeil J (2012) Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Nucl Acids Res 40:1131–1147. https://doi.org/10.1093/nar/gkr834
Real F, Vidal RO, Carazzolle MF, Mondego JM, Costa GG, Herai RH, Würtele M, De Carvalho LM, Carmona-Ferreira R, Mortara RA, Barbiéri CL, Mieczkowski P, Da Silveira JF, Briones MR, Pereira GA, Bahia D (2013) The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models. DNA Res. 20:567–581. https://doi.org/10.1093/dnares/dst031
Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates PA, Depledge DP, Harris D, Her Y, Herzyk P, Imamura H, Otto TD, Sanders M, Seeger K, Dujardin JC, Berriman M, Smith DF, Hertz-Fowler C, Mottram JC (2011) Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res 21:2129–2142. https://doi.org/10.1101/gr.122945.111
Sanchez-Canete MP, Carvalho L, Perez-Victoria FJ, Gamarro F, Castanys S (2009) Low plasma membrane expression of the miltefosine transport complex renders Leishmania braziliensis refractory to the drug. Antimicrob Agents Chemother 53:1305–1313. https://doi.org/10.1128/AAC.01694-08
Teixeira DG, Monteiro GRG, Martins DRA, Fernandes MZ, Macedo-Silva V, Ansaldi M, Nascimento PRP, Kurtz MA, Streit JA, Ximenes MFFM, Pearson RD, Miles A, Blackwell JM, Wilson ME, Kitchen A, Donelson JE, Lima JPMS, Jeronimo SMB (2017) Comparative analyses of whole genome sequences of Leishmania infantum isolates from humans and dogs in northeastern Brazil. Int J Parasitol 47(10–11):655–665. https://doi.org/10.1016/j.ijpara.2017.04.004(Epub 2017 Jun 10)
TriTrypDB (The Kinetoplastid Genomics Resource, 2018) https://tritrypdb.org/tritrypdb/. Accessed: 14 Oct 2019
Yardley V, Croft SL, De Doncker S, Dujardin JC, Koirala S, Rijal S, Miranda C, Llanos-Cuentas A, Chappuis F (2005) The sensitivity of clinical isolates of Leishmania from Peru and Nepal to miltefosine. Am J Trop Med Hyg 73:272–275
WHO (World Health Organization) (2010) Control of the leishmaniasis: report of a meeting of the WHO Expert Committee on the Control of Leishmaniases, Geneva, 22–26 March. https://whqlibdoc.who.int/trs/WHO_TRS_949_eng.pdf. Accessed: 14 Oct 2019
Acknowledgements
This article was produced of BAP (Scientific Research Projects) project 17L0239002, supported by the Ankara University BAP Coordination Unit Coordinator, and as a part of doctoral thesis under the same title.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflıct of ınterest
The authors declare that they have no conflicts of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Guldemir, D., Usluca, S. & Nalbantoglu, A.S. Genome Sequencing of Leishmania infantum Causing Cutaneous Leishmaniosis from a Turkish Isolate with Next-Generation Sequencing Technology. Acta Parasit. 66, 75–80 (2021). https://doi.org/10.1007/s11686-020-00252-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11686-020-00252-9