Complete and De Novo Assembly of the Leishmania Braziliensis (M2904) Genome

Overview

Journal Mem Inst Oswaldo Cruz

Specialties Parasitology
Tropical Medicine

Date 2018 Dec 13

PMID 30540030

Citations 10

Authors

Sandra Gonzalez-de la Fuente

Esther Camacho

Ramon Peiro-Pastor

Alberto Rastrojo

Fernando Carrasco-Ramiro

Begona Aguado

Jose M Requena

Affiliations

Soon will be listed here.

Abstract

Leishmania braziliensis is the etiological agent of American mucosal leishmaniasis, one of the most severe clinical forms of leishmaniasis. Here, we report the assembly of the L. braziliensis (M2904) genome into 35 continuous chromosomes. Also, the annotation of 8395 genes is provided. The public availability of this information will contribute to a better knowledge of this pathogen and help in the search for vaccines and novel drug targets aimed to control the disease caused by this Leishmania species.

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References

Ivens A, Peacock C, Worthey E, Murphy L, Aggarwal G, Berriman M . The genome of the kinetoplastid parasite, Leishmania major. Science. 2005; 309(5733):436-42. PMC: 1470643. DOI: 10.1126/science.1112680. View

Boetzer M, Henkel C, Jansen H, Butler D, Pirovano W . Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2010; 27(4):578-9. DOI: 10.1093/bioinformatics/btq683. View

Ubeda J, Raymond F, Mukherjee A, Plourde M, Gingras H, Roy G . Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite Leishmania. PLoS Biol. 2014; 12(5):e1001868. PMC: 4028189. DOI: 10.1371/journal.pbio.1001868. View

Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J . SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2013; 1(1):18. PMC: 3626529. DOI: 10.1186/2047-217X-1-18. View

Gonzalez-de la Fuente S, Peiro-Pastor R, Rastrojo A, Moreno J, Carrasco-Ramiro F, Requena J . Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs. Sci Rep. 2017; 7(1):18050. PMC: 5741766. DOI: 10.1038/s41598-017-18374-y. View

Coughlan S, Taylor A, Feane E, Sanders M, Schonian G, Cotton J . and reference genomes highlight genome structure and gene evolution in the subgenus. R Soc Open Sci. 2018; 5(4):172212. PMC: 5936940. DOI: 10.1098/rsos.172212. View

Downing T, Imamura H, Decuypere S, Clark T, Coombs G, Cotton J . Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res. 2011; 21(12):2143-56. PMC: 3227103. DOI: 10.1101/gr.123430.111. View

Li L, Stoeckert Jr C, Roos D . OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9):2178-89. PMC: 403725. DOI: 10.1101/gr.1224503. View

Sommer D, Delcher A, Salzberg S, Pop M . Minimus: a fast, lightweight genome assembler. BMC Bioinformatics. 2007; 8:64. PMC: 1821043. DOI: 10.1186/1471-2105-8-64. View

10.

Walker B, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S . Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9(11):e112963. PMC: 4237348. DOI: 10.1371/journal.pone.0112963. View

11.

Boetzer M, Pirovano W . SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics. 2014; 15:211. PMC: 4076250. DOI: 10.1186/1471-2105-15-211. View

12.

Chin C, Alexander D, Marks P, Klammer A, Drake J, Heiner C . Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013; 10(6):563-9. DOI: 10.1038/nmeth.2474. View

13.

Alonso G, Rastrojo A, Lopez-Perez S, Requena J, Aguado B . Resequencing and assembly of seven complex loci to improve the Leishmania major (Friedlin strain) reference genome. Parasit Vectors. 2016; 9:74. PMC: 4746890. DOI: 10.1186/s13071-016-1329-4. View

14.

Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G . Real-time DNA sequencing from single polymerase molecules. Science. 2008; 323(5910):133-8. DOI: 10.1126/science.1162986. View

15.

Nadalin F, Vezzi F, Policriti A . GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics. 2012; 13 Suppl 14:S8. PMC: 3439727. DOI: 10.1186/1471-2105-13-S14-S8. View

16.

Chiurillo M, Ramirez J . Charaterization of Leishmania major Friedlin telomeric terminus. Mem Inst Oswaldo Cruz. 2002; 97(3):343-6. DOI: 10.1590/s0074-02762002000300011. View

17.

Peacock C, Seeger K, Harris D, Murphy L, Ruiz J, Quail M . Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet. 2007; 39(7):839-47. PMC: 2592530. DOI: 10.1038/ng2053. View

18.

Dumetz F, Imamura H, Sanders M, Seblova V, Myskova J, Pescher P . Modulation of Aneuploidy in during Adaptation to Different and Environments and Its Impact on Gene Expression. mBio. 2017; 8(3). PMC: 5442457. DOI: 10.1128/mBio.00599-17. View

19.

Requena J, Rastrojo A, Garde E, Lopez M, Thomas M, Aguado B . Genomic cartography and proposal of nomenclature for the repeated, interspersed elements of the Leishmania major SIDER2 family and identification of SIDER2-containing transcripts. Mol Biochem Parasitol. 2016; 212:9-15. DOI: 10.1016/j.molbiopara.2016.12.009. View

20.

Rogers M, Hilley J, Dickens N, Wilkes J, Bates P, Depledge D . Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res. 2011; 21(12):2129-42. PMC: 3227102. DOI: 10.1101/gr.122945.111. View