Complete and de novo assembly of the Leishmania braziliensis (M2904) genome

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.

Key words:
genome assembly; next generation sequencing; Illumina short reads; PacBio long reads; chromosomes; gene annotation

Authorship

Sandra González-de la Fuente

Universidad Autónoma de Madrid, Centro de Biología Molecular Severo Ochoa, Madrid, SpainUniversidad Autónoma de MadridSpainMadrid, SpainUniversidad Autónoma de Madrid, Centro de Biología Molecular Severo Ochoa, Madrid, Spain

Esther Camacho

Ramón Peiró-Pastor

Alberto Rastrojo

Fernando Carrasco-Ramiro

Begoña Aguado

Jose M Requena ⁺+ Corresponding author: jmrequena@cbm.csic.es

+ Corresponding author: jmrequena@cbm.csic.es

FCR, BA and JMR - Conceived and designed the experiments; JMR - parasites cultures and preparation of DNA; SGF, RPP and AR - genome assembly; SGF and EC - genome annotation; SGF, EC and JMR - drawing of figures, drafted the manuscript; JMR and BA edited the final manuscript. All authors contributed to the writing, have read and approved the final manuscript.

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Figures | Tables

Figures (3)
Tables (1)

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Fig. 1:
schematic overview of the Leishmania braziliensis genome assembly workflow. Input files (Illumina and PacBio reads) are shown in yellow rhomboids. Both different assembly processes and software used are represented in blue boxes. Output files are shown in green boxes and discarded data are shown in red boxes.

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Fig. 2:
read-depth analysis throughout the chromosomes formed by the union of two or more PacBio-assembled contigs. Coverage (log2 value) was appointed by sliding window analysis (bin 200 bp) with either Illumina (in blue) and PacBio (in red) reads, along chromosomes 2, 8, 9, 10, 20, 22, 27 and 34. Contigs lengths are shown by arrowheads lines. Chromosomes 2, 20, and 22 (panels A, E and F) were joined using the minimus 2 assembler. Chromosomes 8 (panel B) and 9 (panel C) were joined by the SSPACE-standard tool. Moreover, chromosome 27 (panel G) was joined by the SSPACE-LongRead tool and chromosome 10 (panel D) was joined with the pyScaf scaffolder tool. Finally, pyScaf and minimus2 were necessary for joining chromosome 34 (panel H).

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Fig. 3:
schematic illustration of chromosomal fusion (20 and 34) in the chromosome 20 of Leishmania braziliensis genome. Pairwise alignments between the L. braziliensis newly assembled genome (top) and the current reference genome (bottom), which is fragmented in two scaffolds (LbrM.20.1 and LbrM.20.2), were generated using Mauve genome alignment tool with default settings. This tool uses different colors to represent synteny blocks. Sections located underneath the x-axis show inversion events. The sizes of the two contigs of the current reference genome for chromosome 20 are shown by lines with arrow-heads.

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TABLE Features
of the Leishmania braziliensis assembled genomes and sequencing strategies

Fig. 1: schematic overview of the Leishmania braziliensis genome assembly workflow. Input files (Illumina and PacBio reads) are shown in yellow rhomboids. Both different assembly processes and software used are represented in blue boxes. Output files are shown in green boxes and discarded data are shown in red boxes.

Fig. 2: read-depth analysis throughout the chromosomes formed by the union of two or more PacBio-assembled contigs. Coverage (log2 value) was appointed by sliding window analysis (bin 200 bp) with either Illumina (in blue) and PacBio (in red) reads, along chromosomes 2, 8, 9, 10, 20, 22, 27 and 34. Contigs lengths are shown by arrowheads lines. Chromosomes 2, 20, and 22 (panels A, E and F) were joined using the minimus 2 assembler. Chromosomes 8 (panel B) and 9 (panel C) were joined by the SSPACE-standard tool. Moreover, chromosome 27 (panel G) was joined by the SSPACE-LongRead tool and chromosome 10 (panel D) was joined with the pyScaf scaffolder tool. Finally, pyScaf and minimus2 were necessary for joining chromosome 34 (panel H).

Fig. 3: schematic illustration of chromosomal fusion (20 and 34) in the chromosome 20 of Leishmania braziliensis genome. Pairwise alignments between the L. braziliensis newly assembled genome (top) and the current reference genome (bottom), which is fragmented in two scaffolds (LbrM.20.1 and LbrM.20.2), were generated using Mauve genome alignment tool with default settings. This tool uses different colors to represent synteny blocks. Sections located underneath the x-axis show inversion events. The sizes of the two contigs of the current reference genome for chromosome 20 are shown by lines with arrow-heads.

TABLE Features of the Leishmania braziliensis assembled genomes and sequencing strategies

Features	Assembly-2007⁽⁵⁾	Assembly-2011²⁸28. Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates PA, Depledge DP, et al. Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res. 2011; 21(12): 2129-42.	Assembly-2018⁽¹³⁾	This work
Chromosomes (scaffolds)	37	35	3782	35
Number of contigs	1041	103	13601	35
N50	57,784 bp	-	20,600 bp	1,063,631 bp
Annotated genes	8428	-	8161	8395
Annotated CDS:	8153	8357	8001	8244
- Functional annotation	-	-	-	4862
- Hypothetical proteins	-	-	-	3382
Annotated pseudogenes	161	-	65	33
Annotated structural genes	114	-	95	118
Number of gaps	2097	-	3352	0
Number of Ns	92,079	-	~316,778	0
Haploide genome size (bp)	31,996,772	31,997,773	30,009,653	32,301,632
Coverage (mean) [sequencing method]	6× [Capillary sequencing]	105× [Illumina] 7× [Capillary]	88× [Illumina]	363× [Illumina] 96× [PacBio]

-: data not found.

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Instituto Oswaldo Cruz, Ministério da Saúde Av. Brasil, 4365 - Pavilhão Mourisco, Manguinhos, 21040-900 Rio de Janeiro RJ Brazil, Tel.: (55 21) 2562-1222, Fax: (55 21) 2562 1220 - Rio de Janeiro - RJ - Brazil
E-mail: memorias@fiocruz.br

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Complete and de novo assembly of the Leishmania braziliensis (M2904) genome

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[1] + Corresponding author: jmrequena@cbm.csic.es