Mitochondrial genomics of human pathogenic parasiteLeishmania(Viannia)panamensis

Abstract

Background The human parasite Leishmania (V.) panamensis is one of the pathogenic species responsible for cutaneous leishmaniasis in Central and South America. Despite its importance in molecular parasitology, its mitochondrial genome, divided into minicircles and maxicircles, haven’t been described so far. Methods Using NGS-based sequencing (454 and ILLUMINA), and combining de novo genome assembly and mapping strategies, we report the maxicircle kDNA annotated genome of L. (V.) panamensis, the first reference of this molecule for the subgenus Viannia. A comparative genomics approach is performed against other Leishmania and Trypanosoma species. Results The results show synteny of mitochondrial genes of L. (V.) panamensis with other kinetoplastids. It was also possible to identify nucleotide variants within the coding regions of the maxicircle, shared among some of them and others specific to each strain. Furthermore, we compared the minicircles kDNA sequences of two strains and the results show that the conserved and divergent regions of the minicircles exhibit strain-specific associations.

Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae

“…Here we present the sequences of 17 new full trypanosomatid maxicircles. The big problem of maxicircle sequencing is the divergent region, which remains difficult to assemble even using the modern NGS techniques [31,32]. In the current work we used PacBio datasets to assemble maxicircles, but even with this technique the assemblies often suffered from the low coverage in their DR.…”

“…With the development of sequencing technologies some maxicircles were sequenced completely [12,[30][31][32]. However, even paired-end Illumina sequencing was often not sufficient to assemble the complete maxicircle, and, because of that, most studies were focused only on coding region with short flanks [11,13,18], and even the most recent assembly from Illumina data had recovered only 3.5 kb of DR (as in [32]). Analysis of 3.5-kb and 5-kb regions of DR of Trypanosoma lewisi, flanking 12S and ND5 genes, respectively, revealed that these loci have different patterns of repeats [31].…”

Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles

“…Paradoxically, until very recently, the mitochondrial genomes of Leishmania parasites have been neglected in the gold era of nuclear genome sequencing. In the field, a few works, in which NGS technologies are used to determine Leishmania mitochondrial genomes, have been published [5,54,59]. In these studies, either previous kDNA purification [5] or selective PCR-amplification of maxicircles [54] steps were included.…”

Molecular Diagnosis of Leishmaniasis: Quantification of Parasite Load by a Real-Time PCR Assay with High Sensitivity

“…have 35 to 36 chromosomes in their nuclear genomes [ 35 , 36 ], and it is characterized by both mini and maxi circles kinetoplast DNA structures [ 37 ]. Various chromosomal and kinetoplast DNA sequences have been evaluated as targets for diagnostic systems and the extra-chromosomal circles showed always the best sensitivity and represent currently the most employed target with worldwide diffusion [ 38 , 39 ]. The use of high-copy 18S and minicircle kDNA sequences as a target usually allows amplification at the genus or subgenus level, due to their conserved sequences or to the heterogeneity of minicircle classes [ 21 ].…”