Comparative genomic analysis of three Leishmania species that cause diverse human disease

Abstract

Leishmania parasites cause a broad spectrum of clinical disease. Here we report the sequencing of the genomes of two species of Leishmania: Leishmania infantum and Leishmania braziliensis. The comparison of these sequences with the published genome of Leishmania major reveals marked conservation of synteny and identifies only ∼200 genes with a differential distribution between the three species. L. braziliensis, contrary to Leishmania species examined so far, possesses components of a putative RNA-mediated interference pathway, telomere-associated transposable elements and spliced leader–associated SLACS retrotransposons. We show that pseudogene formation and gene loss are the principal forces shaping the different genomes. Genes that are differentially distributed between the species encode proteins implicated in host-pathogen interactions and parasite survival in the macrophage.

Gene expression profiling ofLeishmania (Leishmania) donovani: overcoming technical variation and exploiting biological variation

“…This diversity contrasts with the relative structural conservation of Leishmania genomes (Peacock et al 2007). Possibly, Leishmania's natural phenotypic diversity lies in differential features downstream of the genome, in the transcriptome or in the proteome.…”

“…This type of study has become feasible since the introduction of 2 high-throughput expression profiling techniques : (i) microarrays, used for comparative analysis of thousands of genes in distinct RNA populations (Schena et al 1995), and (ii) quantitative real-time PCR (Q-PCR), used for rapid simultaneous analysis of a specific set of genes in large sample collections (Heid et al 1996 ;Vandesompele et al 2002). Both these techniques are rapidly gaining popularity in Leishmania studies since the Leishmania genome sequences have become available (Duncan, 2004 ;Ivens et al 2005 ;Peacock et al 2007). However, the interpretation and standardization of gene expression studies in Leishmania might be more challenging in comparison to other eukaryotes due to the specific biology of this parasite.…”

Contribution of proteomics of Leishmania spp. to the understanding of differentiation, drug resistance mechanisms, vaccine and drug development

“…Genomes of L. major 6 , L. infantum and L. braziliensis 8 were not available at the time and obtained amino acid sequences were used for identification of homologous proteins by using the BLAST search algorithm that requires a very high degree of sequence conservation to unambiguously identify a protein, hence only two proteins (isocitrate dehydrogenase and triosephosphate isomerase) could be identified. Later the GeneDB database became publicly available which provided a platform for initially the L. major genome and later for all sequenced genomes 24 .…”

“…proteome profiling in pre-genomic era Leishmania spp. have a core genome of 8178 genes shared between the three currently sequenced and annotated genomes of L. major, L. infantum and L. braziliensis, and only few genes are species specific, 5, 27 and 49, respectively 8 . Although it is known that host factors play also a part in disease outcome, it is reasonable to assume that for the course of an infection differences in gene content or expression level in parasite species and isolates determine their respective virulence.…”

“…However, it was the sequencing of the genomes of L. major 6 , L. infantum and L. braziliensis 8 , with data available since the beginning of this millennium that enabled the relatively straight forward identification of protein-species excised from 2DE gels by mass spectrometry or from peptides separated by liquid chromatography (LC) as discussed below.…”