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 approximately 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.

Figure 1

Chromosome 32 of L. major showing the positions of genes with a differential distribution between the three Leishmania species analyzed. The organization of chromosome 32 is shown schematically; both strands containing long, non-overlapping gene clusters. Genes that are restricted to only one or two of the three Leishmania species are not concentrated in the subtelomeric regions or at the breakpoint between polycistronic transcription units, as seen in other kinetoplastid parasites, but are distributed more evenly along the chromosome. Most gene differences are a result of pseudogene formation rather than insertion or deletion of new sequences.

Figure 2

Conserved pseudogenes in Leishmania species. Many Leishmania genes present in all three species retain sequence conservation but have frameshifts and/or in-frame stop codons. Some of these pseudogenes have intact syntenic orthologs in other kinetoplastids. (a) Comparison, using the sequence tool ACT, of a region of conserved synteny containing orthologs of the beta-adaptin 4 gene (gray/yellow) and the adjacent syntenic genes (brown) from L. major, L. infantum, L. braziliensis, T. cruzi and T. brucei. Gray bars represent the forward and reverse strands of DNA. The red-pink lines between sequences represent sequence similarity (tBLASTx). Each of the Leishmania orthologs of the beta-adaptin 4 gene (gray) contains several frameshifts and stop codons, whereas the two trypanosome species have uninterrupted intact copies (yellow). Gene prediction of the Leishmania pseudogenes was done by using similarity and codon bias. (b) Alignment of amino acid sequences from the three Leishmania species with their orthologs in T. cruzi, T. brucei and Trypanosoma vivax, showing that there are conserved domains across all species. The N-terminal β-adaptin domain (boxed region) shows conservation between all six species, and the most conserved residues correspond to residues that are restricted in higher eukaryotes.