Leishmania naiffiandLeishmania guyanensisreference genomes highlight genome structure and gene evolution in theVianniasubgenus

Abstract

The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America, where the Viannia subgenus predominates, so far only L. (Viannia) braziliensis and L. (V.) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi and L. (V.) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with 10 other Viannia genomes revealed four traits common to all Viannia: aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar L. lainsoni, L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3’ end of chromosome 34. This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.

In-depth quantitative proteomics uncovers specie-specific metabolic programs in Leishmania (Viannia) species

“…Principal component analysis (PCA) of the protein concentrations showed tight clustering for each set of biological replicates and revealed a clear separation among the strains representing L. braziliensis, L. panamensis and L. guyanensis samples ( Fig 1A). Although proteomes are highly dynamic and may vary according to parasite stage, culture conditions and probably to intra-specific diversity of Leishmania, our results show that global protein abundances obtained by deep proteomics are able to clearly distinguish the three species, in a similar way that deep genome sequencing allows such distinction [9,12].…”

“…Heterogeneous clinical manifestations are the result of a complex interaction among host immune responses, host genetic background and parasite characteristics such as virulence, infectivity and pathogenicity [5]. Among others, to understand the parasite contribution for the clinical outcome, complete genome sequences of most of the pathogenic Leishmania species and hundreds of strains have been obtained [6][7][8][9][10][11][12][13][14][15][16][17], paving the way for the analyses of their proteomes. However, such a massive effort has not been followed by proteomics studies.…”

Aneuploidy in yeast: Segregation error or adaptation mechanism?

“…Trypanosomatids, including Leishmania and Trypanozoma , are responsible for diseases such as sleeping sickness ( Trypanosoma brucei ) and Chagas disease ( Trypanosoma cruzi ). Aneuploidy is particularly widespread across Leishmania and has been shown to vary from few aneuploid chromosomes (Valdivia et al, ) to many (Coughlan et al, ; Coughlan et al, ; Iantorno et al, ; Kumar et al, ; Prieto Barja et al, ; Reis‐Cunha et al, ; Rogers et al, ; Ubeda et al, ) depending on the species, with large phenotypic effects, including resistance to various drugs. For example, Leishmania major gains resistance to the drugs methotrexate and antimonial through aneuploidy, Leishmania donovani to the drug nelfinavi and Leishmania infantum to methotrexate (Kumar et al, ; Mukherjee et al, ; Ubeda et al, ).…”

LmxM.22.0250-Encoded Dual Specificity Protein/Lipid Phosphatase Impairs Leishmania mexicana Virulence In Vitro

“…Our data, demonstrating that ablation of LmxM.22.0250 does not change the expression of the paralogous LmxM.32.2840 gene, are in agreement with this hypothesis. We also noted that the DUSP1-encoding gene has been pseudogenized in members of the subgenus Leishmania (Viannia), suggesting that these parasites rely on other factors determining their virulence [40,41].…”