<i>Leishmania naiffi</i> and <i>Leishmania guyanensis</i> reference genomes highlight genome structure and gene evolution in the <i>Viannia</i> subgenus

Abstract

The unicellular protozoan parasite <i>Leishmania</i> causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America, where the <i>Viannia</i> subgenus predominates, so far only <i>L.</i> (<i>Viannia</i>) <i>braziliensis</i> and <i>L.</i> (<i>V.</i>) <i>panamensis</i> 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, <i>L.</i> (<i>V.</i>) <i>naiffi</i> and <i>L.</i> (<i>V.</i>) <i>guyanensis</i> 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 <i>L. braziliensis</i> 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 <i>L. guyanensis</i> and <i>L. naiffi</i> with 10 other <i>Viannia</i> genomes revealed four traits common to all <i>Viannia</i>: aneuploidy, 22 orthologous groups of genes absent in other <i>Leishmania</i> subgenera, elevated TATE transposon copies and a high NADH-dependent fumarate reductase gene copy number. Within the <i>Viannia</i>, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar <i>L. lainsoni</i>, <i>L. naiffi</i> had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate <i>L. shawi</i> M8408 had a possible minichromosome derived from the 3' end of chromosome 34<i>.</i> This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse <i>Viannia</i> has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.