Global genome diversity of the Leishmania donovani complex

Abstract

Protozoan parasites of the <i>Leishmania donovani</i> complex - <i>L. donovani</i> and <i>L. infantum</i> - cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. <i>L. donovani</i> isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of <i>L. infantum</i> samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the <i>Leishmania donovani</i> complex.