Global genome diversity of theLeishmania donovanicomplex

AbstractProtozoan parasites of theLeishmania donovanicomplex –L. donovaniandL. infantum– 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.L. donovaniisolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority ofL. infantumsamples 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 theLeishmania donovanicomplex.