Genome diversity ofLeishmania aethiopica

Leishmania aethiopicais a zoonotic Old World parasite transmitted by Phlebotomine sand flies and causing cutaneous leishmaniasis in Ethiopia and Kenya. Despite a range of clinical manifestations and a high prevalence of treatment failure,L. aethiopicais the most neglected species of theLeishmaniagenus in terms of scientific attention. Here, we explored the genome diversity ofL. aethiopicaby analyzing the genomes of twenty isolates from Ethiopia. Phylogenomic analyses identified two strains as interspecific hybrids involvingL. aethiopicaas one parent andL. donovaniandL. tropicarespectively as the other parent. High levels of genome-wide heterozygosity suggest that these two hybrids are equivalent to F1 progeny that propagated mitotically since the initial hybridization event. Analyses of allelic read depths further revealed that theL. aethiopica-L. tropicahybrid was diploid and theL. aethiopica-L. donovanihybrid was triploid, as has been described for other interspecificLeishmaniahybrids. When focusing onL. aethiopica, we show that this species is genetically highly diverse and consists of both asexually evolving strains and groups of recombining parasites. A remarkable observation is that someL. aethiopicastrains showed an extensive loss of heterozygosity across large regions of the chromosomal genome, which likely arose from gene conversion/mitotic recombination. Hence, our prospection ofL. aethiopicagenomics revealed new insights into the genomic consequences of both meiotic and mitotic recombination inLeishmania.