Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani.

James A Cotton,Asrat Hailu,Susanne U Franssen,Michael A Miles,Matthew Berriman,Mandy J Sanders,Matthew Yeo,Petr Volf,David Mateus,Caroline Durrant,Tesfaye Gelanew,Ananias A Escalante

doi:10.1371/journal.pntd.0007143

Abstract

Parasites of the genus Leishmania (Kinetoplastida: Trypanosomatidae) cause widespread and devastating human diseases. Visceral leishmaniasis due to Leishmania donovani is endemic in Ethiopia where it has also been responsible for major epidemics. The presence of hybrid genotypes has been widely reported in surveys of natural populations, genetic variation reported in a number of Leishmania species, and the extant capacity for genetic exchange demonstrated in laboratory experiments. However, patterns of recombination and the evolutionary history of admixture that produced these hybrid populations remain unclear. Here, we use whole-genome sequence data to investigate Ethiopian L. donovani isolates previously characterized as hybrids by microsatellite and multi-locus sequencing. To date there is only one previous study on a natural population of Leishmania hybrids based on whole-genome sequences. We propose that these hybrids originate from recombination between two different lineages of Ethiopian L. donovani occurring in the same region. Patterns of inheritance are more complex than previously reported with multiple, apparently independent, origins from similar parents that include backcrossing with parental types. Analysis indicates that hybrids are representative of at least three different histories. Furthermore, isolates were highly polysomic at the level of chromosomes with differences between parasites recovered from a recrudescent infection from a previously treated individual. The results demonstrate that recombination is a significant feature of natural populations and contributes to the growing body of data that shows how recombination, and gene flow, shape natural populations of Leishmania.

Highlights

Leishmania is a diverse genus of kinetoplastid protozoan parasites from the family Trypanosomatidae
Leishmaniasis is a spectrum of diseases caused by the protozoan parasite Leishmania
Genomic analysis of natural Ethiopian Hybrid isolates of Leishmania donovani funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Summary

Introduction

Leishmania is a diverse genus of kinetoplastid protozoan parasites from the family Trypanosomatidae. These parasites are best known as the cause of human and animal leishmaniasis, which is a clinically important neglected tropical disease affecting millions of people and causing a tremendous burden of mortality and morbidity [1,2]. Vertebrate hosts encompass a wide range of mammals or reptiles, and around 20 species of Leishmania have been reported to infect humans [4]. The population structure of Leishmania, other trypanosomatids and most protozoan parasites was considered to be largely clonal [6]: the presumption was that admixture between members of the same clone, or between very closely related parasites was absent or rare, with minimal impact on population structure. There is a growing body of evidence for genetic exchange in natural populations of several Leishmania species

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Results

Conclusion