Discussion

Mating is not an obligatory part of the trypanosome life cycle with its frequency in natural populations depending on the species and the disease focus. Here we provide for the first time extensive genomic evidence for frequent mating in the putatively clonal Trypanosoma congolense, a parasite with detrimental effects on livestock productivity in sub-Saharan Africa. A genome-wide study in 54 isolates from across Africa revealed a large body of SNPs, indels and gene deletions that segregate in divergent T. congolense populations. We present unique data of a hybrid population of trypanosomes at a single focus in Zambia, resulting from outcrossing between phylogenetically distinct T. congolense parasites that led to a substantial increase in standing genomic variation. Subsequent cycles of sexual recombination produced a patchy genomic landscape varying in haplotypic ancestry and marker variability.  We outline the genomic consequences of hybridization in trypanosomes and discuss potential associations with the spread of drug resistance.