Signatures of hybridization in Trypanosoma brucei

Genetic exchange among disease-causing micro-organisms can generate
progeny that combine different pathogenic traits. Though sexual
reproduction has been described in trypanosomes, its impact on the
epidemiology of Human African Trypanosomiasis (HAT) remains controversial.
However, human infective and non-human infective strains of Trypanosoma
brucei circulate in the same transmission cycles in HAT endemic areas in
sub-Saharan Africa, providing the opportunity for mating during the
developmental cycle in the tsetse fly vector. Here we investigated
inheritance among progeny from a laboratory cross of T. brucei and then
applied these insights to genomic analysis of field-collected isolates to
identify signatures of past genetic exchange. Genomes of two parental and
four hybrid progeny clones with a range of DNA contents were assembled and
analysed by k-mer and single nucleotide polymorphism (SNP) frequencies to
determine heterozygosity and chromosomal inheritance. Variant surface
glycoprotein (VSG) genes and kinetoplast (mitochondrial) DNA maxi- and
minicircles were extracted from each genome to examine how each of these
components was inherited in the hybrid progeny. The same bioinformatic
approaches were applied to an additional 37 genomes representing the
diversity of T. brucei in sub-Saharan Africa and T. evansi. SNP analysis
provided evidence of crossover events affecting all 11 pairs of megabase
chromosomes and demonstrated that polyploid hybrids were formed
post-meiotically and not by fusion of the parental diploid cells. VSGs and
kinetoplast DNA minicircles were inherited biparentally, with
approximately equal numbers from each parent, whereas maxicircles were
inherited uniparentally. Extrapolation of these findings to field isolates
allowed us to distinguish clonal descent from hybridization by comparing
maxicircle genotype to VSG and minicircle repertoires. Discordance between
maxicircle genotype and VSG and minicircle repertoires indicated
inter-lineage hybridization. Significantly, some of the hybridization
events we identified involved human infective and non-human infective
trypanosomes circulating in the same geographic areas.