DOI: 10.5061/dryad.xd2547djb
title: Signatures of hybridization in Trypanosoma brucei

description: 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.
description: # Signatures of hybridization in *Trypanosoma brucei* Dataset DOI:
 [10.5061/dryad.xd2547djb](10.5061/dryad.xd2547djb) ## Description of the
 data and file structure Read data for the hybrid clones from the
 experimental cross is available from the NCBI SRA (Sequence Read Archive
 [https://www.ncbi.nlm.nih.gov/sra](https://www.ncbi.nlm.nih.gov/sra)
 Project no. PRJNA795331 All other data have been deposited here. The
 project contains the folders listed below. Each folder contains a “Readme”
 file with further details of the contents. ### assembled\_genomes The
 genomic SPAdes assembled genomes used to predict ORFs and subsequently
 VSGs, contigs are of the form:
 \&gt;NODE_166886_length_56_cov_1939465.000000
 GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG ###
 introgression\_maps Contains the VCF files used to construct the
 introgression maps, the script to derive them, and breakdowns of SNP
 types/density. ### Hybrid\_and\_parent\_maxicircle\_whole\_coding\_region
 FASTA file containing the commonly oriented and trimmed coding regions of
 maxicircle contigs ### Hybrid\_pooled\_minicircles Contains the identified
 contigs from the selective subassembly of minicircles. Contig headers
 inherit their numbering from the SPAdes contigs header (Contig number,
 contig length, coverage depth) \&gt;Tbb_F1G2#59#1030#370##
 GGGCGTGCAGATTTCACCATACACAAATACCGTGCTATTTTCGGGCATTTTTGAGGGCCGTGGTACTTCGAAAGGGG ### Hybrid\_VSG\_pool Contains a fasta of identified VSGs, entry headers include information about their origin. # separated fields indicate, isolate, SPAdes contig, contig length, coverage depth, position/orientation of ORF, HMM used, and HMM e-values \&gt;Tbb_F1G2_k-121#1576#5315#45#1836-3419(+)#Trypan_glycop_C#8e-2 MLKKLALTAIVLAFSNGRKATGAALNDGDNAKYFKPLCGIIRAASAAPEAVPEQPVLDDLEATALLINLSYASPKAMSELTA ### MES\_promoter The HMM used to identify MES contigs. ### MES\_loci Presented as a fasta in the form: \&gt;Cluster_1#Tbb_FIG2#114#31951#R CCAGACACCCTTAGAGACAGAGGGGGTATGCAATCAACAAGCAACAGAAACAGAAAGAGGGGAAGAGAATAATA Where contig, isolate, genomic SPAdes assembly contig number, length, and orientation relative to assembly (R indicates the sequence has been reversed) ### Maxicircle\_sequences Identified maxicircle contigs from the field isolates. ### Sistrom\_pooled\_minicircles As for the minicircles fasta above, except includes other isolates, and does not include hybrids ### Sistrom\_VSG\_pool As for the VSG fasta above, except includes other isolates, and does not include hybrids ### Tbb\_minicircles The derived HMM from our assembled minicircles ### Trypan\_glycop\_C The PFAM HMM for the VSG C-terminal domain at the time of submission ## Code/software Text editor, fasta files