High-resolution genotyping and mapping of recombination and gene conversion in the protozoan Theileria parva using whole genome sequencing

Abstract

BackgroundTheileria parva is a tick-borne protozoan parasite, which causes East Coast Fever, a disease of cattle in sub-Saharan Africa. Like Plasmodium falciparum, the parasite undergoes a transient diploid life-cycle stage in the gut of the arthropod vector, which involves an obligate sexual cycle. As assessed using low-resolution VNTR markers, the crossover (CO) rate in T. parva is relatively high and has been reported to vary across different regions of the genome; non-crossovers (NCOs) and CO-associated gene conversions have not yet been characterised due to the lack of informative markers. To examine all recombination events at high marker resolution, we sequenced the haploid genomes of two parental strains, and two recombinant clones derived from ticks fed on cattle that had been simultaneously co-infected with two different parasite isolates.ResultsBy comparing the genome sequences, we were able to genotype over 64 thousand SNP markers with an average spacing of 127 bp in the two progeny clones. Previously unrecognized COs in sub-telomeric regions were detected. About 50% of CO breakpoints were accompanied by gene conversion events. Such a high fraction of COs accompanied by gene conversions demonstrated the contributions of meiotic recombination to the diversity and evolutionary success of T. parva, as the process not only redistributed existing genetic variations, but also altered allelic frequencies. Compared to COs, NCOs were more frequently observed and more uniformly distributed across the genome. In both progeny clones, genomic regions with more SNP markers had a reduced frequency of COs or NCOs, suggesting that the sequence divergence between the parental strains was high enough to adversely affect recombination frequencies. Intra-species polymorphism analysis identified 81 loci as likely to be under selection in the sequenced genomes.ConclusionsUsing whole genome sequencing of two recombinant clones and their parents, we generated maps of COs, NCOs, and CO-associated gene conversion events for T. parva. The data comprises one of the highest-resolution genome-wide analyses of the multiple outcomes of meiotic recombination for this pathogen. The study also demonstrates the usefulness of high throughput sequencing typing for detailed analysis of recombination in organisms in which conventional genetic analysis is technically difficult.

DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis

“…It is also possible to map recombination events at high resolution, by crossing strains with defined sequence polymorphisms, followed by wholegenome sequencing of the resulting progenies. High-resolution maps of genome-wide recombination events are now available for Saccharomyces cerevisiae, Drosophila, maize, and Theileria parva (Mancera et al, 2008;Comeron et al, 2012;Henson et al, 2012;Li et al, 2015;Rodgers-Melnick et al, 2015). Furthermore, highthroughput sequencing, combined with single-cell technology, contributed to the detection of meiotic recombination of single sperm (Lu et al, 2012b;Wang et al, 2012) and single oocyte (Hou et al, 2013) genotyping.…”

Antigen gene and variable number tandem repeat ( VNTR ) diversity in Theileria parva parasites from Ankole cattle in south‐western Uganda: Evidence for conservation in antigen gene sequences combined with extensive polymorphism at VNTR loci

“…The high T. parva diversity and frequency of multiple infections may be explained by heavy tick infestations resulting from irregular tick control regimes (Wambura, Gwakisa, Silayo, & Rugaimukamu, ). Additionally, as demonstrated by earlier studies, a high degree of genetic diversity within a population may be a result of high levels of recombination and associated gene conversion within the R. appendiculatus tick vector (Katzer, Lizundia, Ngugi, Blake, & McKeever, ; Henson et al., ;., Hayashida et al., ).…”

Multilocus genotyping of Theileria parva isolates associated with a live vaccination trial in Kenya provides evidence for transmission of immunizing parasites into local tick and cattle populations

“…It is possible that stocks with VNTR MLGs identical to Kiambu V and Serengeti/Muguga circulate among ticks and cattle in East Africa, including Western Kenya. However it might be expected that given the high numbers of 22 VNTR, dispersed throughout the genome analysed, with an average number alleles of approximately 5 per locus (Table S2), that these combinations would not persist intact over long periods of time given the high levels of recombination observed on passage of T. parva through the tick vector (Henson et al, ; Katzer, Lizundia, Ngugi, Blake, & McKeever, ). An alternative explanation is that, since at the time of this study (1997–2000), there had been no field trials of the trivalent Muguga cocktail in Kenya, the T. parva isolates Kiambu V and Serengeti/Muguga, (both originally isolated from central Kenya) may have originated from trials of the Muguga cocktail conducted in eastern Uganda a few years prior to the present study (Moran & Ntsubuga‐Mutaka, ; Mutugi, Otim, & Ntsubuga‐Mutaka, ).…”

“…In the longer term the consequences are harder to predict, as recombination within the tick vector is likely to create novel genotypes. However given the diversity of the T. parva in endemic areas (Odongo et al, ; Oura, Tait, Asiimwe, Lubega, & Weir, , ) and the obligate sexual cycle Gauer et al, ; Katzer et al, ; Henson et al, ) it seems probable that new genotypes are continuously being created in the field.…”