NextGen sequencing reveals short double crossovers contribute disproportionately to genetic diversity in Toxoplasma gondii

Abstract

BackgroundToxoplasma gondii is a widespread protozoan parasite of animals that causes zoonotic disease in humans. Three clonal variants predominate in North America and Europe, while South American strains are genetically diverse, and undergo more frequent recombination. All three northern clonal variants share a monomorphic version of chromosome Ia (ChrIa), which is also found in unrelated, but successful southern lineages. Although this pattern could reflect a selective advantage, it might also arise from non-Mendelian segregation during meiosis. To understand the inheritance of ChrIa, we performed a genetic cross between the northern clonal type 2 ME49 strain and a divergent southern type 10 strain called VAND, which harbors a divergent ChrIa.ResultsNextGen sequencing of haploid F1 progeny was used to generate a genetic map revealing a low level of conventional recombination, with an unexpectedly high frequency of short, double crossovers. Notably, both the monomorphic and divergent versions of ChrIa were isolated with equal frequency. As well, ChrIa showed no evidence of being a sex chromosome, of harboring an inversion, or distorting patterns of segregation. Although VAND was unable to self fertilize in the cat, it underwent successful out-crossing with ME49 and hybrid survival was strongly associated with inheritance of ChrIII from ME49 and ChrIb from VAND.ConclusionsOur findings suggest that the successful spread of the monomorphic ChrIa in the wild has not been driven by meiotic drive or related processes, but rather is due to a fitness advantage. As well, the high frequency of short double crossovers is expected to greatly increase genetic diversity among progeny from genetic crosses, thereby providing an unexpected and likely important source of diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1168) contains supplementary material, which is available to authorized users.

Genetic Mapping of Pathogenesis Determinants inToxoplasma gondii

“…With NextGen sequencing, genomes can be completely sequenced to identify all the SNPs in the parents and progeny, yielding many thousands of markers (106). The type 2 × type 10 cross was genotyped using whole-genome sequencing allowing for the identification of recombination breakpoints and short double-crossover events in the progeny (60). Regardless of the density of markers, the limiting factor for linkage mapping is the frequency of crossovers, and this can only be increased by analyzing more progeny.…”

Genetic Mapping Reveals that Sinefungin Resistance in Toxoplasma gondii Is Controlled by a Putative Amino Acid Transporter Locus That Can Be Used as a Negative Selectable Marker

“…1A). The SNF r phenotype was mapped in jQTL as a binary distribution using the ME49-FUDR r ϫ VAND-SNF r genetic map generated previously (39). The primary scan generated one significant peak with a log of odds ratio (LOD) score of 6.57 on chromosome IX between markers MV358 and MV365, corresponding to ME49 region IX:3187822-4202044 (Fig.…”

“…Quantitative trait locus (QTL) mapping has been used to map the basis of SNF r to chromosome IX (15), although the precise locus responsible has not been identified. A recently described cross between type 2 ME49-FUDR r and type 10 VAND-SNF r parental lines (type 2 ϫ type 10 cross) used the parental strain VAND, which was resistant to sinefungin (39). Importantly, the genomes of the progeny of this cross were sequenced in order to generate a genetic map, which was constructed by identifying single nucleotide polymorphisms (SNPs) inherited from the parents (39).…”

Toxoplasmosis and Public Health Genomics

“…The recent researchers have been shown that T. gondii has unusual population structure with different growth rates [20], frequency of differentiation, motility [21] virulence, persistence, and migration capacity [15,[21][22][23]. Recent developments in molecular tools allow enhancing their success to identify the genetic diversity of the parasite [24,25]. Su et al [25,26] have analyzed the nuclear and plastid genome of 950 isolates from all over word and reported six major clades dividing 15 haplotypes with 138 unique genotypes.…”