The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model

Abstract

Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa. We fine-map one locus associated with D. magna resistance to P. ramosa and genetically characterize two haplotypes of the Pasteuria resistance (PR-) locus using de novo genome and transcriptome sequencing. Sequence comparison of PR-locus haplotypes finds dramatic structural polymorphisms between PR-locus haplotypes including a large portion of each haplotype being composed of non-homologous sequences resulting in haplotypes differing in size by 66 kb. The high divergence of PR-locus haplotypes suggest a history of multiple, diverse and repeated instances of structural mutation events and restricted recombination. Annotation of the haplotypes reveals striking differences in gene content. In particular, a group of glycosyltransferase genes that is present in the susceptible but absent in the resistant haplotype. Moreover, in natural populations, we find that the PR-locus polymorphism is associated with variation in resistance to different P. ramosa genotypes, pointing to the PR-locus polymorphism as being responsible for the matching-allele interactions that have been previously described for this system. Our results conclusively identify a genetic basis for the matching-allele interaction observed in a coevolving host-parasite system and provide a first insight into its molecular basis.

Fig 1. Fine-mapping of the Pasteuria resistance locus.

A) Quantitative Trait Locus (QTL) analysis of Daphnia magna resistance to infection by Pasteuria ramosa C19 clone. One large-effect QTL found that explains 59% of variation [25]. B) Break-point mapping of D. magna PR-locus. Recombination breakpoints analysis determined that the resistance locus is located between markers P34 and g311b. This reduced PR-locus to 136 kb. C) Region within the PR-locus with presumed structural genetic variation–NHR. Markers g292 and g351 are the closest that can be amplified in both parental genotypes of the QTL panel (Xinb3 and Iinb1).

Fig 2. Schematic representation of polymorphism between Xinb3 and Iinb1 PR-locus haplotypes.

A) Haplotype xPR-locus. B) Haplotype iPR-locus. iPR-locus is considerably longer than xPR-locus (215 kb to 159 kb). Most of this difference can be explained by differences in the centrally located NHR (121 kb to 55 kb), where little homology between Xinb3 and Iinb1 haplotypes can be found (red line) (expanded for detail). The remaining PR-locus sequence is homologous between the haplotypes (black line). A short region left of NHR is largely made of extra-locus repeats (black dashed line). Extra-locus repeats (grey bars) and intra-locus repeats (red bars) are concentrated in and around the NHR (See expansion for detail).

Fig 3. Alignment of Daphnia magna Xinb3 and Iinb1 PR-locus haplotypes to itself and to the other.

A) Alignment of xPR-locus haplotype to iPR-locus haplotype. B) Alignment of iPR-locus haplotype to xPR-locus haplotype. Reciprocal alignments between PR-locus haplotypes show that at the center (indicated by dashed boxes) is a genomic region with little homology between the haplotypes, whereas at the flanking regions homology between the haplotypes is continuous. This non-homologous region defines the NHR. C) Alignment of iPR-locus to itself. D) Alignment of xPR-locus haplotype to itself. Alignments of each PR-locus haplotype to self reveal that the iPR-locus haplotype has a higher number to intra-locus repeats and that these are repeated more often than in xPR-locus. Intra-locus repeats are concentrated in the NHR.

Fig 4. The ABC genetic model for Daphnia magna resistance to Pasteuria ramosa.

D. magna resistance to P. ramosa C1 and C19 genotypes was suggested to be controlled by three linked loci (A, B and C) and epistasis between them [22]. Arrows represent dominant epistasis. When dominant allele C is present, the host’s phenotype is RR, irrespectively of the genotypes at loci A and B. Allele C is present within the here described iPR-locus. When the C-locus is homozygote for the recessive allele c, the A-locus is unmasked. With the dominant allele A present at the A-locus, the host’s resistance phenotype is RS irrespectively of genotype at locus B. Allele A is present in the xNHR haplotype. With loci A and C being homozygote for the recessive alleles (cc_aa) and the dominant allele B is present, the host’s phenotype is SR. When all three loci have double recessive genotypes the phenotype is SS. All three loci are located within the here described PR-locus.

Fig 5. xNHR haplotype association to Daphnia magna resistance phenotypes in natural populations.

Number of D. magna genotypes collected in Tvärminne archipelago sorted by resistance phenotype: RR–C1/ C19 double resistant; RS–P. ramosa C1 resistant and C19 susceptible; SR–P. ramosa C1 susceptible and C19 resistant; SS—double susceptible. Presence of xNHR haplotype diagnostic markers is denoted in black bars while white denotes absence. Chi-square tests on contingency tables of expected values were applied to the full dataset (P<0.0001) and in pairwise comparisons between phenotypes. Bars indicate comparisons where P-values were significant (P<0.0001). xNHR-haplotype presence is associated to RS phenotype whereas absence is associated to SR and SS phenotypes.