Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system

Abstract

In many systems, host-parasite evolutionary dynamics have led to the emergence and maintenance of diverse parasite and host genotypes within the same population. Genotypes vary in key attributes: Parasite genotypes vary in ability to infect, host genotypes vary in susceptibility, and infection outcome is frequently the result of both parties' genotypic identities. These host-parasite genotype-by-genotype (GH × GP) interactions influence evolutionary and ecological dynamics in important ways. Interactions can be produced through genetic variation; however, here, we assess the role of variable gene expression as an additional source of GH × GP interactions. The bumblebee Bombus terrestris and its trypanosome gut parasite Crithidia bombi are a model system for host-parasite matching. Full-transcriptome sequencing of the bumblebee host revealed that different parasite genotypes indeed induce fundamentally different host expression responses and host genotypes vary in their responses to the infecting parasite genotype. It appears that broadly and successfully infecting parasite genotypes lead to reduced host immune gene expression relative to unexposed bees but induce the expression of genes responsible for controlling gene expression. Contrastingly, a poorly infecting parasite genotype induced the expression of immunologically important genes, including antimicrobial peptides. A targeted expression assay confirmed the transcriptome results and also revealed strong host genotype effects. In all, the expression of a number of genes depends on the host genotype and the parasite genotype and the interaction between both host and parasite genotypes. These results suggest that alongside sequence variation in coding immunological genes, variation that controls immune gene expression can also produce patterns of host-parasite specificity.

Keywords: Red Queen; coevolution; manipulation.

Fig. 1.

Mean number of C. bombi cells ± SE per microliter of feces according to C. bombi genotype and host genotype (colonies K, L, S, and T). The upper squares represent the number of experimentally exposed individuals checked for infection, with squares being filled if subsequent visual inspection of their feces revealed an established infection. In each panel, the x axis lists the parasite genotypes (nos. 68, 75, and 161; and are colored orange, blue, and red, respectively). Both infection intensity and whether or not an individual becomes infected varied according to the interaction between host and parasite genotypes (G_H × G_P intensity: F_6,59 = 2.52, P = 0.031; infection: χ²_6,59 = 14.10, P = 0.029). Both parasite and host genotype alone significantly influenced infection success (G_P: χ²_2,65 = 22.01, P < 0.001, G_H: χ²_3,67 = 11.04, P = 0.012).

Fig. 2.

(A) Venn diagrams of the number of differentially expressed genes upon exposure to three genotypes of C. bombi relative to unexposed workers [no. 68 (orange), no. 75 (blue), and no. 161 (red)] across all host colonies at a false discovery rate of 0.05. (B) Venn diagrams of the number of differentially expressed genes (P < 0.05) when bees with different genotypes (colonies K, L, S, and T) are given the same genotype of parasite (nos. 68, 75, and 161) relative to unexposed workers from the same host genotype. For example, “S_161” indicates colony “S” exposed to parasite genotype “161.”

Fig. 3.

Logfold change in expression of genes based on qPCR, where there is a significant interaction of host genotype and parasite genotype [G_H × G_P interaction for apidaecin, abaecin, and esterase FE4 (F_6,42 = 2.73, F_6,42 = 2.32, and F_6,42 = 2.75, respectively; P < 0.05)] determining expression; where the interaction approached significance [limkain-b1, LRR GPCR4, and SPN 3 (F_6,42 = 2.09, F_6,42 = 1.95, and F_6,42 = 2.25, respectively; P < 0.1)], expression of both limkain-b1 and LRR GPCR4 also varied based on G_H (F_3,42 = 3.15, P < 0.05; F_3,42 = 5.67, P < 0.01) and G_P (F_2,42 = 7.51, F_2,42 = 5.75; P < 0.01). In each panel, the x axis lists the parasite genotypes (nos. 68, 75, and 161; bars are color-coded orange, blue, and red, respectively), whereas boxes labeled with letters refer to colonies (K, L, S, and T). The respective gene is indicated at the top of each panel, together with its GenBank accession number.

Fig. 4.

Logfold change in expression of genes that differ by parasite genotype (G_P: F_2,42 = 3.30*, F_2,42 = 8.44***, F_2,42 = 7.00**, F_2,42 = 10.28***, F_2,42 = 10.47***, F_2,42 = 3.64*, F_2,42 = 12.87***, F_2,42 = 6.41**, F_2,42 = 5.88**, F_2,42 = 8.11**, F_2,42 = 11.61***, F_2,42 = 3.99*; *P < 0.05, **P < 0.01, ***P < 0.001) irrespective of host genotype. In each panel, the x axis lists the parasite genotypes (nos. 68, 75, and 161; bars are color-coded orange, blue, and red, respectively). Genes and their accession numbers are indicated at the top of each panel.

Fig. 5.

Relationship of the expression among genes according to the strength of correlation among all genes. Clustering is produced based on Euclidean distances. ATP-bindg cassette sub-fam G 1, ATP-binding cassette subfamily G1; d-arab-1-dehyg, d-arabinose-1-dehydrogenase; Def, defensin; Maj. Roy. Jell. Prot, major royal jelly protein; Synaptic vesc. glycopr. 2B, synaptic vesicle glycoprotein 2B; Trp, transient receptor potential protein.