Transcriptome profiling during a natural host-parasite interaction

Abstract

Background: Infection outcome in some coevolving host-pathogens is characterised by host-pathogen genetic interactions, where particular host genotypes are susceptible only to a subset of pathogen genotypes. To identify candidate genes responsible for the infection status of the host, we exposed a Daphnia magna host genotype to two bacterial strains of Pasteuria ramosa, one of which results in infection, while the other does not. At three time points (four, eight and 12 h) post pathogen exposure, we sequenced the complete transcriptome of the hosts using RNA-Seq (Illumina).

Results: We observed a rapid and transient response to pathogen treatment. Specifically, at the four-hour time point, eight genes were differentially expressed. At the eight-hour time point, a single gene was differentially expressed in the resistant combination only, and no genes were differentially expressed at the 12-h time point.

Conclusions: We found that pathogen-associated transcriptional activity is greatest soon after exposure. Genome-wide resistant combinations were more likely to show upregulation of genes, while susceptible combinations were more likely to be downregulated, relative to controls. Our results also provide several novel candidate genes that may play a pivotal role in determining infection outcomes.

Fig. 1

Log2 fold change in gene expression of Daphnia magna hosts exposed to Pasteuria S1 (an infective combination) compared to controls (black bars) and S8 (a non-infective combination) and controls (grey bars) four hours post exposure to the pathogen/control solution. Asterisks indicate that the pairwise comparison in the change in gene expression between pathogen treatment and control was significant at a FDR of 0.10. Functional annotation of the genes was carried out with BLASTp to the NCBI database

Fig. 2

Log2 fold change in gene expression of D. magna hosts exposed to P. ramosa S1 (an infective combination) compared to controls (black bar) and S8 (a non-infective combination) and controls (grey bar) eight hours post exposure to the pathogen/control solution. The pairwise comparison in the change in gene expression between pathogen treatment and control was significant at a FDR of 0.10. Functional annotation of the genes was carried out with BLASTp to the NCBI database

Fig. 3

Expression values (in normalized mapped read count values) of a putative sulphotransferase (D. magna gene ID mu8AUG24b_p1s00687g88) identified as significantly different between the two treatments in the GLM (see methods). Data are shown for all three treatments (exposure to infecting Pasteuria ramosa S1, non-infecting S8 or a control solution) and three time points after treatment exposure (4, 8 and 12 h respectively). Error bars represent standard deviations

Fig. 4

The proportion of up- versus downregulated genes in infective and non-infective treatments at 4,8 and 12 h post exposure. Genes were first ranked by uncorrected p-value, and the top 100 genes were selected. The first column displays the number of genes that are up-regulated. The second column displays the number of genes that are down-regulated. Dashed circles indicate the infective treatment, while solid circles indicate the non-infective treatment

Fig. 5

Quantitative PCR expression values of a putative aldo-keto reductase gene (D. magna gene ID mu8AUGep24bs00704g138) and Unknown gene 1 (containing 2 CUB domains) (D. magna gene ID mu8PASAgasmbl_16197) relative to actin (internal control) in three treatments at timepoint 4 h post exposure. Error bars represent standard deviations