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Background  Coccidiosis is an infectious disease with large negative impact on the poultry industry worldwide. It is an enteric infection caused by unicellular Apicomplexan parasites of the genus  Eimeria . The present study aimed to gain more knowledge about interactions between parasites and the host immune system during the early asexual replication phase of  E. tenella  in chicken caeca. For this purpose, chickens were experimentally infected with  E. tenella  oocysts, sacrificed on days 1–4 and 10 after infection and mRNA from caecal tissues was extracted and sequenced.    Results  Dual RNA-seq analysis revealed time-dependent changes in both host and parasite gene expression during the course of the infection. Chicken immune activation was detected from day 3 and onwards with the highest number of differentially expressed immune genes recorded on day 10. Among early (days 3–4) responses up-regulation of genes for matrix metalloproteinases, several chemokines, interferon (IFN)-γ along with IFN-stimulated genes  GBP, IRF1  and  RSAD2  were noted. Increased expression of genes with immune suppressive/regulatory effects, e.g.  IL10, SOCS1 ,  SOCS3 , was also observed among early responses. For  E. tenella  a general up-regulation of genes involved in protein expression and energy metabolism as well as a general down-regulation genes for DNA and RNA processing were observed during the infection. Specific  E. tenella  genes with altered expression during the experiment include those for proteins in rhoptry and microneme organelles.    Conclusions  The present study provides novel information on both the transcriptional activity of  E. tenella  during schizogony in ceacal tissue and of the local host responses to parasite invasion during this phase of infection. Results indicate a role for IFN-γ and IFN-stimulated genes in the innate defence against  Eimeria  replication.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07959-7.

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens