Comparative Transcriptome Analyses of Drug-sensitive and Drug-resistant Strains of Eimeria tenella by RNA-sequencing

To gain insights into the molecular mechnism governing the drug resistance of Eimeria tenella, two drug-resistant strains of E. tenella, maduramicin-resistant (MRR) strain and diclazuril-resistant (DZR) strain were induced.We carried out comparative transcriptome analyses of a drug-sensitive strain (DS) and two drug-resistant strains (MRR and DZR) of E. tenella by RNA-seqencing. A total of 1070 DEGs, 672 upregulated and 398 downregulated, were identified in MRR vs. DS; and 379 DEGs, 330 upregulated and 49 downregulated, were detected in DZR vs. DS. Functional annotation analysis identified several DEGs coding for proteins associated with catalytic activity in the DZR strain that were involved in glycolysis and the tricarboxylic acid (TCA) cycle. Other DEGs were associated with ion binding and ion transmembrane transporter activity in the MRR strain. Some DEGs coded for surface antigens that were downregulated in two drug-resistant strains involved invasion, pathogenesis, and host–parasite interactions.These results contribute to developing rapid molecular methods to detect drug resistance of Eimeria spp. in poultry. Eimeria tenella sporulated oocysts mRNA profiles of the drug-sensitive strain (DS) and two drug-resistant strains (maduramicin-resistant (MRR) strain and diclazuril-resistant (DZR) strain) were generated by deep RNA-sequencing, in triplicate, using Illumina HiSeq 2000