Combined transcriptome and whole genome sequencing analyses reveal candidate drug-resistance genes of Eimeria tenella

Avian coccidiosis is a widespread intestinal disease found in poultry that causes substantial economic losses. To extensively investigate the molecular mechanism of drug resistance in <i>Eimeria tenella</i>, we analyzed the sporozoites and second-generation merozoites of drug-sensitive (DS), diclazuril-resistant (DZR) strain, and salinomycin-resistant (SMR) strains of <i>E. tenella</i> through transcriptome sequencing. Whole genome sequencing analyses were performed on resistant strains at different concentrations-11 sensitive strains, 16 field diclazuril-resistant strains, and 15 field salinomycin-resistant strains of <i>E. tenella</i>. Co-analysis indicated that the ABC transporter protein showed differential expression and base mutations in the two resistant strains compared with the DS strain. KEGG pathway analysis demonstrated that the expression of pABAS and HPPK-DHPS, which are associated with the folate biosynthetic pathway, showed downregulation only in the DZR strain with respect to the DS strain. Several key enzymes in the glycolytic pathway were differentially expressed between DS and SMR strains.