Genomic sequence diversity in the Eimeria tenella surface antigen superfamily

Abstract

Coccidiosis, caused by the protozoan Eimeria tenella, poses a significant threat to the poultry industry, leading to considerable economic losses globally. Eimeria tenella surface antigens (EtSAGs) involved in host-parasite interactions are potential candidates for coccidiosis control management. However, the extent of genetic diversity of these surface proteins and its impact on EtSAGs-based control strategies remain unknown. The objectives of this study were to explore the genetic diversity of EtSAGs and its potential implication on protein structure and function. Sequencing reads from five geographically distinct E. tenella isolates were aligned to the E. tenella Houghton (EtH) reference genome, yielding high-quality genome assemblies. A total of 87 full-length EtSAG genomic sequences were identified per isolate. Comparative analysis revealed conserved number, sequence length and sequence identities across isolates. Variant calling detected sparsely distributed polymorphisms, with unique single nucleotide polymorphisms (SNPs) exclusive to specific geographical regions. Notably, a high number of shared variants were observed between the two Malaysian isolates, EtNSN6 and EtSGR6, suggesting regional-specific polymorphisms. Further genetic statistical assessment included 127 EtSAG sequences from public databases, revealing limited diversity within EtSAGs. Non-significant Tajima’s D, Fu and Li’s D* and F* indicated neutral evolution. However, sliding window analysis identified balancing selection in EtSAG10 within nucleotide position 351 to 450, supported by significant Tajima’s D and Fu and Li’s F* values. Structural predictions using AlphaFold2 highlighted the potential impact of non-synonymous SNPs. The conserved N25D mutation in EtSAG1 potentially introduced a strongly negative charge, while the E135K mutation in EtSAG10, within the nucleotide region of balancing selection, predicted to result in a strongly positive charge. These mutations suggest potential importance to protein structure and function, influencing protein-receptor interactions and host-parasite dynamics. Overall, these findings enhance our understanding of EtSAGs and genetic diversity that could inform development of more effective and long-lasting anticoccidial control strategies.