Genomic structures of rDNA clusters in Eimeria acervulina.

Ribosomal RNAs (rRNAs), essential components of ribosomes involved in protein synthesis, are encoded by ribosomal DNAs (rDNAs), which are typically organized as tandem repeats within rDNA clusters. The internal transcribed spacer (ITS) region of rDNA, characterized by low intraspecific but high interspecific divergence, has been a focus of phylogenetic and diagnostic studies. However, comprehensive analysis of rDNA clusters remains challenging due to their repetitive nature and polymorphisms. In apicomplexan genomes, rDNA structure and function remain poorly explored. Here, we developed a pipeline to reconstruct complete rDNA clusters in Eimeria acervulina. We found that rDNA clusters account for approximately 1.6% of the genome and characterized the genomic organization of the 18 S, 28 S, and 5.8 S rRNA genes. By comparing ITS sequences from local E. acervulina with those of E. tenella and other Eimeria species available in GenBank, we investigated both intraspecific and interspecific sequence variation. Additionally, ITS1 (357 bp) and ITS2 (236 bp) sequences on chromosome 12 were amplified by polymerase chain reaction (PCR). The amplification was detected exclusively in E. acervulina, but not in E. tenella or E. necatrix, confirming their potential as diagnostic markers for E. acervulina identification. Our rDNA detection pipeline and the characterized rDNA cluster structures provide a valuable resource for molecular diagnosis and phylogenetic analysis in Eimeria and other apicomplexan species, thereby advancing our understanding of these important protozoan parasites.