Genomic structures of rDNA clusters in Eimeria acervulina

Ribosomal RNAs (rRNAs), as essential components of ribosomes in protein synthesis, are encoded by ribosomal DNAs (rDNAs) arranged in tandem repeats within rDNA clusters. The internal transcribed spacer (ITS) region in rDNA, with low intraspecific and high interspecific divergence, has been a focus in phylogenetic studies. However, analyzing rDNA clusters is complex due to their repetitive nature and polymorphisms. In the Apicomplexan genome, rDNA structure and function remain under-explored. Here, we developed a pipeline to construct complete rDNA clusters in Eimeria acervulina . We found that rDNA clusters are distributed across 1.6% of its genome and characterized the 18S, 28S, and 5.8S rRNA-encoding regions. By comparing rDNA ITS sequences of local E. acervulina with those of E. tenella and other Eimeria species in GenBank, we investigated intraspecific and interspecific differences. Additionally, amplification targeting the ITS1 (357 bp) and ITS2 (236 bp) genes on chromosome 12 were performed, and amplification was detected exclusively in E. acervulina with no amplification observed in E. tenella , confirming the potential as novel diagnostic target genes for E. acervulina identification. Our rDNA detection pipeline and reported cluster structures offer a foundation for molecular diagnosis and phylogenetic analysis in Eimeria and other Apicomplexan species, advancing our understanding of these important protozoan parasites.