Purpose: In different apicomplexan parasites multicopy organellar DNA such as mitochondrion genomes have been used for detection and genetic traceback analysis. A complete C. cayetanensis mitochondrial genome sequence was obtained in this study and it will be used to design alternative molecular methods for enhanced detection and characterization of the parasite.
Methods: We sequenced the C. cayetanensis genomic DNA obtained from stool samples from patients infected with Cyclospora in Nepal using the Illumina MiSeq platform. By the use of bioinfiormatics the metagenomic reads of non-coccidian origin sequences were filtered out and by targeted alignment, we were able to obtain contigs containing Eimeria-like mitochondrial, apicoplastic and chromosomal genomic fragments.
Results: A complete Cyclospora mitochondrial genome was assembled and confirmed by sequencing of cloned PCR amplicons obtained with primers designed on the basis of the draft assembly sequence. The results show that the C. cayetanensis mitochondrion genome is 6274 bp long, with a 33% GC content and appears to exist in concatemeric arrays, similar to Eimeria spp. mitochondrial genomes. Phylogenetic analysis of the C. cayetanensis mitochondrial genome placed this organism in closely related cluster with Eimeria species. The mitochondrial genome of C. cayetanensis contains coding genes for Cytochrome B (cytb), Cytochrome C oxidase subunit 1(cox1), and Cytochrome C oxidase subunit 3 (cox3) in addition to 14 large subunit (LSU) and nine small subunit (SSU) fragmented rRNA genes.
Significance: The complete mitochondrial genome sequence presented here will provide novel molecular targets for detection and characterization of C. cayetanensis during foodborne outbreaks.