Complete Mitochondrial Sequences from Fish-Infecting Coccidia (Goussia Species) Reveal Highly Divergent Genome Organizations

To date, no complete genomes from any species of fish-infecting coccidia have been sequenced, including any from one of the most speciose genera of fish-infecting coccidia, Goussia. To address this data gap, we generated and annotated complete mitochondrial (mt) genomes of 2 local fish-infecting Goussia species: Goussia degiustii and Goussia leucisci. Parasite DNA was extracted from infected spleen and kidney samples from common shiner (Luxilus cornutus) specimens. PCR and Sanger sequencing were conducted to generate whole nuclear (nu) 18S rDNA sequences and complete mt genomes from each species. Despite being members of the same genus, the mt genomes of G. degiustii and G. leucisci are highly divergent with respect to both content and organization. The mt genome of G. degiustii has the same organization as the mt genomes of parasites in the family Eimeriidae (sensu stricto). A phylogenetic analysis of nu 18S rDNA sequences combined with mt cytochrome c oxidase subunit I sequences (where available) from 56 species of related coccidia placed G. degiustii in a clade with 5 fish-infecting enteric species exhibiting nodular development and G. leucisci in a different clade with 5 fish-infecting species exhibiting epicellular development. Additional molecular data, but especially mt coding sequences and whole-genome data, need to be obtained from other fish-infecting Goussia species to resolve the apparent paraphyly of this genus and uncover the genome organizations of these parasites.