Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities

Abstract

Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.

Keywords: Eimeria; chickens; genetics; genome; population structure.

Figure 1

Neighbor joining phylogeny of partial coccidian mitochondrial cytochrome c oxidase subunit I (COI) sequences. The optimal tree is shown with the percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) indicated next to the branches. GenBank accession numbers are shown for each sequence, followed by the parasite species and host (common name) identity. Sequences were aligned using CLC Main Workbench (version 8.0.1), creating a 788 bp alignment. The phylogeny was inferred using MEGA X [56], with the evolutionary distances computed using the Kimura 2-parameter method.