Eimeria genomics: where are we now and where are we going?
Damer P. Blake
Pathology and Pathogen Biology, Royal Veterinary College, Hawkshead Lane, North
Mymms, AL9 7TA, UK
The evolution of sequencing technologies, from Sanger to next generation (NGS) and now the
emerging third generation, has prompted a radical frameshift moving genomics from the specialist to
the mainstream. For parasitology, genomics has moved fastest for the protozoa, with sequence
assemblies becoming available for multiple genera. Progress has commonly been slower for
parasites of animals which lack zoonotic potential, but the deficit is being redressed with impact likely
in the areas of drug and vaccine development, molecular diagnostics and population biology.
Genomics studies with the apicomplexan Eimeria species clearly illustrate the approaches and
opportunities available. Eimeria cause the disease coccidiosis, most notably in chickens where the
global cost is thought to exceed US$3 billion every year. Farmers commonly rely on
chemoprophylaxis to control Eimeria, but drug resistance develops rapidly and is now widespread.
Vaccines are available, but production capacity and relative cost limit uptake. New methods of control
are required, but progress has been undermined by the lack of genomic resources. Now, more than
ten years after sequencing started, a genome sequence assembly has been published for Eimeria
tenella. Additional sequence assemblies for all other Eimeria species which infect the chicken and
Eimeria falciformis, a parasite of the mouse, offer powerful opportunities for comparative analysis,
enhancing development of novel diagnostic and control strategies. The current status of Eimeria
genomic resources will be reviewed and their application to define population structure for E. tenella
described, revealing an intriguing dichotomy between Northern and Southern populations
characterised by distinctive spatial haplotype occurrence with evidence of both clonality and panmixia.