1 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet2 Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;3 The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;4 Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia;5 Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada;6 Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan;7 Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom;8 Natural History Museum of Denmark, Faculty of Science, Københavns Universitet9 European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;10 Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico;11 School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia; Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor DE, Malaysia;12 MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;13 Department of Microbiology, Monash University, Clayton VIC 3800, Australia;14 Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil;15 Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;16 The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF, United Kingdom.17 Natural History Museum of Denmark, Faculty of Science, Københavns Universitet
Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.