title: Genomic analysis of the causative agents of coccidiosis in domestic chickens.
abstract: 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.
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Reid
authors.affiliation: Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;
authors.forename: Damer P
authors.initials: DP
authors.lastname: Blake
authors.affiliation: 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;
authors.forename: Hifzur R
authors.initials: HR
authors.lastname: Ansari
authors.affiliation: The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;
authors.forename: Karen
authors.initials: K
authors.lastname: Billington
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Hilary P
authors.initials: HP
authors.lastname: Browne
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Josephine
authors.initials: J
authors.lastname: Bryant
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Matt
authors.initials: M
authors.lastname: Dunn
authors.affiliation: 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;
authors.forename: Stacy S
authors.initials: SS
authors.lastname: Hung
authors.affiliation: Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan;
authors.forename: Fumiya
authors.initials: F
authors.lastname: Kawahara
authors.affiliation: Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom;
authors.forename: Diego
authors.initials: D
authors.lastname: Miranda-Saavedra
authors.affiliation: 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;
authors.forename: Tareq B
authors.initials: TB
authors.lastname: Malas
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
authors.forename: Tobias
authors.initials: T
authors.lastname: Mourier
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom;
authors.forename: Hardeep
authors.initials: H
authors.lastname: Naghra
authors.affiliation: 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;
authors.forename: Mridul
authors.initials: M
authors.lastname: Nair
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
authors.affiliation: European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Neil D
authors.initials: ND
authors.lastname: Rawlings
authors.affiliation: The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA;
authors.forename: Pierre
authors.initials: P
authors.lastname: Rivailler
authors.affiliation: Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico;
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sanchez-Flores
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Mandy
authors.initials: M
authors.lastname: Sanders
authors.affiliation: The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;
authors.forename: Chandra
authors.initials: C
authors.lastname: Subramaniam
authors.affiliation: 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;
authors.forename: Yea-Ling
authors.initials: YL
authors.lastname: Tay
authors.affiliation: 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;
authors.forename: Yong
authors.initials: Y
authors.lastname: Woo
authors.affiliation: The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Amgen Limited, Uxbridge UB8 1DH, United Kingdom;
authors.forename: Xikun
authors.initials: X
authors.lastname: Wu
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Bart
authors.initials: B
authors.lastname: Barrell
authors.affiliation: MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
authors.forename: Paul H
authors.initials: PH
authors.lastname: Dear
authors.affiliation: Department of Microbiology, Monash University, Clayton VIC 3800, Australia;
authors.forename: Christian
authors.initials: C
authors.lastname: Doerig
authors.affiliation: Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil;
authors.forename: Arthur
authors.initials: A
authors.lastname: Gruber
authors.affiliation: Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;
authors.forename: Alasdair C
authors.initials: AC
authors.lastname: Ivens
authors.affiliation: 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;
authors.forename: John
authors.initials: J
authors.lastname: Parkinson
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Marie-Adèle
authors.initials: MA
authors.lastname: Rajandream
authors.affiliation: The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF, United Kingdom.
authors.forename: Martin W
authors.initials: MW
authors.lastname: Shirley
authors.affiliation: 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;
authors.forename: Kiew-Lian
authors.initials: KL
authors.lastname: Wan
authors.affiliation: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
authors.affiliation: Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; ar11@sanger.ac.uk ftomley@rvc.ac.uk arnab.pain@kaust.edu.sa.
authors.forename: Fiona M
authors.initials: FM
authors.lastname: Tomley
authors.affiliation: 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; ar11@sanger.ac.uk ftomley@rvc.ac.uk arnab.pain@kaust.edu.sa.
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
mesh_terms: D000818:Animals; D002460:Cell Line; D002645:Chickens; D002874:Chromosome Mapping; D003048:Coccidiosis / Q000469:parasitology / Q000662:veterinary; D004539:Eimeria / Q000145:classification / Q000235:genetics*; D020869:Gene Expression Profiling; D018503:Genome, Protozoan; D010802:Phylogeny; D011201:Poultry Diseases / Q000469:parasitology; D020543:Proteome; D015800:Protozoan Proteins / Q000235:genetics*; D026801:Synteny
chemical_list: D020543:Proteome; D015800:Protozoan Proteins