Genomic analysis of the causative agents of coccidiosis in domestic chickens

  1. Arnab Pain4
  1. 1Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
  2. 2Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom;
  3. 3The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;
  4. 4Computational 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. 5Program 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. 6Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan;
  7. 7Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom;
  8. 8Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
  9. 9School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom;
  10. 10European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
  11. 11Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA;
  12. 12Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico;
  13. 13School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia;
  14. 14Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor DE, Malaysia;
  15. 15Amgen Limited, Uxbridge UB8 1DH, United Kingdom;
  16. 16MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
  17. 17Department of Microbiology, Monash University, Clayton VIC 3800, Australia;
  18. 18Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil;
  19. 19Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;
  20. 20The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF, United Kingdom
  1. Corresponding authors: ar11{at}sanger.ac.uk, ftomley{at}rvc.ac.uk, arnab.pain{at}kaust.edu.sa

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.

Footnotes

  • ↵21 Retired.

  • ↵22 Deceased.

  • [Supplemental material is available for this article.]

  • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.168955.113.

    Freely available online through the Genome Research Open Access option.

  • Received October 29, 2013.
  • Accepted July 8, 2014.

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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  1. Published in Advance July 11, 2014, doi: 10.1101/gr.168955.113 Genome Res. 24: 1676-1685 © 2014 Reid et al.; Published by Cold Spring Harbor Laboratory Press

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