Genomic analysis of the causative agents of coccidiosis in domestic chickens.
Identifieur interne : 000668 ( PubMed/Curation ); précédent : 000667; suivant : 000669Genomic analysis of the causative agents of coccidiosis in domestic chickens.
Auteurs : Adam J. Reid [Royaume-Uni] ; Damer P. Blake [Royaume-Uni] ; Hifzur R. Ansari ; Karen Billington [Royaume-Uni] ; Hilary P. Browne [Royaume-Uni] ; Josephine Bryant [Royaume-Uni] ; Matt Dunn [Royaume-Uni] ; Stacy S. Hung [Canada] ; Fumiya Kawahara [Japon] ; Diego Miranda-Saavedra [Royaume-Uni] ; Tareq B. Malas ; Tobias Mourier [Danemark] ; Hardeep Naghra [Royaume-Uni] ; Mridul Nair ; Thomas D. Otto [Royaume-Uni] ; Neil D. Rawlings [Royaume-Uni] ; Pierre Rivailler [États-Unis] ; Alejandro Sanchez-Flores [Mexique] ; Mandy Sanders [Royaume-Uni] ; Chandra Subramaniam [Royaume-Uni] ; Yea-Ling Tay [Malaisie] ; Yong Woo ; Xikun Wu [Royaume-Uni] ; Bart Barrell [Royaume-Uni] ; Paul H. Dear [Royaume-Uni] ; Christian Doerig [Australie] ; Arthur Gruber [Brésil] ; Alasdair C. Ivens [Royaume-Uni] ; John Parkinson [Canada] ; Marie-Adèle Rajandream [Royaume-Uni] ; Martin W. Shirley [Royaume-Uni] ; Kiew-Lian Wan [Malaisie] ; Matthew Berriman [Royaume-Uni] ; Fiona M. Tomley [Royaume-Uni] ; Arnab Pain [Royaume-Uni]Source :
- Genome research [ 1549-5469 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Protozoan Proteins.
- chemical : Proteome.
- classification : Eimeria.
- genetics : Eimeria.
- parasitology : Coccidiosis, Poultry Diseases.
- veterinary : Coccidiosis.
- Animals, Cell Line, Chickens, Chromosome Mapping, Gene Expression Profiling, Genome, Protozoan, Phylogeny, Synteny.
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.
DOI: 10.1101/gr.168955.113
PubMed: 25015382
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Hifzur R. Ansari<affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation>Le document en format XML
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Browne</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Bryant, Josephine" sort="Bryant, Josephine" uniqKey="Bryant J" first="Josephine" last="Bryant">Josephine Bryant</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Dunn, Matt" sort="Dunn, Matt" uniqKey="Dunn M" first="Matt" last="Dunn">Matt Dunn</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Hung, Stacy S" sort="Hung, Stacy S" uniqKey="Hung S" first="Stacy S" last="Hung">Stacy S. Hung</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8</wicri:regionArea></affiliation></author><author><name sortKey="Kawahara, Fumiya" sort="Kawahara, Fumiya" uniqKey="Kawahara F" first="Fumiya" last="Kawahara">Fumiya Kawahara</name><affiliation wicri:level="1"><nlm:affiliation>Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan;</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Nippon Institute for Biological Science, Ome, Tokyo 198-0024</wicri:regionArea></affiliation></author><author><name sortKey="Miranda Saavedra, Diego" sort="Miranda Saavedra, Diego" uniqKey="Miranda Saavedra D" first="Diego" last="Miranda-Saavedra">Diego Miranda-Saavedra</name><affiliation wicri:level="1"><nlm:affiliation>Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH</wicri:regionArea></affiliation></author><author><name sortKey="Malas, Tareq B" sort="Malas, Tareq B" uniqKey="Malas T" first="Tareq B" last="Malas">Tareq B. Malas</name><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Mourier, Tobias" sort="Mourier, Tobias" uniqKey="Mourier T" first="Tobias" last="Mourier">Tobias Mourier</name><affiliation wicri:level="1"><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen</wicri:regionArea></affiliation></author><author><name sortKey="Naghra, Hardeep" sort="Naghra, Hardeep" uniqKey="Naghra H" first="Hardeep" last="Naghra">Hardeep Naghra</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Nair, Mridul" sort="Nair, Mridul" uniqKey="Nair M" first="Mridul" last="Nair">Mridul Nair</name><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Otto, Thomas D" sort="Otto, Thomas D" uniqKey="Otto T" first="Thomas D" last="Otto">Thomas D. Otto</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Rawlings, Neil D" sort="Rawlings, Neil D" uniqKey="Rawlings N" first="Neil D" last="Rawlings">Neil D. Rawlings</name><affiliation wicri:level="1"><nlm:affiliation>European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Rivailler, Pierre" sort="Rivailler, Pierre" uniqKey="Rivailler P" first="Pierre" last="Rivailler">Pierre Rivailler</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333</wicri:regionArea></affiliation></author><author><name sortKey="Sanchez Flores, Alejandro" sort="Sanchez Flores, Alejandro" uniqKey="Sanchez Flores A" first="Alejandro" last="Sanchez-Flores">Alejandro Sanchez-Flores</name><affiliation wicri:level="1"><nlm:affiliation>Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico;</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210</wicri:regionArea></affiliation></author><author><name sortKey="Sanders, Mandy" sort="Sanders, Mandy" uniqKey="Sanders M" first="Mandy" last="Sanders">Mandy Sanders</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Subramaniam, Chandra" sort="Subramaniam, Chandra" uniqKey="Subramaniam C" first="Chandra" last="Subramaniam">Chandra Subramaniam</name><affiliation wicri:level="1"><nlm:affiliation>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN</wicri:regionArea></affiliation></author><author><name sortKey="Tay, Yea Ling" sort="Tay, Yea Ling" uniqKey="Tay Y" first="Yea-Ling" last="Tay">Yea-Ling Tay</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Woo, Yong" sort="Woo, Yong" uniqKey="Woo Y" first="Yong" last="Woo">Yong Woo</name><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Wu, Xikun" sort="Wu, Xikun" uniqKey="Wu X" first="Xikun" last="Wu">Xikun Wu</name><affiliation wicri:level="1"><nlm:affiliation>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Amgen Limited, Uxbridge UB8 1DH, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Amgen Limited, Uxbridge UB8 1DH</wicri:regionArea></affiliation></author><author><name sortKey="Barrell, Bart" sort="Barrell, Bart" uniqKey="Barrell B" first="Bart" last="Barrell">Bart Barrell</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Dear, Paul H" sort="Dear, Paul H" uniqKey="Dear P" first="Paul H" last="Dear">Paul H. Dear</name><affiliation wicri:level="1"><nlm:affiliation>MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC Laboratory of Molecular Biology, Cambridge CB2 0QH</wicri:regionArea></affiliation></author><author><name sortKey="Doerig, Christian" sort="Doerig, Christian" uniqKey="Doerig C" first="Christian" last="Doerig">Christian Doerig</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, Monash University, Clayton VIC 3800, Australia;</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Microbiology, Monash University, Clayton VIC 3800</wicri:regionArea></affiliation></author><author><name sortKey="Gruber, Arthur" sort="Gruber, Arthur" uniqKey="Gruber A" first="Arthur" last="Gruber">Arthur Gruber</name><affiliation wicri:level="1"><nlm:affiliation>Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil;</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000</wicri:regionArea></affiliation></author><author><name sortKey="Ivens, Alasdair C" sort="Ivens, Alasdair C" uniqKey="Ivens A" first="Alasdair C" last="Ivens">Alasdair C. Ivens</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT</wicri:regionArea></affiliation></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8</wicri:regionArea></affiliation></author><author><name sortKey="Rajandream, Marie Adele" sort="Rajandream, Marie Adele" uniqKey="Rajandream M" first="Marie-Adèle" last="Rajandream">Marie-Adèle Rajandream</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Shirley, Martin W" sort="Shirley, Martin W" uniqKey="Shirley M" first="Martin W" last="Shirley">Martin W. Shirley</name><affiliation wicri:level="1"><nlm:affiliation>The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF</wicri:regionArea></affiliation></author><author><name sortKey="Wan, Kiew Lian" sort="Wan, Kiew Lian" uniqKey="Wan K" first="Kiew-Lian" last="Wan">Kiew-Lian Wan</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Berriman, Matthew" sort="Berriman, Matthew" uniqKey="Berriman M" first="Matthew" last="Berriman">Matthew Berriman</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Tomley, Fiona M" sort="Tomley, Fiona M" uniqKey="Tomley F" first="Fiona M" last="Tomley">Fiona M. Tomley</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country wicri:rule="url">Royaume-Uni</country><wicri:regionArea>Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN</wicri:regionArea></affiliation></author><author><name sortKey="Pain, Arnab" sort="Pain, Arnab" uniqKey="Pain A" first="Arnab" last="Pain">Arnab Pain</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country wicri:rule="url">Royaume-Uni</country><wicri:regionArea>Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25015382</idno><idno type="pmid">25015382</idno><idno type="doi">10.1101/gr.168955.113</idno><idno type="wicri:Area/PubMed/Corpus">000668</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000668</idno><idno type="wicri:Area/PubMed/Curation">000668</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000668</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genomic analysis of the causative agents of coccidiosis in domestic chickens.</title><author><name sortKey="Reid, Adam J" sort="Reid, Adam J" uniqKey="Reid A" first="Adam J" last="Reid">Adam J. Reid</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Blake, Damer P" sort="Blake, Damer P" uniqKey="Blake D" first="Damer P" last="Blake">Damer P. Blake</name><affiliation wicri:level="1"><nlm:affiliation>Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN</wicri:regionArea></affiliation></author><author><name sortKey="Ansari, Hifzur R" sort="Ansari, Hifzur R" uniqKey="Ansari H" first="Hifzur R" last="Ansari">Hifzur R. Ansari</name><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Billington, Karen" sort="Billington, Karen" uniqKey="Billington K" first="Karen" last="Billington">Karen Billington</name><affiliation wicri:level="1"><nlm:affiliation>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN</wicri:regionArea></affiliation></author><author><name sortKey="Browne, Hilary P" sort="Browne, Hilary P" uniqKey="Browne H" first="Hilary P" last="Browne">Hilary P. Browne</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Bryant, Josephine" sort="Bryant, Josephine" uniqKey="Bryant J" first="Josephine" last="Bryant">Josephine Bryant</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Dunn, Matt" sort="Dunn, Matt" uniqKey="Dunn M" first="Matt" last="Dunn">Matt Dunn</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Hung, Stacy S" sort="Hung, Stacy S" uniqKey="Hung S" first="Stacy S" last="Hung">Stacy S. Hung</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8</wicri:regionArea></affiliation></author><author><name sortKey="Kawahara, Fumiya" sort="Kawahara, Fumiya" uniqKey="Kawahara F" first="Fumiya" last="Kawahara">Fumiya Kawahara</name><affiliation wicri:level="1"><nlm:affiliation>Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan;</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Nippon Institute for Biological Science, Ome, Tokyo 198-0024</wicri:regionArea></affiliation></author><author><name sortKey="Miranda Saavedra, Diego" sort="Miranda Saavedra, Diego" uniqKey="Miranda Saavedra D" first="Diego" last="Miranda-Saavedra">Diego Miranda-Saavedra</name><affiliation wicri:level="1"><nlm:affiliation>Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH</wicri:regionArea></affiliation></author><author><name sortKey="Malas, Tareq B" sort="Malas, Tareq B" uniqKey="Malas T" first="Tareq B" last="Malas">Tareq B. Malas</name><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Mourier, Tobias" sort="Mourier, Tobias" uniqKey="Mourier T" first="Tobias" last="Mourier">Tobias Mourier</name><affiliation wicri:level="1"><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen</wicri:regionArea></affiliation></author><author><name sortKey="Naghra, Hardeep" sort="Naghra, Hardeep" uniqKey="Naghra H" first="Hardeep" last="Naghra">Hardeep Naghra</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Nair, Mridul" sort="Nair, Mridul" uniqKey="Nair M" first="Mridul" last="Nair">Mridul Nair</name><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Otto, Thomas D" sort="Otto, Thomas D" uniqKey="Otto T" first="Thomas D" last="Otto">Thomas D. Otto</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Rawlings, Neil D" sort="Rawlings, Neil D" uniqKey="Rawlings N" first="Neil D" last="Rawlings">Neil D. Rawlings</name><affiliation wicri:level="1"><nlm:affiliation>European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Rivailler, Pierre" sort="Rivailler, Pierre" uniqKey="Rivailler P" first="Pierre" last="Rivailler">Pierre Rivailler</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333</wicri:regionArea></affiliation></author><author><name sortKey="Sanchez Flores, Alejandro" sort="Sanchez Flores, Alejandro" uniqKey="Sanchez Flores A" first="Alejandro" last="Sanchez-Flores">Alejandro Sanchez-Flores</name><affiliation wicri:level="1"><nlm:affiliation>Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico;</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210</wicri:regionArea></affiliation></author><author><name sortKey="Sanders, Mandy" sort="Sanders, Mandy" uniqKey="Sanders M" first="Mandy" last="Sanders">Mandy Sanders</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Subramaniam, Chandra" sort="Subramaniam, Chandra" uniqKey="Subramaniam C" first="Chandra" last="Subramaniam">Chandra Subramaniam</name><affiliation wicri:level="1"><nlm:affiliation>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN</wicri:regionArea></affiliation></author><author><name sortKey="Tay, Yea Ling" sort="Tay, Yea Ling" uniqKey="Tay Y" first="Yea-Ling" last="Tay">Yea-Ling Tay</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Woo, Yong" sort="Woo, Yong" uniqKey="Woo Y" first="Yong" last="Woo">Yong Woo</name><affiliation><nlm: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;</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Wu, Xikun" sort="Wu, Xikun" uniqKey="Wu X" first="Xikun" last="Wu">Xikun Wu</name><affiliation wicri:level="1"><nlm:affiliation>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Amgen Limited, Uxbridge UB8 1DH, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Amgen Limited, Uxbridge UB8 1DH</wicri:regionArea></affiliation></author><author><name sortKey="Barrell, Bart" sort="Barrell, Bart" uniqKey="Barrell B" first="Bart" last="Barrell">Bart Barrell</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Dear, Paul H" sort="Dear, Paul H" uniqKey="Dear P" first="Paul H" last="Dear">Paul H. Dear</name><affiliation wicri:level="1"><nlm:affiliation>MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC Laboratory of Molecular Biology, Cambridge CB2 0QH</wicri:regionArea></affiliation></author><author><name sortKey="Doerig, Christian" sort="Doerig, Christian" uniqKey="Doerig C" first="Christian" last="Doerig">Christian Doerig</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, Monash University, Clayton VIC 3800, Australia;</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Microbiology, Monash University, Clayton VIC 3800</wicri:regionArea></affiliation></author><author><name sortKey="Gruber, Arthur" sort="Gruber, Arthur" uniqKey="Gruber A" first="Arthur" last="Gruber">Arthur Gruber</name><affiliation wicri:level="1"><nlm:affiliation>Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil;</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000</wicri:regionArea></affiliation></author><author><name sortKey="Ivens, Alasdair C" sort="Ivens, Alasdair C" uniqKey="Ivens A" first="Alasdair C" last="Ivens">Alasdair C. Ivens</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT</wicri:regionArea></affiliation></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8</wicri:regionArea></affiliation></author><author><name sortKey="Rajandream, Marie Adele" sort="Rajandream, Marie Adele" uniqKey="Rajandream M" first="Marie-Adèle" last="Rajandream">Marie-Adèle Rajandream</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Shirley, Martin W" sort="Shirley, Martin W" uniqKey="Shirley M" first="Martin W" last="Shirley">Martin W. Shirley</name><affiliation wicri:level="1"><nlm:affiliation>The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF</wicri:regionArea></affiliation></author><author><name sortKey="Wan, Kiew Lian" sort="Wan, Kiew Lian" uniqKey="Wan K" first="Kiew-Lian" last="Wan">Kiew-Lian Wan</name><affiliation wicri:level="1"><nlm: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;</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Berriman, Matthew" sort="Berriman, Matthew" uniqKey="Berriman M" first="Matthew" last="Berriman">Matthew Berriman</name><affiliation wicri:level="1"><nlm:affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Tomley, Fiona M" sort="Tomley, Fiona M" uniqKey="Tomley F" first="Fiona M" last="Tomley">Fiona M. Tomley</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country wicri:rule="url">Royaume-Uni</country><wicri:regionArea>Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN</wicri:regionArea></affiliation></author><author><name sortKey="Pain, Arnab" sort="Pain, Arnab" uniqKey="Pain A" first="Arnab" last="Pain">Arnab Pain</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country wicri:rule="url">Royaume-Uni</country><wicri:regionArea>Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900</wicri:regionArea></affiliation></author></analytic><series><title level="j">Genome research</title><idno type="eISSN">1549-5469</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Cell Line</term><term>Chickens</term><term>Chromosome Mapping</term><term>Coccidiosis (parasitology)</term><term>Coccidiosis (veterinary)</term><term>Eimeria (classification)</term><term>Eimeria (genetics)</term><term>Gene Expression Profiling</term><term>Genome, Protozoan</term><term>Phylogeny</term><term>Poultry Diseases (parasitology)</term><term>Proteome</term><term>Protozoan Proteins (genetics)</term><term>Synteny</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Protozoan Proteins</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Eimeria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Eimeria</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Coccidiosis</term><term>Poultry Diseases</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Coccidiosis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Cell Line</term><term>Chickens</term><term>Chromosome Mapping</term><term>Gene Expression Profiling</term><term>Genome, Protozoan</term><term>Phylogeny</term><term>Synteny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25015382</PMID><DateCreated><Year>2014</Year><Month>10</Month><Day>02</Day></DateCreated><DateCompleted><Year>2015</Year><Month>06</Month><Day>15</Day></DateCompleted><DateRevised><Year>2017</Year><Month>03</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1549-5469</ISSN><JournalIssue CitedMedium="Internet"><Volume>24</Volume><Issue>10</Issue><PubDate><Year>2014</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res.</ISOAbbreviation></Journal><ArticleTitle>Genomic analysis of the causative agents of coccidiosis in domestic chickens.</ArticleTitle><Pagination><MedlinePgn>1676-85</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1101/gr.168955.113</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>© 2014 Reid et al.; Published by Cold Spring Harbor Laboratory Press.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Reid</LastName><ForeName>Adam J</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Blake</LastName><ForeName>Damer P</ForeName><Initials>DP</Initials><AffiliationInfo><Affiliation>Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ansari</LastName><ForeName>Hifzur R</ForeName><Initials>HR</Initials><AffiliationInfo><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;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Billington</LastName><ForeName>Karen</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Browne</LastName><ForeName>Hilary P</ForeName><Initials>HP</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bryant</LastName><ForeName>Josephine</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dunn</LastName><ForeName>Matt</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hung</LastName><ForeName>Stacy S</ForeName><Initials>SS</Initials><AffiliationInfo><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;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kawahara</LastName><ForeName>Fumiya</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Miranda-Saavedra</LastName><ForeName>Diego</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Malas</LastName><ForeName>Tareq B</ForeName><Initials>TB</Initials><AffiliationInfo><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;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mourier</LastName><ForeName>Tobias</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Naghra</LastName><ForeName>Hardeep</ForeName><Initials>H</Initials><AffiliationInfo><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;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nair</LastName><ForeName>Mridul</ForeName><Initials>M</Initials><AffiliationInfo><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;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Otto</LastName><ForeName>Thomas D</ForeName><Initials>TD</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rawlings</LastName><ForeName>Neil D</ForeName><Initials>ND</Initials><AffiliationInfo><Affiliation>European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rivailler</LastName><ForeName>Pierre</ForeName><Initials>P</Initials><AffiliationInfo><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;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sanchez-Flores</LastName><ForeName>Alejandro</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sanders</LastName><ForeName>Mandy</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Subramaniam</LastName><ForeName>Chandra</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tay</LastName><ForeName>Yea-Ling</ForeName><Initials>YL</Initials><AffiliationInfo><Affiliation>School of Biosciences and 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ValidYN="Y"><LastName>Barrell</LastName><ForeName>Bart</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dear</LastName><ForeName>Paul H</ForeName><Initials>PH</Initials><AffiliationInfo><Affiliation>MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Doerig</LastName><ForeName>Christian</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Microbiology, Monash University, Clayton VIC 3800, Australia;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gruber</LastName><ForeName>Arthur</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, 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ValidYN="Y"><LastName>Tomley</LastName><ForeName>Fiona M</ForeName><Initials>FM</Initials><AffiliationInfo><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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pain</LastName><ForeName>Arnab</ForeName><Initials>A</Initials><AffiliationInfo><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.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>BBS/E/I/00001421</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>S17413</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>MOP84556</GrantID><Agency>Canadian Institutes of Health Research</Agency><Country>Canada</Country></Grant><Grant><GrantID>S19705/6</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>MC_U105131672</GrantID><Agency>Medical Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>BBS/B/04196</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>BB/F002564/1</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>S19705</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>07</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genome Res</MedlineTA><NlmUniqueID>9518021</NlmUniqueID><ISSNLinking>1088-9051</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015800">Protozoan Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2006 Feb 1;22(3):361-2</RefSource><PMID 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MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018503" MajorTopicYN="Y">Genome, Protozoan</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011201" MajorTopicYN="N">Poultry Diseases</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015800" MajorTopicYN="N">Protozoan Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D026801" 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