title: Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken.
abstract: BACKGROUND
  EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data.
  
  
  RESULTS
  An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05).
  
  
  CONCLUSIONS
  Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.
authors.affiliation: Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK. david.wragg@toulouse.inra.fr.|Institut National de la Recherche Agronomique (INRA), UMR 1338 GenPhySE, 31326, Castanet-Tolosan, France. david.wragg@toulouse.inra.fr.
authors.forename: David
authors.initials: D
authors.lastname: Wragg
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK. andrew.mason@roslin.ed.ac.uk.
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Mason
authors.affiliation: GAIC Co. Ltd. Jing Chen Buiding, Science Park, South Street, Chao Yang District, Beijing, People's Republic Popular of China. leyu@genekang.com.
authors.forename: Le
authors.initials: L
authors.lastname: Yu
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK. richard.kuo@roslin.ed.ac.uk.
authors.forename: Richard
authors.initials: R
authors.lastname: Kuo
authors.affiliation: Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK. plxral@nottingham.ac.uk.
authors.forename: Raman A
authors.initials: RA
authors.lastname: Lawal
authors.affiliation: Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK. plxtd@nottingham.ac.uk.
authors.forename: Takele Taye
authors.initials: TT
authors.lastname: Desta
authors.affiliation: Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK. j.mwacharo@cgiar.org.|International Centre for Agricultural Research in Dry Areas, c/o International Livestock Research Institute, Addis Ababa, Ethiopia. j.mwacharo@cgiar.org.
authors.forename: Joram M
authors.initials: JM
authors.lastname: Mwacharo
authors.affiliation: Animal Genetic Resources Station, National Institute of Animal Science, Namwon, Republic of Korea. bloodtype@korea.kr.
authors.forename: Chang-Yeon
authors.initials: CY
authors.lastname: Cho
authors.affiliation: International Livestock Research Institute, Naivasha Road, P.O. Box 30709, Nairobi, Kenya. s.kemp@cgiar.org.
authors.forename: Steve
authors.initials: S
authors.lastname: Kemp
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK. dave.burt@roslin.ed.ac.uk.
authors.forename: David W
authors.initials: DW
authors.lastname: Burt
authors.affiliation: Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK. olivier.hanotte@nottingham.ac.uk.
authors.forename: Olivier
authors.initials: O
authors.lastname: Hanotte
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000235:genetics* / Q000821:virology; D002645:Chickens / Q000235:genetics* / Q000821:virology; D019143:Evolution, Molecular; D016678:Genome; D010802:Phylogeny; D011200:Poultry / Q000235:genetics / Q000821:virology; D012190:Retroviridae / Q000235:genetics* / Q000472:pathogenicity; D016662:Virus Integration / Q000235:genetics