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Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

Wragg, David; Mason, Andrew S.; Yu, Le; Kuo, Richard; Lawal, Raman A.; Desta, Takele Taye; Mwacharo, Joram M.; Cho, Chang-Yeon; Kemp, Steve; Burt, David W.; Hanotte, Olivier

Authors

David Wragg

Andrew S. Mason

Le Yu

Richard Kuo

Raman A. Lawal

Takele Taye Desta

Joram M. Mwacharo

Chang-Yeon Cho

Steve Kemp

David W. Burt

OLIVIER HANOTTE OLIVIER.HANOTTE@NOTTINGHAM.AC.UK
Director of Frozen Ark Project & Professor of Genetics & Conservation



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 Gallusgallus 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

Journal Article Type Article
Publication Date Oct 14, 2015
Journal BMC Genomics
Electronic ISSN 1471-2164
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 16
Article Number 784
APA6 Citation Wragg, D., Mason, A. S., Yu, L., Kuo, R., Lawal, R. A., Desta, T. T., …Hanotte, O. (2015). Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics, 16, https://doi.org/10.1186/s12864-015-1954-x
DOI https://doi.org/10.1186/s12864-015-1954-x
Keywords Retrovirus, Symbiosis, Adaptation, Immunogenetics, Genetics, NGS, Gallus
Publisher URL http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1954-x
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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