David Wragg
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
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
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, Article 784. https://doi.org/10.1186/s12864-015-1954-x
Journal Article Type | Article |
---|---|
Acceptance Date | Sep 2, 2015 |
Publication Date | Oct 14, 2015 |
Deposit Date | Jun 30, 2016 |
Publicly Available Date | Mar 29, 2024 |
Journal | BMC Genomics |
Electronic ISSN | 1471-2164 |
Publisher | Springer Verlag |
Peer Reviewed | Peer Reviewed |
Volume | 16 |
Article Number | 784 |
DOI | https://doi.org/10.1186/s12864-015-1954-x |
Keywords | Retrovirus, Symbiosis, Adaptation, Immunogenetics, Genetics, NGS, Gallus |
Public URL | https://nottingham-repository.worktribe.com/output/763866 |
Publisher URL | http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1954-x |
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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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