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

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<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.

Citation

Wragg, D., Mason, A. S., Yu, L., Kuo, R., Lawal, R. A., Desta, T. T., Mwacharo, J. M., Cho, C.-Y., Kemp, S., Burt, D. W., & 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: Jun 30, 2016
• 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
• Contract Date: Jun 30, 2016