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

Wragg, David and Mason, Andrew S. and Yu, Le and Kuo, Richard and Lawal, Raman A. and Desta, Takele Taye and Mwacharo, Joram M. and Cho, Chang-Yeon and Kemp, Steve and Burt, David W. and Hanotte, Olivier (2015) Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics, 16 . 784/1-784/10. ISSN 1471-2164

[img]
Preview
PDF (Article only no supplementary) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
Available under Licence Creative Commons Attribution.
Download (2MB) | Preview

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.

Item Type: Article
Keywords: Retrovirus, Symbiosis, Adaptation, Immunogenetics, Genetics, NGS, Gallus
Schools/Departments: University of Nottingham UK Campus > Faculty of Medicine and Health Sciences > School of Life Sciences
Identification Number: https://doi.org/10.1186/s12864-015-1954-x
Depositing User: Hanotte, Olivier
Date Deposited: 30 Jun 2016 08:41
Last Modified: 23 Sep 2016 21:54
URI: http://eprints.nottingham.ac.uk/id/eprint/34507

Actions (Archive Staff Only)

Edit View Edit View