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. 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
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.
Actions (Archive Staff Only)
 |
Edit View |
Tools
Tools
