@article { , title = {Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken}, 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}, doi = {10.1186/s12864-015-1954-x}, eissn = {1471-2164}, journal = {BMC Genomics}, publicationstatus = {Published}, publisher = {Springer Verlag}, url = {https://nottingham-repository.worktribe.com/output/763866}, volume = {16}, keyword = {Retrovirus, Symbiosis, Adaptation, Immunogenetics, Genetics, NGS, Gallus}, year = {2015}, author = {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} }