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 Gallus gallus 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 immunerelated
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