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

David Wragg, Andrew S Mason, Le Yu, Richard Kuo, Raman A Lawal, Takele Taye Desta, Joram M Mwacharo, Chang-Yeon Cho, Stephen Kemp, David W Burt, Olivier Hanotte

Research output: Contribution to journalArticlepeer-review

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 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.

Original languageEnglish
Pages (from-to)784
JournalBMC Genomics
Volume16
Issue number1
DOIs
Publication statusPublished - 14 Oct 2015

Fingerprint

Dive into the research topics of 'Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken'. Together they form a unique fingerprint.

Cite this