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BioMed Central, BMC Genomics, 1(16), 2015

DOI: 10.1186/s12864-015-1954-x

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

Journal article published in 2015 by David Wragg, Andrew S. Mason ORCID, Le Yu, Richard Kuo, Raman A. Lawal, Takele Taye Desta, Joram M. Mwacharo, Chang-Yeon Cho, Steve Kemp, David W. Burt, Olivier Hanotte
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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).