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

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

doi:10.1186/s12864-015-1954-x

Abstract

BackgroundEAV-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.ResultsAn 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).ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1954-x) contains supplementary material, which is available to authorized users.

Highlights

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
Some EAV elements might be related to the avian leukosis virus (ALV) genus [Dimcheff et al 2000 in 2], and owing to high env sequence identity between EAV and ALV genomes, recombination events involving EAV-HP may have led to the emergence of the ALV subgroup J (ALV-J; [3])
Further support for recombination as the origin of ALV-J is evident in the avian retrotransposon ART-CH, where the R and U5 regions of the ART-CH long terminal repeat (LTR) are 97 % identical to the EAV-HP LTR, while the U3 region is distinct from any other retrovirus [3]

Summary

Introduction

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. The EAV retrovirus family likely originated from a primordial integration event prior to the evolutionary speciation of Gallus sp. Some EAV elements might be related to the avian leukosis virus (ALV) genus [Dimcheff et al 2000 in 2], and owing to high env sequence identity between EAV and ALV genomes, recombination events involving EAV-HP may have led to the emergence of the ALV subgroup J (ALV-J; [3]). Remnants of endogenous retroviruses (ERVs) at varying states of integrity are present in vertebrate genomes and can be observed in re-sequencing data. An analysis of reference genome sequences by Stoye [5] suggests that 4–10 % of vertebrate DNA is composed of retroviral remnants

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