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Article Dans Une Revue BMC Genomics Année : 2015

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

Résumé

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. 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). 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.
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Dates et versions

hal-02641230 , version 1 (28-05-2020)

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David Wragg, Andrew S. Mason, Le Yu, Richard Kuo, Raman A. Lawal, et al.. Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics, 2015, 16 (1), pp.784. ⟨10.1186/s12864-015-1954-x⟩. ⟨hal-02641230⟩
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