Title | Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. |
Publication Type | Journal Article |
Year of Publication | 2015 |
Authors | Wragg, D, Mason, AS, Yu, L, Kuo, R, Lawal, RA, Desta, TTaye, Mwacharo, JM, Cho, C-Y, Kemp, S, Burt, DW, Hanotte, O |
Journal | BMC Genomics |
Volume | 16 |
Issue | 1 |
Pagination | 784 |
Date Published | 2015 |
ISSN | 1471-2164 |
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. |
DOI | 10.1186/s12864-015-1954-x |
Alternate Journal | BMC Genomics |
PubMed ID | 26466991 |
PubMed Central ID | PMC4607243 |
Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken.
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