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Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken.
- Source :
- BMC Genomics; 10/14/2015, Vol. 16, p1-10, 10p, 3 Diagrams
- Publication Year :
- 2015
-
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<superscript>-6</superscript>), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immunerelated 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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 16
- Database :
- Complementary Index
- Journal :
- BMC Genomics
- Publication Type :
- Academic Journal
- Accession number :
- 110548016
- Full Text :
- https://doi.org/10.1186/s12864-015-1954-x