Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
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 Ethiopi...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
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BioMed Central
2015
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| Online Access: | https://eprints.nottingham.ac.uk/34507/ |
| _version_ | 1848794871074127872 |
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| author | Wragg, David Mason, Andrew S. Yu, Le Kuo, Richard Lawal, Raman A. Desta, Takele Taye Mwacharo, Joram M. Cho, Chang-Yeon Kemp, Steve Burt, David W. Hanotte, Olivier |
| author_facet | Wragg, David Mason, Andrew S. Yu, Le Kuo, Richard Lawal, Raman A. Desta, Takele Taye Mwacharo, Joram M. Cho, Chang-Yeon Kemp, Steve Burt, David W. Hanotte, Olivier |
| author_sort | Wragg, David |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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 Gallusgallus 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. |
| first_indexed | 2025-11-14T19:23:04Z |
| format | Article |
| id | nottingham-34507 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:23:04Z |
| publishDate | 2015 |
| publisher | BioMed Central |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-345072024-08-15T15:17:33Z https://eprints.nottingham.ac.uk/34507/ Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken Wragg, David Mason, Andrew S. Yu, Le Kuo, Richard Lawal, Raman A. Desta, Takele Taye Mwacharo, Joram M. Cho, Chang-Yeon Kemp, Steve Burt, David W. Hanotte, Olivier 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 Gallusgallus 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. BioMed Central 2015-10-14 Article PeerReviewed Wragg, David, Mason, Andrew S., Yu, Le, Kuo, Richard, Lawal, Raman A., Desta, Takele Taye, Mwacharo, Joram M., Cho, Chang-Yeon, Kemp, Steve, Burt, David W. and Hanotte, Olivier (2015) Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics, 16 . 784/1-784/10. ISSN 1471-2164 Retrovirus Symbiosis Adaptation Immunogenetics Genetics NGS Gallus http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1954-x doi:10.1186/s12864-015-1954-x doi:10.1186/s12864-015-1954-x |
| spellingShingle | Retrovirus Symbiosis Adaptation Immunogenetics Genetics NGS Gallus Wragg, David Mason, Andrew S. Yu, Le Kuo, Richard Lawal, Raman A. Desta, Takele Taye Mwacharo, Joram M. Cho, Chang-Yeon Kemp, Steve Burt, David W. Hanotte, Olivier Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken |
| title | Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken |
| title_full | Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken |
| title_fullStr | Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken |
| title_full_unstemmed | Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken |
| title_short | Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken |
| title_sort | genome-wide analysis reveals the extent of eav-hp integration in domestic chicken |
| topic | Retrovirus Symbiosis Adaptation Immunogenetics Genetics NGS Gallus |
| url | https://eprints.nottingham.ac.uk/34507/ https://eprints.nottingham.ac.uk/34507/ https://eprints.nottingham.ac.uk/34507/ |