Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
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 c...
| Autores principales: | , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2015
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/129459 |
| _version_ | 1855517465600065536 |
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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, Stephen J. Burt, David W. Hanotte, Olivier H. |
| author_browse | Burt, David W. Cho, Chang-Yeon Desta, Takele Taye Hanotte, Olivier H. Kemp, Stephen J. Kuo, Richard Lawal, Raman A. Mason, Andrew S. Mwacharo, Joram M. Wragg, David Yu, Le |
| author_facet | Wragg, David Mason, Andrew S. Yu, Le Kuo, Richard Lawal, Raman A. Desta, Takele Taye Mwacharo, Joram M. Cho, Chang-Yeon Kemp, Stephen J. Burt, David W. Hanotte, Olivier H. |
| author_sort | Wragg, David |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace129459 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1294592024-10-03T07:40:47Z 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, Stephen J. Burt, David W. Hanotte, Olivier H. analysis integration genetics biotechnology 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. 2015-12 2023-03-10T14:35:50Z 2023-03-10T14:35:50Z Journal Article https://hdl.handle.net/10568/129459 en Open Access Springer Wragg, David; Mason, Andrew S.; Yu, Le; Kuo, Richard; Lawal, Raman A.; Desta, Takele Taye; Mwacharo, Joram M.; Cho, Chang-Yeon; Kemp, Stephen J.; Burt, David W.; Hanotte, Olivier H. 2015. Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics 16: |
| spellingShingle | analysis integration genetics biotechnology Wragg, David Mason, Andrew S. Yu, Le Kuo, Richard Lawal, Raman A. Desta, Takele Taye Mwacharo, Joram M. Cho, Chang-Yeon Kemp, Stephen J. Burt, David W. Hanotte, Olivier H. 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 | analysis integration genetics biotechnology |
| url | https://hdl.handle.net/10568/129459 |
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