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

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cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationNational Institute of Animal Science, Republic of Koreaen
cg.contributor.affiliationNational Research Institute for Agriculture, Food and Environmenten
cg.contributor.affiliationUniversity of Edinburghen
cg.contributor.affiliationUniversity of Nottinghamen
cg.contributor.donorBiotechnology and Biological Sciences Research Council, United Kingdomen
cg.contributor.donorScottish Governmenten
cg.contributor.donorWellcome Trusten
cg.creator.identifierJoram Mwacharo: 0000-0001-6981-8140
cg.creator.identifierOlivier Hanotte: 0000-0002-2877-4767
cg.creator.identifierStephen J Kemp: 0000-0003-4041-1720
cg.identifier.doihttps://doi.org/10.1186/s12864-015-1954-xen
cg.issn1471-2164en
cg.issue1en
cg.journalBMC Genomicsen
cg.subject.ilriCHICKENSen
cg.subject.ilriGENOMICSen
cg.volume16en
dc.contributor.authorWragg, Daviden
dc.contributor.authorMason, Andrew S.en
dc.contributor.authorYu, Leen
dc.contributor.authorKuo, Richarden
dc.contributor.authorLawal, Raman A.en
dc.contributor.authorDesta, Takele Tayeen
dc.contributor.authorMwacharo, Joram M.en
dc.contributor.authorCho, Chang-Yeonen
dc.contributor.authorKemp, Stephen J.en
dc.contributor.authorBurt, David W.en
dc.contributor.authorHanotte, Olivier H.en
dc.date.accessioned2023-03-10T14:35:50Zen
dc.date.available2023-03-10T14:35:50Zen
dc.identifier.urihttps://hdl.handle.net/10568/129459
dc.titleGenome-wide analysis reveals the extent of EAV-HP integration in domestic chickenen
dcterms.abstractEAV-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.en
dcterms.accessRightsOpen Access
dcterms.available2015-10-14
dcterms.bibliographicCitationWragg, 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:en
dcterms.issued2015-12
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectanalysisen
dcterms.subjectintegrationen
dcterms.subjectgeneticsen
dcterms.subjectbiotechnologyen
dcterms.typeJournal Article

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