Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
In: ISSN: 1471-2164 ; BMC Genomics ; https://hal.inrae.fr/hal-02641230 ; BMC Genomics, 2015, 2015
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Zugriff:
International audience ; 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.
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Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
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Autor/in / Beteiligte Person: | 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 ; Génétique Physiologie et Systèmes d'Elevage (GenPhySE ) ; Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT) ; Université de Toulouse (UT)-Université de Toulouse (UT) ; University of Nottingham, UK (UON) ; The Roslin Institute ; Biotechnology and Biological Sciences Research Council (BBSRC) ; University of Edinburgh (Edin.) ; GAIC Co Ltd ; Partenaires, INRAE ; International Center for Agricultural Research in the Dry Areas Syrie (ICARDA) ; National Institute of Animal Science |
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Zeitschrift: | ISSN: 1471-2164 ; BMC Genomics ; https://hal.inrae.fr/hal-02641230 ; BMC Genomics, 2015, 2015 |
Veröffentlichung: | HAL CCSD ; BioMed Central, 2015 |
Medientyp: | academicJournal |
DOI: | 10.1186/s12864-015-1954-x |
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