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Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3

I. Bassano, SH. Ong, M. Sanz-Hernandez, M. Vinkler, A. Kebede, O. Hanotte, E. Onuigbo, M. Fife, P. Kellam,

. 2019 ; 20 (1) : 272. [pub] 20190405

Language English Country England, Great Britain

Document type Comparative Study, Journal Article

Persistent link   https://www.medvik.cz/link/bmc19034655

Grant support
BB/L003996/1 Biotechnology and Biological Sciences Research Council - United Kingdom
BBS/OS/GC/000015/2 Biotechnology and Biological Sciences Research Council - United Kingdom
LTC18060 Inter-COST

BACKGROUND: The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well documented in several animal species, but their genetic variation and biological mechanism is less well understood, particularly in avian species. RESULTS: Here we report the complete sequence of the domestic chicken Gallus gallus IFITM locus from a wide variety of chicken breeds to examine the detailed pattern of genetic variation of the locus on chromosome 5, including the flanking genes ATHL1 and B4GALNT4. We have generated chIFITM sequences from commercial breeds (supermarket-derived chicken breasts), indigenous chickens from Nigeria (Nsukka) and Ethiopia, European breeds and inbred chicken lines from the Pirbright Institute, totalling of 206 chickens. Through mapping of genetic variants to the latest chIFITM consensus sequence our data reveal that the chIFITM locus does not show structural variation in the locus across the populations analysed, despite spanning diverse breeds from different geographic locations. However, single nucleotide variants (SNVs) in functionally important regions of the proteins within certain groups of chickens were detected, in particular the European breeds and indigenous birds from Ethiopia and Nigeria. In addition, we also found that two out of four SNVs located in the chIFITM1 (Ser36 and Arg77) and chIFITM3 (Val103) proteins were simultaneously under positive selection. CONCLUSIONS: Together these data suggest that IFITM genetic variation may contribute to the capacities of different chicken populations to resist virus infection.

References provided by Crossref.org

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$a Bassano, Irene $u Department of Medicine, Division of Infectious Diseases, Wright Fleming Wing, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK.
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$a Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3 / $c I. Bassano, SH. Ong, M. Sanz-Hernandez, M. Vinkler, A. Kebede, O. Hanotte, E. Onuigbo, M. Fife, P. Kellam,
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$a BACKGROUND: The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well documented in several animal species, but their genetic variation and biological mechanism is less well understood, particularly in avian species. RESULTS: Here we report the complete sequence of the domestic chicken Gallus gallus IFITM locus from a wide variety of chicken breeds to examine the detailed pattern of genetic variation of the locus on chromosome 5, including the flanking genes ATHL1 and B4GALNT4. We have generated chIFITM sequences from commercial breeds (supermarket-derived chicken breasts), indigenous chickens from Nigeria (Nsukka) and Ethiopia, European breeds and inbred chicken lines from the Pirbright Institute, totalling of 206 chickens. Through mapping of genetic variants to the latest chIFITM consensus sequence our data reveal that the chIFITM locus does not show structural variation in the locus across the populations analysed, despite spanning diverse breeds from different geographic locations. However, single nucleotide variants (SNVs) in functionally important regions of the proteins within certain groups of chickens were detected, in particular the European breeds and indigenous birds from Ethiopia and Nigeria. In addition, we also found that two out of four SNVs located in the chIFITM1 (Ser36 and Arg77) and chIFITM3 (Val103) proteins were simultaneously under positive selection. CONCLUSIONS: Together these data suggest that IFITM genetic variation may contribute to the capacities of different chicken populations to resist virus infection.
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$a Ong, Swee Hoe $u Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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$a Sanz-Hernandez, Maximo $u Imperial College London, Department of Life Sciences, South Kensington, London, SW7 2AZ, UK.
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$a Vinkler, Michal $u Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
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$a Kebede, Adebabay $u Addis Ababa University (AAU), P.O. Box 32853, Addis Ababa, Ethiopia. Amhara Regional Agricultural Research Institute (ARARI), P.O. Box 527, 100, Bahir Dar, Ethiopia. International Livestock Research Institute (ILRI), P. O. Box 5689, Addis Ababa, Ethiopia.
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$a Hanotte, Olivier $u School of Life Sciences, University of Nottingham, University Park, Nottingham, NG72RD, UK. Center for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
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$a Onuigbo, Ebele $u Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria.
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$a Kellam, Paul $u Department of Medicine, Division of Infectious Diseases, Wright Fleming Wing, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK. p.kellam@imperial.ac.uk. Kymab Ltd The Bennet Building (B930) Babraham Research Campus, Cambridge, CB22 3AT, UK. p.kellam@imperial.ac.uk.
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