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

Bassano, Irene; Ong, Swee Hoe; Sanz-Hernandez, Maximo; Vinkler, Michal; Kebede, Adebabay; Hanotte, Olivier; Onuigbo, Ebele; Fife, Mark; Kellam, Paul

Abstract

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.

Citation

Bassano, I., Ong, S. H., Sanz-Hernandez, M., Vinkler, M., Kebede, A., Hanotte, O., Onuigbo, E., Fife, M., & Kellam, P. (2019). Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3. BMC Genomics, 20(1), Article 272. https://doi.org/10.1186/s12864-019-5621-5

• Journal Article Type: Article
• Acceptance Date: Mar 18, 2019
• Online Publication Date: Apr 5, 2019
• Publication Date: 2019-12
• Deposit Date: Sep 2, 2019
• Publicly Available Date: Sep 2, 2019
• Journal: BMC Genomics
• Electronic ISSN: 1471-2164
• Publisher: Springer Verlag
• Peer Reviewed: Peer Reviewed
• Volume: 20
• Issue: 1
• Article Number: 272
• DOI: https://doi.org/10.1186/s12864-019-5621-5
• Keywords: Biotechnology; Genetics
• Public URL: https://nottingham-repository.worktribe.com/output/2547494
• Publisher URL: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5621-5
• Additional Information: Received: 26 October 2018; Accepted: 18 March 2019; First Online: 5 April 2019; : Ethiopian samples were collected as part of Mr. Abebabay Kebede PhD study, blood samples procedures were approved by and followed International Livestock Research IAUC guidelines (Reference Number IACUC-RC2017–21). Samples were dispatched in the UK following International Guidelines (Nagoya Protocol) and the approval of the Ethiopian Institute of Biodiversity. Czech Republic samples were collected under the approval of the Czech Ministry of Education, Youth and Sports (permits no. 34712/2010–30 and 13,882/2011–30). Nigerian birds handling and experiments were conducted following the guidelines stipulated by University of Nigeria Research Ethics Committee on animal handling and use. Pirbright inbred samples were collected from birds housed at The Pirbright Institute, as authorised under its Home Office Establishment Licence and in accordance with the Code of Practice for the Housing and Care of Animals Bred, Supplied or Used for Scientific Purposes. Birds were euthanized following neck dislocation. The method results in immediate death and is recognized as an approved method under the UK Home Office legislation, Animals (Scientific Procedures) Act 1986.; : All authors consented to this publication. All authors read and approved the final manuscript.; : The authors declare that they have no competing interests.; : Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
• Contract Date: Sep 2, 2019