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

Adebabay Kebede¹  Irene Bassano²  Paul Kellam²  Ebele Onuigbo³  Michal Vinkler⁴  Maximo Sanz-Hernandez⁵  Olivier Hanotte⁶  Mark Fife⁷  Swee Hoe Ong⁸ 

[1] Addis Ababa University (AAU);Department of Medicine, Division of Infectious Diseases, Wright Fleming Wing, St Mary’s Campus, Imperial College London;Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, University of Nigeria;Department of Zoology, Faculty of Science, Charles University;Imperial College London, Department of Life Sciences;School of Life Sciences, University of Nottingham, University Park;The Pirbright Institute;Wellcome Sanger Institute, Wellcome Genome Campus;

关键词: Variant calling;    SNPs;    INDELs;    GATK;    Positive selection;   

DOI  :  10.1186/s12864-019-5621-5

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown