Abstract
BackgroundInterferon inducible transmembrane (IFITM) proteins are effectors of the immune system widely characterized for their role in restricting infection by diverse enveloped and non-enveloped viruses. The chicken IFITM (chIFITM) genes are clustered on chromosome 5 and to date four genes have been annotated, namely chIFITM1, chIFITM3, chIFITM5 and chIFITM10. However, due to poor assembly of this locus in the Gallus Gallus v4 genome, accurate characterization has so far proven problematic. Recently, a new chicken reference genome assembly Gallus Gallus v5 was generated using Sanger, 454, Illumina and PacBio sequencing technologies identifying considerable differences in the chIFITM locus over the previous genome releases.MethodsWe re-sequenced the locus using both Illumina MiSeq and PacBio RS II sequencing technologies and we mapped RNA-seq data from the European Nucleotide Archive (ENA) to this finalized chIFITM locus. Using SureSelect probes capture probes designed to the finalized chIFITM locus, we sequenced the locus of a different chicken breed, namely a White Leghorn, and a turkey.ResultsWe confirmed the Gallus Gallus v5 consensus except for two insertions of 5 and 1 base pair within the chIFITM3 and B4GALNT4 genes, respectively, and a single base pair deletion within the B4GALNT4 gene. The pull down revealed a single amino acid substitution of A63V in the CIL domain of IFITM2 compared to Red Jungle fowl and 13, 13 and 11 differences between IFITM1, 2 and 3 of chickens and turkeys, respectively. RNA-seq shows chIFITM2 and chIFITM3 expression in numerous tissue types of different chicken breeds and avian cell lines, while the expression of the putative chIFITM1 is limited to the testis, caecum and ileum tissues.ConclusionsLocus resequencing using these capture probes and RNA-seq based expression analysis will allow the further characterization of genetic diversity within Galliformes.
Highlights
Interferon inducible transmembrane (IFITM) proteins are effectors of the immune system widely characterized for their role in restricting infection by diverse enveloped and non-enveloped viruses
Four IFITM genes have been annotated to date by the chicken gene nomenclature consortium (CGNC), namely chIFITM1 (LOC422993-3-like), chIFITM3 (LOC770612-1-like), chIFITM5, and chIFITM10 [15,16,17,18,19,20,21,22]
Not yet annotated by the CGNC, we have previously shown the existence of chIFITM2 and suggested a hypothetical genetic structure of the locus based on the human syntenic genome region [23]
Summary
Interferon inducible transmembrane (IFITM) proteins are effectors of the immune system widely characterized for their role in restricting infection by diverse enveloped and non-enveloped viruses. Poultry accounts for almost half of all meat consumed in the UK, with 875 million chickens, 17 million turkeys, 16 million ducks and 250,000 geese a year supplied by over 2500 poultry farms [1] Their production can be adversely affected by infection with avian specific viruses such as infectious bursal disease virus (IBDV), infectious. Binding of the IFNα/β to their cell surface receptors induces translocation of the transcription factor complex IFN-stimulated gene factor 3 (ISGF3) into the nucleus [24]. This induces the transcription of several ISGs, among which are the IFITM genes. It is suggested that the membrane-defined site of fusion, namely plasma membrane and endosomes, is critical for the antiviral activity of these proteins [15]
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