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Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes

Title: Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes
Authors: Bassano, I
Ong, SH
Lawless, N
Whitehead, T
Fife, M
Kellam, P
Item Type: Journal Article
Abstract: Background 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. 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. Methods We 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. Results We 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. Conclusions Locus resequencing using these capture probes and RNA-seq based expression analysis will allow the further characterization of genetic diversity within Galliformes.
Issue Date: 30-May-2017
Date of Acceptance: 16-May-2017
URI: http://hdl.handle.net/10044/1/69613
DOI: https://dx.doi.org/10.1186/s12864-017-3801-8
ISSN: 1471-2164
Publisher: BioMed Central
Journal / Book Title: BMC Genomics
Volume: 18
Issue: 1
Copyright Statement: © 2017 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Sponsor/Funder: Biotechnology and Biological Sciences Research Council (BBSRC)
Funder's Grant Number: BB/L00397X/2
Keywords: Science & Technology
Life Sciences & Biomedicine
Biotechnology & Applied Microbiology
Genetics & Heredity
PacBio RSII
Illumina MiSeq
Chicken IFITM
Genetic characterization
RNA-seq
INDUCED TRANSMEMBRANE PROTEINS
RNA-SEQ ANALYSIS
TRANSCRIPTOME ANALYSIS
VIRUS-INFECTION
IN-VITRO
INFLUENZA
CHICKEN
REVEALS
REPLICATION
DISEASE
Animals
Galliformes
Genetic Loci
Genetic Variation
Sequence Analysis, RNA
06 Biological Sciences
11 Medical and Health Sciences
08 Information and Computing Sciences
Bioinformatics
Publication Status: Published
Article Number: 419
Online Publication Date: 2017-05-30
Appears in Collections:Department of Medicine



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