Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes.
Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes.
复制标题
DOI：
10.1186/s12864-017-3801-8
复制
发表时间：
2017-05-30
期刊：
影响因子：
4.4
通讯作者：
Kellam P
中科院分区：
文献类型：
--
作者：
Bassano I;Ong SH;Lawless N;Whitehead T;Fife M;Kellam P
干扰素诱导跨膜（IFITM）蛋白是免疫系统的效应器，其广泛的特点是在限制各种包膜和非包膜病毒的感染中发挥作用。鸡IFITM （chIFITM）基因聚集在第5染色体上，迄今为止已注释了4个基因，分别是chIFITM1、chIFITM3、chIFITM5和chIFITM10。然而，由于该基因座在Gallus Gallus v4基因组中的组装不良，迄今为止，准确的表征一直存在问题。最近，使用Sanger， 454， Illumina和PacBio测序技术生成了一个新的鸡参考基因组组合Gallus Gallus v5，发现chIFITM位点与以前的基因组版本存在很大差异。我们使用Illumina MiSeq和PacBio RS II测序技术对该位点进行了重新测序，并将来自欧洲核苷酸档案（ENA）的RNA-seq数据映射到最终确定的chIFITM位点。使用SureSelect探针捕获设计到最终chIFITM位点的探针，我们对不同鸡品种（即白来角鸡和火鸡）的位点进行了测序。我们证实了Gallus Gallus v5的一致性，除了chIFITM3和B4GALNT4基因中分别有5个和1个碱基对的插入，以及B4GALNT4基因中单个碱基对的缺失。下拉结果显示，与红丛林鸡相比，IFITM2的CIL结构域的A63V有一个氨基酸的替换，而与鸡和火鸡相比，IFITM2、2和3分别有13,13和11个氨基酸的差异。RNA-seq显示，chIFITM2和chIFITM3在许多组织类型的不同鸡品种和禽细胞系中表达，而推测的chIFITM1的表达仅限于睾丸、盲肠和回肠组织。使用这些捕获探针和基于RNA-seq的表达分析的位点重测序将允许进一步表征Galliformes内的遗传多样性。本文的在线版本（doi:10.1186/s12864-017-3801-8）包含补充材料，授权用户可以使用。
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. 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. 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. Locus resequencing using these capture probes and RNA-seq based expression analysis will allow the further characterization of genetic diversity within Galliformes. The online version of this article (doi:10.1186/s12864-017-3801-8) contains supplementary material, which is available to authorized users.