Long-read sequence capture of the haemoglobin gene clusters across codfish species
Long-read sequence capture of the haemoglobin gene clusters across codfish species
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DOI：
10.1111/1755-0998.12955
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发表时间：
2019-01-01
影响因子：
7.7
通讯作者：
Jentoft, Sissel
中科院分区：
文献类型：
--
作者：
Hoff, Siv Nam Khang;Baalsrud, Helle T.;Jentoft, Sissel
结合高通量测序和靶向序列捕获已经成为研究特定基因组区域的一种有吸引力的工具。迄今为止，大多数研究都集中在使用短读技术的外显子组上。这些方法并不是为了捕获重建基因组组织所需的基因间区域而设计的，包括调控区域和基因合成。在这里，我们展示了将靶向序列捕获与长读测序技术相结合的力量，用于对相隔7000万年的8个物种的血红蛋白（Hb）基因簇进行比较基因组分析。以大西洋鳕鱼（Gadus morhua）的参考基因组组装为指导，结合选定鳕鱼的草图组装的基因组信息，我们设计了覆盖两个Hb基因簇的探针。使用定制条形码与PacBio RSII测序相结合，导致LA（类似于100 kb）和MN（类似于200 kb）簇的高度连续组装，其中包括编码和基因间序列的合成区域。我们的结果揭示了Hb基因在这个谱系中的整体保守的基因组组织，但有几个谱系特异性的基因重复。此外，对于一些被研究的物种，我们在Hbb1基因的两个位点上发现了氨基酸替换，以及其调节区域的长度多态性，这与大西洋鳕鱼种群的温度适应有关。这项研究强调了利用靶向长读捕获作为一种通用的方法，通过跨物种基因组资源的产生来进行比较基因组研究，阐明了Hb基因家族在高度分化的鳕鱼群中的进化史。
Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (similar to 100 kb) and MN (similar to 200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.