Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing
Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing
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DOI：
10.1038/s41598-019-48867-x
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发表时间：
2019-08
影响因子：
4.6
通讯作者：
Takahiro Sanada;K. Tsukiyama-Kohara;T. Shin-I;Naoki Yamamoto;M. E. H. Kayesh;D. Yamane;Jun-ichiro Takano;Yumiko Shiogama;Y. Yasutomi;K. Ikeo;T. Gojobori;M. Mizokami;M. Kohara
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文献类型：
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作者：
Takahiro Sanada;K. Tsukiyama-Kohara;T. Shin-I;Naoki Yamamoto;M. E. H. Kayesh;D. Yamane;Jun-ichiro Takano;Yumiko Shiogama;Y. Yasutomi;K. Ikeo;T. Gojobori;M. Mizokami;M. Kohara
鉴于其与灵长类动物的遗传相似性，北方树鼩（Tupaia belangeri）作为人类疾病和生物学的动物模型具有很高的潜力。虽然树鼩的遗传信息已经被公开，但树鼩基因的一些完整编码序列（CDSs）仍然不完整，而且这些CDSs的可靠性仍然难以确定。为了改进树鼩CDSs的测定，我们对树鼩的全基因组、mRNA和总RNA进行了测序，并整合了结果数据。此外，我们建立了可靠的CDSs选择标准，并通过与人类转录组比较对这些序列进行注释，从而鉴定出12,612个树鼩基因的完整CDSs，并产生更准确的树鼩基因组数据库（TupaiaBase: http://tupaiabase.org）。对乙型肝炎病毒感染树鼩肝脏的转录组谱进行了分析以验证。基因本体论分析显示，感染后1天转录调控富集，即“I型干扰素信号通路”。此外，还诱导了I型干扰素的负调节因子SOCS3。这项工作提供了一个基于基因组DNA和RNA测序的树鼩CDS数据库，有望成为进一步开发树鼩模型的有力工具。
The northern tree shrew (Tupaia belangeri) possesses high potential as an animal model of human diseases and biology, given its genetic similarity to primates. Although genetic information on the tree shrew has already been published, some of the entire coding sequences (CDSs) of tree shrew genes remained incomplete, and the reliability of these CDSs remained difficult to determine. To improve the determination of tree shrew CDSs, we performed sequencing of the whole-genome, mRNA, and total RNA and integrated the resulting data. Additionally, we established criteria for the selection of reliable CDSs and annotated these sequences by comparison to the human transcriptome, resulting in the identification of complete CDSs for 12,612 tree shrew genes and yielding a more accurate tree shrew genome database (TupaiaBase: http://tupaiabase.org). Transcriptome profiles in hepatitis B virus infected tree shrew livers were analyzed for validation. Gene ontology analysis showed enriched transcriptional regulation at 1 day post-infection, namely in the “type I interferon signaling pathway”. Moreover, a negative regulator of type I interferon,SOCS3, was induced. This work, which provides a tree shrew CDS database based on genomic DNA and RNA sequencing, is expected to serve as a powerful tool for further development of the tree shrew model.