Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing

Takahiro Sanada, Kyoko Tsukiyama-Kohara, Tadasu Shin-I, Naoki Yamamoto, Mohammad Enamul Hoque Kayesh, Daisuke Yamane, Jun ichiro Takano, Yumiko Shiogama, Yasuhiro Yasutomi, Kazuho Ikeo, Takashi Gojobori, Masashi Mizokami, Michinori Kohara

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


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: 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.
Original languageEnglish (US)
JournalScientific Reports
Issue number1
StatePublished - Aug 26 2019

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: The authors thank Dr. Yukiko Yamazaki for construction of database and Dr. Hayying Chi, Dr. Bouchra Kitab, Rika Matsuyama, Takumi Haraguchi, and Takuya Kato for their help in tree shrew care. This study was supported by grants from the Ministry of Health, Labour and Welfare of Japan (H24-HBV-general-014) and the Research Program on Hepatitis from the Japanese Agency for Medical Research and Development, AMED (JP16fk0310513, JP16fk0210108, and JP17fk0310111). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Dive into the research topics of 'Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing'. Together they form a unique fingerprint.

Cite this