TupaiaBase

TupaiaBase provides a curated transcriptome database for Tupaia belangeri by integrating whole-genome sequencing (WGS), mRNA sequencing, and total RNA sequencing to identify 12,612 complete coding sequences (CDSs) and support comparative and infection-response genomic studies.

Key Features:

• Comprehensive CDS identification: Identified complete CDSs for 12,612 Tupaia belangeri genes by integrating genomic DNA and RNA sequencing data (WGS, mRNA-seq, total RNA-seq).
• Reliability criteria: Incorporates specific criteria for selecting reliable CDSs established through comparison with the human transcriptome.
• Validation via infection transcriptomics: Validated CDS reliability by analyzing transcriptome profiles from hepatitis B virus-infected tree shrew livers, revealing regulation of the type I interferon signaling pathway at 1 day post-infection, including induction of SOCS3.

Scientific Applications:

• Model development: Enables development of Tupaia belangeri as a model organism for human-disease studies due to its primate-like genetic features and comprehensive CDS set.
• Gene function and regulation studies: Supports investigation of gene expression and regulatory responses to viral infections such as hepatitis B virus.
• Comparative genomics: Facilitates comparative analyses between tree shrew and human transcriptomes to assess translational relevance.

Methodology:

Integration of whole-genome sequencing (WGS), mRNA sequencing, and total RNA sequencing data; selection of reliable CDSs through comparison with the human transcriptome; transcriptome profiling of hepatitis B virus-infected tree shrew livers to assess differential regulation of the type I interferon signaling pathway and SOCS3 at 1 day post-infection.