TreeshrewDB

TreeshrewDB provides a comprehensive genomic resource for the Chinese tree shrew (Tupaia belangeri chinensis), including a chromosome-scale assembly (KIZ version 2: TS_2.0), a ~12.8 million SNP variation map from six individuals, and updated genome annotations to support comparative genomics, population genetics, and immunogenetics.

Key Features:

• Chromosome-scale genome assembly: KIZ version 2 (TS_2.0) produced using long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C), resolving large and complex repeat regions, gene structures, and species-specific structural variants.
• Comprehensive genetic variation map: Whole-genome sequencing of six Chinese tree shrews produced a detailed map of approximately 12.8 million single nucleotide polymorphisms (SNPs) and revealed high nucleotide diversity in major histocompatibility complex (MHC) loci and the immunoglobulin gene family.
• Updated genome annotation: Integrated genome annotation information enhancing interpretation of gene function and regulation in Tupaia belangeri chinensis.

Scientific Applications:

• Biomedical research: Comparative genomics and evolutionary analyses leveraging the primate-relatedness of tree shrews for human disease modeling.
• Genetic studies: Population genetics and evolutionary dynamics investigations using the SNP map and genome annotations.
• Immunological research: Studies of immune system function and disease resistance informed by high nucleotide diversity in MHC loci and immunoglobulin genes.

Methodology:

Long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) were used to generate the chromosome-scale assembly (KIZ version 2: TS_2.0), and whole-genome sequencing of six individuals generated the ~12.8 million SNP dataset.