| URL: | http://www.treeshrewdb.org |
| Full name: | tree shrew database |
| Description: | The tree shrew (Tupaia belangeri), currently placed in the order Scandentia, has a wide distribution in South Asia, Southeast Asia and Southwest China. For several decades, tree shrew, the closest relative of primates, has attracted increasing attention in modeling human diseases and therapeutic responses. It has been used as a viable animal model alternative to rodents and primates in biomedical researches such as hepatitis virus infection, myopia, social stress and depression. |
| Year founded: | 2014 |
| Last update: | 2017-12-06 |
| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | China |
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| University/Institution: | Kunming Institute of Zoology, Chinese Academy of Sciences |
| Address: | Key Laboratory of Animal Models and Human Disease Mechanisms Kunming Institute of Zoology, Chinese Academy of Sciences Kunming, Yunnan, China 650223 |
| City: | Kunming |
| Province/State: | Yunnan |
| Country/Region: | China |
| Contact name (PI/Team): | Yong-Gang Yao |
| Contact email (PI/Helpdesk): | yaoyg@mail.kiz.ac.cn |
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Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. [PMID: 31418539]
Chinese tree shrews () have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://www.treeshrewdb.org) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research. |
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Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew. [PMID: 25413576]
The tree shrew (Tupaia belangeri) is a small mammal with a close relationship to primates and it has been proposed as an alternative experimental animal to primates in biomedical research. The recent release of a high-quality Chinese tree shrew genome enables more researchers to use this species as the model animal in their studies. With the aim to making the access to an extensively annotated genome database straightforward and easy, we have created the Tree shrew Database (TreeshrewDB). This is a web-based platform that integrates the currently available data from the tree shrew genome, including an updated gene set, with a systematic functional annotation and a mRNA expression pattern. In addition, to assist with automatic gene sequence analysis, we have integrated the common programs Blast, Muscle, GBrowse, GeneWise and codeml, into TreeshrewDB. We have also developed a pipeline for the analysis of positive selection. The user-friendly interface of TreeshrewDB, which is available at http://www.treeshrewdb.org, will undoubtedly help in many areas of biological research into the tree shrew. |