Zoological Research ›› 2019, Vol. 40 ›› Issue (6): 506-521.doi: 10.24272/j.issn.2095-8137.2019.063

Special Issue: Tree shrew biology Animal models

• Articles • Previous Articles     Next Articles

Chromosomal level assembly and population sequencing of the Chinese tree shrew genome

Yu Fan1,2,Mao-Sen Ye1,3,Jin-Yan Zhang1,3,Ling Xu1,2,Dan-Dan Yu1,2,Tian-Le Gu1,3,Yu-Lin Yao1,3,Jia-Qi Chen4,Long-Bao Lv4,Ping Zheng2,3,4,5,6,7,Dong-Dong Wu2,6,Guo-Jie Zhang2,6,Yong-Gang Yao1,2,3,4,5()   

  1. 1. Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
    2. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan 650223, China
    3. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
    4. Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
    5. KIZ–CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
    6. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
    7. Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
  • Received:2019-07-12 Accepted:2019-08-09 Online:2019-11-18 Published:2019-08-15
  • Contact: Yong-Gang Yao E-mail:yaoyg@mail.kiz.ac.cn
  • Supported by:
    the National Natural Science Foundation of China(U1402224);Yunnan Province(2015HA038 and 2018FB054);Chinese Academy of Sciences(CAS zsys-02)

Abstract:

Chinese tree shrews (Tupaia belangeri chinensis) 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.

Key words: Tupaia belangeri, Chromosomal level assembly genome, Population sequencing, Database