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

Yu Fan; Mao-Sen Ye; Jin-Yan Zhang; Ling Xu; Dan-Dan Yu; Tian-Le Gu; Yu-Lin Yao; Jia-Qi Chen; Long-Bao Lv; Ping Zheng; Dong-Dong Wu; Guo-Jie Zhang; Yong-Gang Yao

doi:10.24272/j.issn.2095-8137.2019.063

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Volume 40 Issue 6

Nov. 2019

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Article Navigation > Zoological Research > 2019 > 40(6): 506-521

Yu Fan, Mao-Sen Ye, Jin-Yan Zhang, Ling Xu, Dan-Dan Yu, Tian-Le Gu, Yu-Lin Yao, Jia-Qi Chen, Long-Bao Lv, Ping Zheng, Dong-Dong Wu, Guo-Jie Zhang, Yong-Gang Yao. Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. Zoological Research, 2019, 40(6): 506-521. doi: 10.24272/j.issn.2095-8137.2019.063

Citation:

Yu Fan, Mao-Sen Ye, Jin-Yan Zhang, Ling Xu, Dan-Dan Yu, Tian-Le Gu, Yu-Lin Yao, Jia-Qi Chen, Long-Bao Lv, Ping Zheng, Dong-Dong Wu, Guo-Jie Zhang, Yong-Gang Yao. Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. Zoological Research, 2019, 40(6): 506-521. doi: 10.24272/j.issn.2095-8137.2019.063

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

doi: 10.24272/j.issn.2095-8137.2019.063

Yu Fan^1,2,
Mao-Sen Ye^1,3,
Jin-Yan Zhang^1,3,
Ling Xu^1,2,
Dan-Dan Yu^1,2,
Tian-Le Gu^1,3,
Yu-Lin Yao^1,3,
Jia-Qi Chen⁴,
Long-Bao Lv⁴,
Ping Zheng^2,3,4,5,6,7,
Dong-Dong Wu^2,6,
Guo-Jie Zhang^2,6,
Yong-Gang Yao^{1,2,3,4,5
,}

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

Funds: the National Natural Science Foundation of China(U1402224);Yunnan Province(2015HA038 and 2018FB054);Chinese Academy of Sciences(CAS zsys-02)

More Information

Corresponding author: Yong-Gang Yao
Received Date: 2019-07-12
Accepted Date: 2019-08-15
Publish Date: 2019-08-15

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.
- Tupaia belangeri,
- Chromosomal level assembly genome,
- Population sequencing,
- Database
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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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

doi: 10.24272/j.issn.2095-8137.2019.063

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

Funds: the National Natural Science Foundation of China(U1402224);Yunnan Province(2015HA038 and 2018FB054);Chinese Academy of Sciences(CAS zsys-02)

Corresponding author: Yong-Gang Yao

Received Date: 2019-07-12
Accepted Date: 2019-08-15
Publish Date: 2019-08-15

Key words:

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.

Citation:

Yu Fan, Mao-Sen Ye, Jin-Yan Zhang, Ling Xu, Dan-Dan Yu, Tian-Le Gu, Yu-Lin Yao, Jia-Qi Chen, Long-Bao Lv, Ping Zheng, Dong-Dong Wu, Guo-Jie Zhang, Yong-Gang Yao. Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. Zoological Research, 2019, 40(6): 506-521. doi: 10.24272/j.issn.2095-8137.2019.063