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Zoological Research
Kunming Institute of Zoology, Chinese Academy of Sciences
ISSN: 2095-8137
Vol. 40, No. 6, 2019, pp. 506-521
Bioline Code: zr19050
Full paper language: English
Document type: Research Article
Document available free of charge

Zoological Research, Vol. 40, No. 6, 2019, pp. 506-521

 en Chromosomal level assembly and population sequencing of the Chinese tree shrew genome
Fan, Yu; Ye, Mao-Sen; Zhang, Jin-Yan; Xu, Ling; Yu, Dan-Dan; Gu, Tian-Le; Yao, Yu-Lin; Chen, Jia-Qi; Lv, Long-Bao; Zheng, Ping; Wu, Dong-Dong; Zhang, Guo-Jie & Yao, Yong-Gang


Chinese tree shrews ( Tupaia belangeri chinensis check for this species in other resources ) 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: 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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