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

作     者：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 

作者机构：Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming Yunnan 650223China Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunming Yunnan 650204China Kunming Primate Research Center of the Chinese Academy of SciencesKunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China KIZ–CUHK Joint Laboratory of Bioresources and Molecular Research in Common DiseasesKunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Yunnan Key Laboratory of Animal ReproductionKunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China 

出 版 物：《Zoological Research》 (动物学研究（英文）)

年 卷 期：2019年第40卷第6期

页      面：506-521页

核心收录：

学科分类：0710[理学-生物学] 1002[医学-临床医学] 07[理学] 09[农学] 

基　　金：supported by the National Natural Science Foundation of China(U1402224,31601010,81571998,and U1702284) Yunnan Province(2015HA038 and 2018FB054) Chinese Academy of Sciences(CAS zsys-02) 

主　　题：Tupaia belangeri Chromosomal level assembly genome Population sequencing Database 

摘      要：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://***) 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.