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

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

doi:10.24272/j.issn.2095-8137.2019.063

Jin-Yan Zhang, Yu-Lin Yao + Show 11 more

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https://doi.org/10.24272/j.issn.2095-8137.2019.063

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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.

Highlights

Tree shrews (Tupaia belangeri) are widely distributed throughout South Asia, Southeast Asia (Fuchs & CorbachSöhle, 2010), and South and Southwest China (Peng et al, 1991)
We successfully sequenced the genome of the Chinese tree shrew (Tupaia belangeri chinensis) using Illumina short-read sequencing (KIZ version 1: TS_1.0) and showed their close relationship to non-human primates, thereby settling a longrunning debate regarding the phylogenetic position of tree shrews within eutherian mammals (Fan et al, 2013)
With the human protein set as a reference, we found the best hit for each protein in the other species, with a criterion that more than 30% of the aligned sequence showed identity above 30%

Summary

Introduction

Tree shrews (Tupaia belangeri) are widely distributed throughout South Asia, Southeast Asia (Fuchs & CorbachSöhle, 2010), and South and Southwest China (Peng et al, 1991). They possesses many unique characteristics that are useful in biomedical research models, such as small adult body size (100–150 g), easy and low cost maintenance, short reproductive cycle (~6 weeks), moderate life span (6–8 years), high brain-to-body mass ratio, and very close relationship to primates (Fan et al, 2013; Xiao et al, 2017; Xu et al, 2012; Yao, 2017; Zheng et al, 2014). The successful genome sequencing (Fan et al, 2013) and genetic manipulation of tree shrews (Li et al, 2017) have opened up new avenues for the wide usage of this species in biomedical research (Yao, 2017)

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