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- Title
Chromosomal level assembly and population sequencing of the Chinese tree shrew genome.
- Authors
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
- 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 singlemolecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-quality chromosomescale 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. Inaddition, 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.
- Subjects
BIOLOGICAL research; NORTHERN tree shrew; SINGLE nucleotide polymorphisms; MAJOR histocompatibility complex; LABORATORY animals
- Publication
Zoological Research, 2019, Vol 40, Issue 6, p506
- ISSN
2095-8137
- Publication type
Article
- DOI
10.24272/j.issn.2095-8137.2019.063