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范宇, 叶茂森, 张金燕, 许凌, 余丹丹, 古天乐, 姚玉林, 陈佳琦, 吕龙宝, 郑萍, 吴东东, 张国捷, 姚永刚. 2019: 树鼩染色体水平参考基因组组装及重测序. 动物学研究, 40(6): 506-521. DOI: 10.24272/j.issn.2095-8137.2019.063
引用本文: 范宇, 叶茂森, 张金燕, 许凌, 余丹丹, 古天乐, 姚玉林, 陈佳琦, 吕龙宝, 郑萍, 吴东东, 张国捷, 姚永刚. 2019: 树鼩染色体水平参考基因组组装及重测序. 动物学研究, 40(6): 506-521. DOI: 10.24272/j.issn.2095-8137.2019.063
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. 2019: Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. Zoological Research, 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. 2019: Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. Zoological Research, 40(6): 506-521. DOI: 10.24272/j.issn.2095-8137.2019.063

树鼩染色体水平参考基因组组装及重测序

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

  • 摘要: 树鼩(Tupaia belangeri chinensis)是一种与灵长类亲缘关系较近的小型哺乳动物,作为实验动物研究引起了广泛的关注。对树鼩基因组高精度的测序及组装,对全面获取遗传特性和了解其生物学特征很有必要。在本研究中,我们使用单分子实时测序技术(Single molecular real-time,SMRT)以及高通量染色质构象捕获技术(High-throughput chromosome conformation capture,Hi-C),完成了新版树鼩基因组(KIZ version 2: TS_2.0)测序,获得高质量染色体水平的参考基因组。新版基因组解决了现存树鼩基因组中存在的问题,并能更加准确地识别基因组上复杂的重复序列、基因结构及物种特异性基因组结构变异。此外,我们对6只野生树鼩进行了全基因组重测序,获得基因组水平上约1280万个单核苷酸变异信息,其中主要组织相容性复合体(Major histocompatibility complex,MHC)及免疫球蛋白基因(Immunoglobulin)家族所在区域在基因组上具有较高的核苷酸多样性。基于上述数据,我们更新了树鼩基因组数据库(TreeshrewDB v2.0: http://www. treeshrewdb.org),发布了新版基因组的注释信息以及遗传变异数据。高质量的树鼩基因组及更新的树鼩基因组数据库将为树鼩应用于各个领域的研究提供相关基础。

     

    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.

     

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