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Evolutionary and biomedical insights from a marmoset diploid genome assembly

机译：来自Marmoset二倍体基因组组装的进化和生物医学洞察

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摘要

The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases~(1). Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an primate model system that is widely used in biomedical research~(2,3). The full spectrum of heterozygosity between the two haplotypes involves 1.36% of the genome-much higher than the 0.13% indicated by the standard estimation based on single-nucleotide heterozygosity alone. The de novo mutation rate is 0.43 × 10~(-8)per site per generation, and the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex-differentiation region and unique evolutionary changes in the marmoset Y chromosome. In addition, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrix biological features. Brain-related genes were highly conserved between marmosets and humans, although several genes experienced lineage-specific copy number variations or diversifying selection, with implications for the use of marmosets as a model system.
机译：二倍体生物的单倍型序列的准确性和完整组装对于了解基因组功能，表型和疾病的变异作用至关重要〜（1）。在这里，使用三进子钻探方法，我们呈现了一种高质量的二倍体参考基因组，两倍于染色体水平独立组装，用于常见的Marmoset（Callithrix jacchus），一种被广泛用于生物医学研究的灵长类动物模型系统〜（2,3）。两个单倍型之间的杂合子的全谱涉及基因组的1.36％ - 高于基于单独的单核苷酸杂合子的标准估计所示的0.13％。每代每次突变率为0.43×10〜（-8），父亲遗传基因组获得了两倍的突变作为母体。我们的二倍体大会使我们能够发现最近的性别分化区域的扩张，以及Marmoset Y染色体的独特进化变化。此外，我们鉴定了许多具有阳性选择的基因，可能导致Callithrix生物学特征的演变。脑与人类和人类之间有高度保守脑相关基因，尽管有几个基因经历了谱系特定的拷贝数变异或多样化的选择，但有影响使用Marmosets作为模型系统。

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  • 来源
    《Nature》 |2021年第7862期|227-233|共7页
  • 作者

    Chentao Yang; Yang Zhou; Stephanie Marcus; Giulio Formenti; Lucie A Bergeron; Zhenzhen Song; Xupeng Bi; Juraj Bergman; Marjolaine Marie C Rousselle; Chengran Zhou; Long Zhou; Yuan Deng; Miaoquan Fang; Duo Xie; Yuanzhen Zhu; Shangjin Tan; Jacquelyn Mountcastle; Bettina Haase; Jennifer Balacco; Jonathan Wood; William Chow; Arang Rhie; Martin Pippel; Margaret M Fabiszak; Sergey Koren; Olivier Fedrigo; Winrich A Freiwald; Kerstin Howe; Huanming Yang; Adam M Phillippy; Mikkel Heide Schierup; Erich D Jarvis; Guojie Zhang;

  • 作者单位

    BGI-Shenzhen|Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen;

    BGI-Shenzhen;

    Laboratory of Neurogenetics of Language The Rockefeller University;

    Laboratory of Neurogenetics of Language The Rockefeller University|Vertebrate Genome Laboratory The Rockefeller University;

    Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen;

    University of the Chinese Academy of Sciences;

    BGI-Shenzhen;

    Bioinformatics Research Centre Aarhus University;

    Bioinformatics Research Centre Aarhus University;

    BGI-Shenzhen;

    BGI-Shenzhen;

    BGI-Shenzhen|Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen;

    BGI-Shenzhen;

    BGI-Shenzhen;

    BGI-Shenzhen;

    BGI-Shenzhen;

    Vertebrate Genome Laboratory The Rockefeller University;

    Vertebrate Genome Laboratory The Rockefeller University;

    Vertebrate Genome Laboratory The Rockefeller University;

    Wellcome Sanger Institute;

    Wellcome Sanger Institute;

    Genome Informatics Section Computational and Statistical Genomics Branch National Human Genome Research Institute National Institutes of Health;

    Max Planck Institute of Molecular Cell Biology and Genetics|Center for Systems Biology;

    Laboratory of Neural Systems The Rockefeller University;

    Genome Informatics Section Computational and Statistical Genomics Branch National Human Genome Research Institute National Institutes of Health;

    Vertebrate Genome Laboratory The Rockefeller University;

    Laboratory of Neural Systems The Rockefeller University|Center for Brains Minds and Machines (CBMM) The Rockefeller University;

    Wellcome Sanger Institute;

    BGI-Shenzhen|University of the Chinese Academy of Sciences|James D. Watson Institute of Genome Sciences|Guangdong Provincial Academician Workstation of BGI Synthetic Genomics BGI-Shenzhen;

    Genome Informatics Section Computational and Statistical Genomics Branch National Human Genome Research Institute National Institutes of Health;

    Bioinformatics Research Centre Aarhus University;

    Laboratory of Neurogenetics of Language The Rockefeller University|Vertebrate Genome Laboratory The Rockefeller University|Howard Hughes Medical Institute;

    Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen|State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences|China National GeneBank BGI-Shenzhen|Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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