A reference genome of the Chinese hamster based on a hybrid assembly strategy

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  • Oliver Rupp
    Bioinformatics and Systems Biology Justus‐Liebig‐University Giessen Giessen Germany
  • Madolyn L. MacDonald
    Department of Computer and Information Sciences University of Delaware Newark Delaware
  • Shangzhong Li
    Department of Bioengineering University of California San Diego California
  • Heena Dhiman
    Austrian Center of Industrial Biotechnology Vienna Austria
  • Shawn Polson
    Department of Computer and Information Sciences University of Delaware Newark Delaware
  • Sven Griep
    Bioinformatics and Systems Biology Justus‐Liebig‐University Giessen Giessen Germany
  • Kelley Heffner
    Chemical and Biomolecular Engineering Johns Hopkins University Baltimore Maryland
  • Inmaculada Hernandez
    Department of Biotechnology University of Natural Resources and Life Sciences Vienna Austria
  • Karina Brinkrolf
    Department of Biorescources Fraunhofer Institute for Molecular Biology and Applied Ecology Giessen Germany
  • Vaibhav Jadhav
    Austrian Center of Industrial Biotechnology Vienna Austria
  • Mojtaba Samoudi
    Novo Nordisk Foundation Center for Biosustainability University of California San Diego California
  • Haiping Hao
    Johns Hopkins University Deep Sequencing and Microarray Core Johns Hopkins University Baltimore Maryland
  • Brewster Kingham
    Delaware Biotechnology Institute Newark Delaware
  • Alexander Goesmann
    Bioinformatics and Systems Biology Justus‐Liebig‐University Giessen Giessen Germany
  • Michael J. Betenbaugh
    Chemical and Biomolecular Engineering Johns Hopkins University Baltimore Maryland
  • Nathan E. Lewis
    Department of Bioengineering University of California San Diego California
  • Nicole Borth
    Austrian Center of Industrial Biotechnology Vienna Austria
  • Kelvin H. Lee
    Delaware Biotechnology Institute Newark Delaware

書誌事項

公開日
2018-05-29
権利情報
  • http://creativecommons.org/licenses/by/4.0/
  • http://creativecommons.org/licenses/by/4.0/
DOI
  • 10.1002/bit.26722
公開者
Wiley

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説明

<jats:title>Abstract</jats:title><jats:p>Accurate and complete genome sequences are essential in biotechnology to facilitate genome‐based cell engineering efforts. The current genome assemblies for <jats:italic>Cricetulus griseus</jats:italic>, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short‐read‐based assemblies. Here, we completely resequenced <jats:italic>C. griseus</jats:italic> using single molecule real time sequencing and merged this with Illumina‐based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28‐fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up‐ and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important Chinese hamster ovary cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.</jats:p>

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