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

Oliver Rupp, Madolyn L. MacDonald, Shangzhong Li, Heena Dhiman, Shawn Polson, Sven Griep, Kelley Heffner, Inmaculada Hernandez, Karina Brinkrolf, Vaibhav Jadhav, Mojtaba Samoudi, Haiping Hao, Brewster Kingham, Alexander Goesmann, Michael J. Betenbaugh, Nathan E. Lewis, Nicole Borth, Kelvin H. Lee

Research output: Contribution to journalArticlepeer-review

74 Scopus citations

Abstract

Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read-based assemblies. Here, we completely resequenced C. griseus 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.

Original languageEnglish (US)
Pages (from-to)2087-2100
Number of pages14
JournalBiotechnology and Bioengineering
Volume115
Issue number8
DOIs
StatePublished - Aug 2018
Externally publishedYes

Keywords

  • Chinese hamster
  • assembly
  • biopharmaceuticals
  • genome

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology

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