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

doi:10.1002/bit.26722

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

Biotechnol Bioeng. 2018 Aug;115(8):2087-2100. doi: 10.1002/bit.26722. Epub 2018 May 29.

Authors

Oliver Rupp¹, Madolyn L MacDonald^{2

3}, Shangzhong Li^{4

5}, Heena Dhiman^{6

7}, Shawn Polson^{2

3}, Sven Griep¹, Kelley Heffner⁸, Inmaculada Hernandez⁷, Karina Brinkrolf⁹, Vaibhav Jadhav⁶, Mojtaba Samoudi^{5

10}, Haiping Hao¹¹, Brewster Kingham³, Alexander Goesmann¹, Michael J Betenbaugh⁸, Nathan E Lewis^{4

5

10}, Nicole Borth^{6

7}, Kelvin H Lee^{3

12}

Affiliations

¹ Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany.
² Department of Computer and Information Sciences, University of Delaware, Newark, Delaware.
³ Delaware Biotechnology Institute, Newark, Delaware.
⁴ Department of Bioengineering, University of California, San Diego, California.
⁵ Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California.
⁶ Austrian Center of Industrial Biotechnology, Vienna, Austria.
⁷ Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.
⁸ Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.
⁹ Department of Biorescources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.
¹⁰ Department of Pediatrics, University of California, San Diego, California.
¹¹ Johns Hopkins University Deep Sequencing and Microarray Core, Johns Hopkins University, Baltimore, Maryland.
¹² Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware.

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.

Keywords: Chinese hamster; assembly; biopharmaceuticals; genome.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Computational Biology
Cricetulus / genetics*
Genome*
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Whole Genome Sequencing*

Abstract

Publication types

MeSH terms

Grants and funding