@article{06995d9976664e6ba04147ba79d9cfc2,
title = "A reference genome of the Chinese hamster based on a hybrid assembly strategy",
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",
author = "Oliver Rupp and MacDonald, {Madolyn L.} and Shangzhong Li and Heena Dhiman and Shawn Polson and Sven Griep and Kelley Heffner and Inmaculada Hernandez and Karina Brinkrolf and Vaibhav Jadhav and Mojtaba Samoudi and Haiping Hao and Brewster Kingham and Alexander Goesmann and Betenbaugh, {Michael J.} and Lewis, {Nathan E.} and Nicole Borth and Lee, {Kelvin H.}",
note = "Funding Information: National Institute of General Medical Sciences, Grant/Award Number: P20 GM103446, R35 GM119850; National Science Foundation, Grant/Award Number: NSF1144726, NSF1412365, NSF1539359, NSF1736123; Technical University of Denmark, Grant/Award Numbers: NNF10CC1016517, NNF16CC0021858 Funding Information: The authors thank George Yarganian for providing hamster tissue. Valerie Schneider and Fran{\c c}oise Thibaud-Nissen from NCBI helped in running a “light” version of the NCBI annotation pipeline on the assemblies. This work was supported with generous funding from Biogen, Genentech, Eli Lilly and Company, Dublin City University, University of Queensland, and University of Tokushima. Grant support was provided by the Novo Nordisk Foundation to the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517 and NNF16CC0021858), NIGMS (R35 GM119850), a FISP fellowship from UC San Diego to S. Li, and NSF (NSF1144726, NSF1412365, NSF1539359, and NSF1736123) to the University of Delaware. H. Dhiman is supported by the EU Horizon 2020 MSCA ITN grant no. 642663. O. Rupp, S. Griep, I. Hernandez, V. Jadhav, K. Brinkrolf, A. Goesmann, and N. Borth received support from the Austrian Center of Industrial Biotechnology Acib, a COMET K2 competence center of the Austrian Research Promotion Agency. I. Hernandez also received support from the Austrian Science Fund PhD Program “Biotop” (Grant Number W1224). Bioinformatics support by the BMBF-funded project “Bielefeld-Gie{\ss}en Center for Microbial Bioinformatics—BiGi (Grant Number 031A533)” within the German Network for Bioinformatics Infrastructure (de.NBI) is gratefully acknowledged. S. Polson and the computational infrastructure provided by the University of Delaware Center for Bioinformatics and Computational Biology Core Facility is supported through Delaware INBRE, NIGMS (P20 GM103446). Publisher Copyright: {\textcopyright} 2018 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.",
year = "2018",
month = aug,
doi = "10.1002/bit.26722",
language = "English (US)",
volume = "115",
pages = "2087--2100",
journal = "Biotechnology and Bioengineering",
issn = "0006-3592",
publisher = "Wiley-VCH Verlag",
number = "8",
}