September 22, 2019  |  

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

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

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.© 2018 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

Journal: Biotechnology and bioengineering
DOI: 10.1002/bit.26722
Year: 2018

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