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

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

doi:10.1002/bit.26722

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.

Highlights

Chinese hamster ovary (CHO) cells have been the primary recombinant protein production host across the biopharmaceutical industry (Walsh, 2014)
For 60 years, CHO cells have been invaluable for biomedical research and fundamental to the study of several biological processes, such as glycosylation (Goh et al, 2014) and DNA repair (Thompson et al, 1987)
The aforementioned research was carried out without genomic resources, new opportunities are arising with published CHO genome sequences (Brinkrolf et al, 2013; Lewis et al, 2013; Xu et al, 2011; Yusufi et al, 2017)

Summary

| INTRODUCTION

Chinese hamster ovary (CHO) cells have been the primary recombinant protein production host across the biopharmaceutical industry (Walsh, 2014). To facilitate CHO cell research and development, the community relies on published genomes for the CHO‐K1 cell line and the parent Chinese hamster, sequenced using short‐read Illumina technologies (Brinkrolf et al, 2013; Lewis et al, 2013; Xu et al, 2011; Yusufi et al, 2017). An important single nucleotide polymorphism (SNP) in the glycosyltransferase, xylosyltransferase 2 (Xylt2), which impacts glycosylation and which was hidden in gaps in previous assemblies, can be detected This resource will serve as an important reference genome for researchers across the biotechnology industry and scientific community

| MATERIALS AND METHODS

| RESULTS

Findings

| DISCUSSION