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 (SMRT) 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 CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

Bioinformatic Identification of Chinese Hamster Ovary (CHO) Cold‐Shock Genes and Biological Evidence of their Cold‐Inducible Promoters

“…Raw sequences were trimmed of adapters and low quality reads using Trimmomatic‐0.36 . Reads were then mapped to the Chinese hamster genome using HiSat2 aligner . Reads mapping in coding genes were counted using “htseq‐count” command in HTSeq python package .…”

CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines

“…With the improved Chinese hamster genome as reference (NCBI Refseq Annotation Release 103) [7], we established an integrated CHO-specific multi-omics platform,'CHOmics', that serves as a one stop-shop for omics data analysis from raw data to comparative pathway analysis across multiple omics data sets. As shown in Figure 1, the tool mainly consists of three modules including data input, analysis (preprocessing pipeline and statistical analysis) and visualization.…”

Expanding the Chinese hamster ovary cell long non-coding RNA transcriptome using RNASeq

“…Despite the availability of several reference genomes for CHO cells (Lewis et al, 2013;Rupp et al, 2018;Xu et al, 2011) and tremendous improvements in transcriptome characterisation, lncRNAs remain poorly annotated severely limiting our ability to associate these molecules with bioprocess phenotypes, and consequently, their utility for cell line engineering. Of the three reference genomes currently available through Ensembl (release 98), the CHOK1 genome contains the largest number of annotated lncRNA genes, yet this number represents only 19% and 14% of the total number of mouse (v23) and human (v32) lncRNAs annotated in GENCODE respectively (Frankish et al, 2019).…”