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Updated chromosome-scale CH assembly and CH/CHO-K1 annotations
January 27, 2021
A significantly more continuous version of the Chinese hamster genome, CH PICRH (GCF_003668045.3), along with its 2020 RefSeq annotation is now on CHOgenome.org. Long-range scaffolding of the previous CH genome assembly was performed using high-throughput chromosome conformation capture (Hi-C) and now 97% of the genome is contained in 11 large scaffolds corresponding to the CH chromosomes. In addition, the updated 2020 RefSeq annotation for the CHO-K1 cell line is available. Both can be searched (gene search and BLAST) and viewed on JBrowse. More information on the most recent version of the Chinese hamster genome can be found here.
Updated CH assembly and CH/CHO-K1 annotations
May 1, 2019
We are excited to announce that the significantly improved Chinese hamster genome, CH PICR (GCF_00366804.1), along with its 2018 RefSeq annotation is now online. In addition, an updated RefSeq annotation for the CHO-K1 cell line is now available. Both can be searched (gene search and BLAST) and viewed on JBrowse. More information on the updated Chinese hamster genome can be found here.
New mRNA Expression Browser (Beta)
June 7, 2017
The browser (beta version) for the visualization of mRNA expression from CHO-K1 cells is now online. The data is from several published DNA-microarray or RNA-Seq experiments. The tutorial on how to use this browser can be found here.
Featured Articles
This webpage contains links to the current and past featured articles. Journal access may be limited to subscribed users for some of the articles.
| Description | Title | Reference |
|---|---|---|
| The genome assembly for the Chinese hamster was further improved and now contains chromosome-scale scaffolds. Long-range scaffolding of the previous CH genome assembly (PICR) was performed using high-throughput chromosome conformation capture to create this significantly more continuous CH assembly (referred to as PICRH). | Chromosome-scale scaffolds for the Chinese hamster reference genome assembly to facilitate the study of the CHO epigenome | Hilliard et al. Biotechnol Bioeng (2020) 117, 2331-2339 |
| The authors created a consensus genome-scale model of CHO cell metabolism with 1,766 genes and 6,663 reactions describing metabolism and protein production during cell growth. Cell line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells were also created and the integration of -omics data revealed amino acid auxotrophy bases in various cell lines. | A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism | Hefzi H et al. Cell Systems (2016) 3, 434-443 |
| The authors evaluated the RNA-seq mapping of four CHO cell reference sequences hosted by the NCBI RefSeq. The reference sequences were the 2012 annotated CHO-K1 genome, the 2014 annotated Chinese hamster genome, and their respective transcriptomes. The 2014 Chinese hamster genome had the best total mapping rate of RNA-seq data (73.5%) and the total mapping rate could be improved by approximately 15% with the addition of the human and mouse genomes. | An evaluation of public genomic references for mapping RNA-Seq data from Chinese hamster ovary cells | Le H et al. Biotechnol. Bioeng. (2015) 112, 2412-2416 |
| Compares host cell protein production in three different CHO cell lines each lacking a recombinant protein product, in order to understand cell culture harvest diversity. | More similar than different: Host cell protein production using three null CHO cell lines | Yuk I et al. Biotechnol. Bioeng. (2015) 112, 2068-83 |
| The authors identified novel miRNAs in CHO by searching the CHO genome for conserved miRNA sequences identified in other species. Further criteria, such as secondary structure prediction, were used to filter the list of novel predicted miRNAs down to 71 expressed novel miRNAs and 56 pre-miRNAs that were added to the hamster miRNome. | Annotation of additional evolutionary conserved microRNAs in CHO cells from updated genomic data | Diendorfer A et al. Biotechnol. Bioeng. (2015) 112, 1488-93 |
| The genome of the DHFR negative CHO DXB11 cell line was sequenced with a depth of 33x. Genome analyses revealed that about 17% of CHO DXB11 genes are single copies and that copy number variations of the currently sequenced CHO cell lines are distinct from each other. | Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy | Kaas C et al. BMC Genomics. 2015; 16(1): 160 |
| The authors use CRISPR Cas9 to disrupt the function of the FUT8 and COSMC genes in CHO cells and introduce a web-based tool called CRISPy to identify sgRNA target sequences in the CHO-K1 genome. The tool has identified about 2 million CRISPR target sites over 27,553 genes. | Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool | Ronda C et al. Biotechnol. Bioeng. (2014) 111, 1604-1616 |