Chinese hamster CHOK1GS assembly and gene annotation

Assembly

The Chinese Hamster Ovary cell line (CHO-K1S GS null) assembly, covering more than 90% of the genome is provided by Horizon Discovery and Welcome Trust Sanger Institute. The strategy for the CHOseq project used a hybrid approach with Illumina short range, Illumina long range with Dovetail Chicago library and Bionanogenomics optical mapping to construct the genome. The assembly is on the Scaffold level, consisting of 71,598 contigs assembled into 8264 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 97,133 while the scaffold N50 is 61,810,576.

Gene annotation

The Chinese hamster (Cricetulus griseus), is a species of hamster originating from the deserts of northern China and Mongolia. More information on the Horizon Discovery CHO-K1 GS null cell line can be found on the following poster: Building on GS Engineering the next generation CHO cell platform.pdf

The gene annotation process is carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For candidate genic region, a selection process was applied to chose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome. lincRNAs will be provided in a future release.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.