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. The genome assembly represented here corresponds to GenBank Assembly ID: GCA_900186095.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_900186095.1

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.

Statistics

Summary

AssemblyCHOK1GS_HDv1, INSDC Assembly GCA_900186095.1, Feb 2017
Base Pairs2,323,924,942
Golden Path Length2,358,167,390
Annotation providerHorizon Eagle
Annotation methodFull genebuild
Genebuild startedMar 2017
Genebuild releasedAug 2017
Genebuild last updated/patchedSep 2017
Database version90.1

Gene counts

Coding genes20,824
Non coding genes4,142
Small non coding genes3,346
Long non coding genes22
Misc non coding genes774
Pseudogenes106
Gene transcripts32,575

Other

Genscan gene predictions50,660

About this species