Golden Hamster assembly and gene annotation

Assembly

The MesAur1.0 assembly was submitted by Broad Institute on 2013/03/29 . The assembly is on the Scaffold level, consisting of 237,700 assembled into 21,484 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 22,511 while the scaffold N50 is 12,753,307 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000349665.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000349665.1

Gene annotation

The golden hamster, or Syrian hamster (Mesocricetus auratus) is a member of the subfamily Cricetinae, the hamsters. In the wild, they are now considered vulnerable. Their natural geographical range is limited to the north of Syria and the south of Turkey, in arid habitats. Their numbers have been declining due to loss of habitat caused by agriculture and deliberate destruction by humans. However, captive-breeding programs are well established, and captive-bred Syrian hamsters are often kept as pets. They are also used as scientific research animals throughout the world.

The gene annotation process was 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 each candidate gene region, a selection process was applied to choose 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 were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

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

AssemblyMesAur1.0, INSDC Assembly GCA_000349665.1, Dec 2012
Base Pairs2,076,176,254
Golden Path Length2,504,925,039
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2016
Genebuild releasedFeb 2017
Genebuild last updated/patchedFeb 2017
Database version90.10

Gene counts

Coding genes18,257
Non coding genes3,720
Small non coding genes2,995
Long non coding genes23
Misc non coding genes702
Pseudogenes306
Gene transcripts29,936

Other

Genscan gene predictions49,829

About this species