Supporting data for "Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus"

Dataset type: Genomic, Transcriptomic
Data released on March 23, 2022

Harris RA; Raveendran M; Lyfoung DT; Sedlazeck FJ; Mahmoud M; Prall TM; Karl JA; Doddapaneni H; Meng Q; Han Y; Muzny DM; Wiseman RW; O’Connor DH; Rogers J (2022): Supporting data for "Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus" GigaScience Database. http://dx.doi.org/10.5524/102203

DOI10.5524/102203

The Syrian hamster (Mesocricetus auratus) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was published in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and higher continuity.
Here, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gbp, similar to the 2.50 Gbp length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein-coding genes and 10,459 non-coding genes were annotated in BCM_Maur_2.0 compared to 20,495 protein-coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where approximately 17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0 in which the number of unresolved bases is reduced to 3.00%.
Access to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 35640223)

Accessions (data generated as part of this study):

BioProject: PRJNA705675
Assembly: GCA_017639785.1

Accessions (data referenced by this study):

BioProject: PRJNA77669
BioProject: PRJNA675865
Assembly: GCA_000349665.1





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SY011-Kidney10036Syrian golden hamstergolden hamsterMesocricetus auratus Description:DNA extracted from SY011 Syrain hamste...
Alternative accession-BioSample:SAMN18096088
Geographic location (country and/or sea,region):US...
...
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SY011-Liver10036Syrian golden hamstergolden hamsterMesocricetus auratus Description:DNA extracted from SY011 Syrain hamste...
Alternative accession-BioSample:SAMN18096087
Geographic location (country and/or sea,region):US...
...
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Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
ScriptTEXT2.62 KB2022-03-15
Sequence assemblyGZIP663.01 MB2022-03-15
BUSCOGZIP426.57 KB2022-03-15
BUSCOTSV10.81 KB2022-03-15
Sequence assemblyGZIP654.27 MB2022-03-15
BUSCOGZIP442.7 KB2022-03-15
BUSCOTSV5.66 KB2022-03-15
BUSCOTEXT0.71 KB2022-03-15
BUSCOTEXT0.69 KB2022-03-15
Sequence assemblyGZIP647.65 MB2022-03-15
Displaying 1-10 of 18 File(s).
Funding body Awardee Award ID Comments
National Institute of Allergy and Infectious Diseases DH O’Connor HHSN272201600007C Division of Intramural Research
Date Action
March 23, 2022 Dataset publish
April 7, 2022 Manuscript Link added : 10.1093/gigascience/giac039
October 7, 2022 Manuscript Link updated : 10.1093/gigascience/giac039
February 9, 2023 Link updated : Assembly:GCA_017639785.1
February 9, 2023 Link updated : Assembly:GCA_000349665.1