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
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 ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
SY011-Kidney | 10036 | Syrian golden hamster | golden hamster | Mesocricetus auratus | Description:DNA extracted from SY011 Syrain hamste... Alternative accession-BioSample:SAMN18096088 Geographic location (country and/or sea,region):US... ... + |
SY011-Liver | 10036 | Syrian golden hamster | golden hamster | Mesocricetus auratus | Description:DNA extracted from SY011 Syrain hamste... Alternative accession-BioSample:SAMN18096087 Geographic location (country and/or sea,region):US... ... + |