|Title||Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus.|
|Publication Type||Journal Article|
|Year of Publication||2022|
|Authors||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|
|Date Published||2022 May 28|
|Keywords||Animals, Chromosomes, Mammalian, Genome, High-Throughput Nucleotide Sequencing, Mesocricetus, Whole Genome Sequencing|
BACKGROUND: 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 generated 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 greater continuity.
FINDINGS: 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 Gb, similar to the 2.50-Gb 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 noncoding genes are 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 ∼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%.
CONCLUSIONS: 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.
|PubMed Central ID||PMC9155146|
|Grant List||P51 OD011106 / OD / NIH HHS / United States |
T32 GM135119 / GM / NIGMS NIH HHS / United States
HHSN272201600007C / AI / NIAID NIH HHS / United States