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

TitleConstruction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus.
Publication TypeJournal Article
Year of Publication2022
AuthorsHarris, 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 Published2022 May 28
KeywordsAnimals, 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.

Alternate JournalGigascience
PubMed ID35640223
PubMed Central IDPMC9155146
Grant ListP51 OD011106 / OD / NIH HHS / United States
T32 GM135119 / GM / NIGMS NIH HHS / United States
HHSN272201600007C / AI / NIAID NIH HHS / United States