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

TitleConstruction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus
Publication TypeJournal Article
Year of PublicationSubmitted
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 Published07/2021
Type of ArticlePreprint
Abstract

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 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.

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 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 noncoding 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%.

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.

Competing Interest Statement

The authors have declared no competing interest.
DOI10.1101/2021.07.05.451071
Refereed DesignationNon-Refereed