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

Ronald Alan Harris; Muthuswamy Raveendran; Dustin T. Lyfoung; Fritz Joachim Sedlazeck; Medhat Mahmoud; Trent M. Prall; Julie A. Karl; HarshaVardhan Doddapaneni; Qingchang Meng; Yi Han; Donna Marie Muzny; Roger W. Wiseman; David H. O’Connor; Jeffrey Rogers

doi:10.1093/gigascience/giac039

GenomicsGigaScienceJan 1, 2022

Peer-reviewed journal article

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

Ronald Alan Harris iD, Muthuswamy Raveendran iD, Dustin T. Lyfoung iD, Fritz Joachim Sedlazeck iD, Medhat Mahmoud iD, Trent M. Prall iD, Julie A. Karl iD, HarshaVardhan Doddapaneni iD, Qingchang Meng iD, Yi Han iD, Donna Marie Muzny iD, Roger W. Wiseman iD, David H. O’Connor iD, Jeffrey Rogers iD

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Abstract

BackgroundThe 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. FindingsHere, 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 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 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%. ConclusionsAccess 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.