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

2022; University of Oxford; Volume: 11; Linguagem: Inglês

10.1093/gigascience/giac039

2047-217X

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

Viral Infectious Diseases and Gene Expression in Insects

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 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.