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

• Published in: Gigascience 2022-05, Vol.11
• Main Authors: Harris, R Alan, Raveendran, Muthuswamy, Lyfoung, Dustin T, Sedlazeck, Fritz J, Mahmoud, Medhat, Prall, Trent M, Karl, Julie A, Doddapaneni, Harshavardhan, Meng, Qingchang, Han, Yi, Muzny, Donna, Wiseman, Roger W, O'Connor, David H, Rogers, Jeffrey
• Format: Article
• Language: English
• Subjects: Animal models; Animals; Assembly; Chromosomes; Chromosomes, Mammalian - genetics; Data Note; Gene sequencing; Genes; Genome; Genomes; Hamsters; High-Throughput Nucleotide Sequencing - methods; Mathematical models; Mesocricetus - genetics; Mesocricetus auratus; Nucleotide sequence; Nucleotides; Proteins; Severe acute respiratory syndrome coronavirus 2; Viral diseases; Whole Genome Sequencing
• ISSN: 2047-217X; 2047-217X
• DOI: 10.1093/gigascience/giac039

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.