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Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus.
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.
  • Harris RA; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Raveendran M; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Lyfoung DT; Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA.
  • Sedlazeck FJ; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Mahmoud M; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Prall TM; Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA.
  • Karl JA; Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA.
  • Doddapaneni H; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Meng Q; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Han Y; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Muzny D; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Wiseman RW; Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA.
  • O'Connor DH; Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA.
  • Rogers J; Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA.
Gigascience ; 112022 05 28.
Article in English | MEDLINE | ID: covidwho-1873910
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Mesocricetus / Chromosomes, Mammalian Limits: Animals Language: English Year: 2022 Document Type: Article Affiliation country: Gigascience

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Mesocricetus / Chromosomes, Mammalian Limits: Animals Language: English Year: 2022 Document Type: Article Affiliation country: Gigascience