De Novo-Whole Genome Assembly of the Roborovski Dwarf Hamster ( Phodopus roborovskii ) Genome: An Animal Model for Severe/Critical COVID-19

  1. Sandro Andreotti
  2. Janine Altmüller
  3. Claudia Quedenau
  4. Tatiana Borodina
  5. Geraldine Nouailles
  6. Luiz Gustavo Teixeira Alves
  7. Markus Landthaler
  8. Maximilian Bieniara
  9. Jakob Trimpert
  10. Emanuel Wyler

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Abstract

The Roborovski dwarf hamster Phodopus roborovskii belongs to the Phodopus genus, one of the seven within Cricetinae subfamily. Like other rodents such as mice, rats, or ferrets, hamsters can be important animal models for a range of diseases. Whereas the Syrian hamster from the genus Mesocricetus is now widely used as a model for mild-to-moderate coronavirus disease 2019, Roborovski dwarf hamster shows a severe-to-lethal course of disease upon infection with the novel human coronavirus severe acute respiratory syndrome coronavirus 2.

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  1. Version published to 10.1093/gbe/evac100
  2. Version published to 10.1101/2021.10.02.462569v3 on bioRxiv
  3. Version published to 10.1101/2021.10.02.462569v2 on bioRxiv
  4. ScreenIT

    SciScore for 10.1101/2021.10.02.462569: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    De novo genome assembly: Raw unprocessed reads were assembled using Canu assembler (Koren et al. 2017) with an estimated genome size of 2.1gb and default parameters.
    Canu
    suggested: (Canu, RRID:SCR_015880)
    For evaluation of assembly quality and polishing effects, we applied the quality assessment tools QUAST (Mikheenko et al. 2018) and BUSCO (Simão et al. 2015) for estimation of genome completeness.
    BUSCO
    suggested: (BUSCO, RRID:SCR_015008)
    Contigs classified as bacteria were removed and those classified as human were further analyzed using BLASTN (Altschul et al. 1990) with database nt to eliminate possible contamination with human genetic material.
    BLASTN
    suggested: (BLASTN, RRID:SCR_001598)
    Genome annotation: RNA-Seq reads were quality trimmed and adapter sequences were removed with Cutadapt (Martin 2011) and filtered reads were mapped to the final polished assembly using the mapper STAR (Dobin et al. 2013).
    STAR
    suggested: (STAR, RRID:SCR_004463)
    The mapped reads, together with closely related reference genomes and annotations of Mus musculus (GRCm38.102), Rattus norvegicus (Rnor_6.0.102) and Mesocricetus auratus (MesAur1.0.100) - obtained from ENSEMBL - were used a input for the hybrid genome annotation tool GeMoMa (Keilwagen et al. 2016, 2018) to predict gene loci.
    GeMoMa
    suggested: (GeMoMa, RRID:SCR_017646)
    Finally, resulting gff files were converted to gtf format using GffRead (Pertea & Pertea 2020) and augmented with the original gene name(s) of the associated gene from the reference genomes with a custom Python script.
    Python
    suggested: (IPython, RRID:SCR_001658)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  5. Version published to 10.1101/2021.10.02.462569v1 on bioRxiv