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De novo assembly of the Mongolian gerbil genome and transcriptome

Shifeng Cheng, Yuan Fu, Yaolei Zhang, Wenfei Xian, Hongli Wang, Benedikt Grothe, Xin Liu, Xun Xu, Achim Klug, View ORCID ProfileElizabeth A McCullagh
doi: https://doi.org/10.1101/522516
Shifeng Cheng
1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
2Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Yuan Fu
1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
3China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
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Yaolei Zhang
1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
3China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
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Wenfei Xian
1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
2Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Hongli Wang
1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
3China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
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Benedikt Grothe
4Division of Neurobiology, Ludwig-Maximilians-Universitaet Munich, Planegg-Martinsried 82152,Germany
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Xin Liu
1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
3China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
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Xun Xu
1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
3China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
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Achim Klug
5Department of Physiology and Biophysics, School of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
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Elizabeth A McCullagh
5Department of Physiology and Biophysics, School of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
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  • ORCID record for Elizabeth A McCullagh
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Abstract

BACKGROUND The Mongolian gerbil (Meriones unguiculatus) has historically been used as a model organism for the auditory and visual systems, stroke/ischemia, epilepsy and aging related research since 1935 when laboratory gerbils were separated from their wild counterparts. In this study we report genome sequencing, assembly, and annotation further supported by transcriptome data from 27 different tissues samples.

FINDINGS The genome was assembled using Illumina HiSeq 2000 and resulted in a final genome size of 2.54 Gbp with contig and scaffold N50 values of 31.4 Kbp and 500.0 Kbp, respectively. Based on the k-mer estimated genome size of 2.48 Gbp, the assembly appears to be complete. The genome annotation was supported by transcriptome data that identified 36 019 predicted protein-coding genes across 27 tissue samples. A BUSCO search of 3023 mammalian groups resulted in 86% of curated single copy orthologs present among predicted genes, indicating a high level of completeness of the genome.

CONCLUSIONS We report a de novo assembly of the Mongolian gerbil genome that was further enhanced by annotation of transcriptome data from several tissues. Sequencing of this genome increases the utility of the gerbil as a model organism, opening the availability of now widely used genetic tools.

The data sets supporting the results of this article are available in the China National GeneBank CNSA repository, Accession id: CNP0000340.

Footnotes

  • Email Addresses for Authors: Shifeng Cheng: chengshifeng{at}caas.cn Yuan Fu: fuyuan{at}genomics.cn Yaolei Zhang: zhangyaolei{at}genomics.cn Wenfei Xian: xianwenfei{at}caas.cn Hongli Wang: wanghongli{at}genomics.cn Benedikt Grothe: grothe{at}lmu.de Xin Lu: liuxig{at}genomics.cn Xun Xu: xuxun{at}genomics.cn Achim Klug: achim.klug{at}ucdenver.edu Elizabeth A McCullagh: elizabeth.mccullagh{at}ucdenver.edu

  • ↵* co first authors

  • Abbreviations

    bp
    base pair
    BUSCO
    Benchmarking Universal Single-Copy Orthologs
    CDS
    coding sequence
    LINEs
    long interspersed elements
    LTRs
    long terminal repeats
    Myr
    million years
    NCBI
    National Center for Biotechnology Information
    RefSeq
    Reference sequence
    RNA-seq
    high-throughput messenger RNA sequencing
    RIN
    RNA integrity number
    SINEs
    short interspersed elements
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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    Posted January 24, 2019.
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    De novo assembly of the Mongolian gerbil genome and transcriptome
    Shifeng Cheng, Yuan Fu, Yaolei Zhang, Wenfei Xian, Hongli Wang, Benedikt Grothe, Xin Liu, Xun Xu, Achim Klug, Elizabeth A McCullagh
    bioRxiv 522516; doi: https://doi.org/10.1101/522516
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    De novo assembly of the Mongolian gerbil genome and transcriptome
    Shifeng Cheng, Yuan Fu, Yaolei Zhang, Wenfei Xian, Hongli Wang, Benedikt Grothe, Xin Liu, Xun Xu, Achim Klug, Elizabeth A McCullagh
    bioRxiv 522516; doi: https://doi.org/10.1101/522516

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