Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)

Elizabeth Dong Nguyen^{1

2

3}, Vahid Nikoonejad Fard⁴, Bernard Y Kim⁵, Sarah Collins², Miranda Galey⁶, Branden R Nelson⁷, Paul Wakenight⁷, Simone M Gable⁴, Aaron McKenna⁸, Theo K Bammler⁹, Jim MacDonald⁹, Daryl M Okamura^{1

2}, Jay Shendure^{3

10

11

12

13}, David R Beier^{1

2}, Jan Marino Ramirez^{7

14}, Mark W Majesky^{1

2

13

15}, Kathleen J Millen^{1

3

7}, Marc Tollis⁴, Danny E Miller^{3

6

15}

Affiliations

¹ Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
² Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA.
³ Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.
⁴ School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA.
⁵ Department of Biology, Stanford University, Stanford, CA 94305, USA.
⁶ Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
⁷ Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
⁸ Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH 03755, USA.
⁹ Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA.
¹⁰ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
¹¹ Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA.
¹² Howard Hughes Medical Institute, Seattle, WA 98195, USA.
¹³ Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
¹⁴ Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA.
¹⁵ Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA.

PMID: 37552705
PMCID: PMC10542272
DOI: 10.1093/g3journal/jkad177

Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)

Elizabeth Dong Nguyen et al. G3 (Bethesda). 2023.

. 2023 Sep 30;13(10):jkad177.

doi: 10.1093/g3journal/jkad177.

Authors

Affiliations

¹ Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
² Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA.
³ Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.
⁴ School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA.
⁵ Department of Biology, Stanford University, Stanford, CA 94305, USA.
⁶ Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
⁷ Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
⁸ Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH 03755, USA.
⁹ Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA.
¹⁰ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
¹¹ Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA.
¹² Howard Hughes Medical Institute, Seattle, WA 98195, USA.
¹³ Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
¹⁴ Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA.
¹⁵ Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA.

PMID: 37552705
PMCID: PMC10542272
DOI: 10.1093/g3journal/jkad177

Abstract

There is increasing interest in the African spiny mouse (Acomys cahirinus) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality reference genome is needed to better understand these regenerative properties at the molecular level. Here, we present an improved reference genome for A. cahirinus generated from long Nanopore sequencing reads. We confirm the quality of our annotations using RNA sequencing data from 4 different tissues. Our genome is of higher contiguity and quality than previously reported genomes from this species and will facilitate ongoing efforts to better understand the regenerative properties of this organism.

Keywords: Acomys cahirinus; Nanopore sequencing; genome assembly; regenerative wound healing; spiny mouse.

PubMed Disclaimer

Conflict of interest statement

Conflicts of interest DEM is engaged in a research agreement with Oxford Nanopore, and they have paid for him to travel to speak on their behalf. DEM is on a scientific advisory board at Oxford Nanopore. The other authors have no conflicts to declare.

Figures

**Fig. 1.**
Karyotype of *Acomys cahirinus* and results of Hi-C scaffolding of the assembly. a) Representative karyotype of a male *A. cahirinus* from the same colony that DNA and RNA were obtained from for sequencing and assembly. Autosomes are arranged by size and numbered accordingly. b) Hi-C interaction contact heatmap of 19 *A. cahirinus* pseudo-chromosomes matches the karyotype (bin size is 1 Mb).

**Fig. 2.**
a) Repeat landscapes for *Acomys cahirinus* and *Mus musculus*, visualizing the percent of each genome comprised of different types of repeats according to their Kimura 2-parameter divergence from family consensus. DNA, DNA transposon; LINE, long interspersed nuclear element; LTR, long terminal repeat retrotransposon; SINE, short interspersed nuclear element. b) Venn diagram showing the number of genes per tissue with a TPM value greater than 2. The majority of genes (4,246; 29%) are expressed at this level in all 4 tissues, while testis had the highest number of genes (2,411; 16%) with a TPM greater than 2 not seen in other tissues.

See this image and copyright information in PMC

Update of

GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse ( Acomys cahirinus ).
Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, Majesky MW, Millen KJ, Tollis M, Miller DE. Nguyen ED, et al. bioRxiv [Preprint]. 2023 Apr 5:2023.04.03.535372. doi: 10.1101/2023.04.03.535372. bioRxiv. 2023. Update in: G3 (Bethesda). 2023 Sep 30;13(10):jkad177. doi: 10.1093/g3journal/jkad177. PMID: 37066261 Free PMC article. Updated. Preprint.

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Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)

Affiliations

Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)

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Abstract

Conflict of interest statement

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