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

Elizabeth Dong Nguyen; Vahid Nikoonejad Fard; Bernard Y Kim; Sarah Collins; Miranda Galey; Branden R Nelson; Paul Wakenight; Simone M Gable; Aaron McKenna; Theo K Bammler; Jim MacDonald; Daryl M Okamura; Jay Shendure; David R Beier; Jan Marino Ramirez; Mark W Majesky; Kathleen J Millen; Marc Tollis; Danny E Miller

doi:10.1093/g3journal/jkad177

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

G3 (Bethesda). 2023 Sep 30;13(10):jkad177. doi: 10.1093/g3journal/jkad177.

Authors

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.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Murinae* / genetics
Muscle, Skeletal
Sequence Analysis, RNA
Skin*

Associated data

figshare/10.6084/m9.figshare.23528349

Abstract

Publication types

MeSH terms

Associated data

Grants and funding