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

Author:

Nguyen Elizabeth Dong123,Fard Vahid Nikoonejad4,Kim Bernard Y5,Collins Sarah2,Galey Miranda6,Nelson Branden R7,Wakenight Paul7,Gable Simone M4,McKenna Aaron8,Bammler Theo K9,MacDonald Jim9,Okamura Daryl M12,Shendure Jay310111213,Beier David R12,Ramirez Jan Marino714,Majesky Mark W121315,Millen Kathleen J137,Tollis Marc4,Miller Danny E3615

Affiliation:

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

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.

Funder

Keck Foundation for BioMedical Research

NIH

Impetus Longevity Award

Brotman Baty Institute

Howard Hughes Medical Institute

Seattle Research Institute Center for Developmental Biology and Regenerative Medicine

Seattle Research Institute Center for Integrative Brain Research

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology

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