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)

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

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

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.

Original language	English (US)
Article number	jkad177
Journal	G3: Genes, Genomes, Genetics
Volume	13
Issue number	10
DOIs	https://doi.org/10.1093/g3journal/jkad177
State	Published - Oct 2023
Externally published	Yes

Keywords

Acomys cahirinus
Nanopore sequencing
genome assembly
regenerative wound healing
spiny mouse

ASJC Scopus subject areas

Molecular Biology
Genetics
Genetics(clinical)

Access to Document

10.1093/g3journal/jkad177

Cite this

Nguyen, E. D., Fard, V. N., Kim, B. Y., Collins, S., Galey, M., Nelson, B. R., Wakenight, P., Gable, S. M., McKenna, A., Bammler, T. K., MacDonald, J., Okamura, D. M., Shendure, J., Beier, D. R., Ramirez, J. M., Majesky, M. W., Millen, K. J., Tollis, M., & Miller, D. E. (2023). Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3: Genes, Genomes, Genetics, 13(10), Article jkad177. https://doi.org/10.1093/g3journal/jkad177

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 2023, 'Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)', G3: Genes, Genomes, Genetics, vol. 13, no. 10, jkad177. https://doi.org/10.1093/g3journal/jkad177

@article{fbe6de4b044448f4a15ab652c29d39dc,

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

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",

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

note = "Publisher Copyright: {\textcopyright} The Author(s) 2023.",

year = "2023",

month = oct,

doi = "10.1093/g3journal/jkad177",

language = "English (US)",

volume = "13",

journal = "G3: Genes, Genomes, Genetics",

issn = "2160-1836",

publisher = "Genetics Society of America",

number = "10",

}

TY - JOUR

T1 - Genome Report

T2 - chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)

AU - Nguyen, Elizabeth Dong

AU - Fard, Vahid Nikoonejad

AU - Kim, Bernard Y.

AU - Collins, Sarah

AU - Galey, Miranda

AU - Nelson, Branden R.

AU - Wakenight, Paul

AU - Gable, Simone M.

AU - McKenna, Aaron

AU - Bammler, Theo K.

AU - MacDonald, Jim

AU - Okamura, Daryl M.

AU - Shendure, Jay

AU - Beier, David R.

AU - Ramirez, Jan Marino

AU - Majesky, Mark W.

AU - Millen, Kathleen J.

AU - Tollis, Marc

AU - Miller, Danny E.

PY - 2023/10

Y1 - 2023/10

N2 - 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.

AB - 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.

KW - Acomys cahirinus

KW - Nanopore sequencing

KW - genome assembly

KW - regenerative wound healing

KW - spiny mouse

UR - http://www.scopus.com/inward/record.url?scp=85172940541&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85172940541&partnerID=8YFLogxK

U2 - 10.1093/g3journal/jkad177

DO - 10.1093/g3journal/jkad177

M3 - Article

C2 - 37552705

AN - SCOPUS:85172940541

SN - 2160-1836

VL - 13

JO - G3: Genes, Genomes, Genetics

JF - G3: Genes, Genomes, Genetics

IS - 10

M1 - jkad177

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this