A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.

Humans Animals Haplotypes Diabetes Mellitus, Type 2 / genetics Murinae Genome Genomics
Arvicanthis niloticus Diabetes Diurnal Genome Germline mutation rate Heterozygosity Long-read genome assembly Orthology Positive selection Retrogenes Segmental duplications

Journal

BMC biology
ISSN: 1741-7007
Titre abrégé: BMC Biol
Pays: England
ID NLM: 101190720

Informations de publication

Date de publication:
08 11 2022
Historique:
received: 10 03 2022
accepted: 29 09 2022
entrez: 7 11 2022
pubmed: 8 11 2022
medline: 10 11 2022
Statut: epublish

Résumé

The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.

Sections du résumé

BACKGROUND
The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.
RESULTS
We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.
CONCLUSIONS
Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.

Identifiants

DOI: 10.1186/s12915-022-01427-8 PMID: 36344967 PMC: PMC9641963
pubmed: 36344967
doi: 10.1186/s12915-022-01427-8
pii: 10.1186/s12915-022-01427-8
pmc: PMC9641963
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

245

Informations de copyright

© 2022. The Author(s).

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Auteurs

Huishi Toh (H)

Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93117, USA.

Chentao Yang (C)

BGI-Shenzhen, Shenzhen, 518083, China.

Giulio Formenti (G)

Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY, USA.

Kalpana Raja (K)

Bioinformatics and Regenerative Biology, Morgridge Institute for Research, Madison, WI, USA.
Current address: Sema4, Stamford, CT, USA.

Lily Yan (L)

Department of Psychology & Neuroscience Program, Michigan State University, East Lansing, MI, USA.

Alan Tracey (A)

Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.

William Chow (W)

Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.

Kerstin Howe (K)

Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.

Lucie A Bergeron (LA)

Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.

Guojie Zhang (G)

BGI-Shenzhen, Shenzhen, 518083, China.
Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.

Bettina Haase (B)

Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.

Jacquelyn Mountcastle (J)

Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.

Olivier Fedrigo (O)

Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.

John Fogg (J)

Department of Statistics, University of Wisconsin - Madison, Madison, WI, USA.

Bogdan Kirilenko (B)

LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany.
Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany.
Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.

Chetan Munegowda (C)

LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany.
Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany.
Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.

Michael Hiller (M)

LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany.
Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany.
Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.

Aashish Jain (A)

Department of Computer Science, Purdue University, West Lafayette, IN, USA.

Daisuke Kihara (D)

Department of Computer Science, Purdue University, West Lafayette, IN, USA.
Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.

Arang Rhie (A)

Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA.

Adam M Phillippy (AM)

Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA.

Scott A Swanson (SA)

Bioinformatics and Regenerative Biology, Morgridge Institute for Research, Madison, WI, USA.

Peng Jiang (P)

Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH, USA.
Department of Biological, Geological and Environmental Sciences (BGES), Cleveland State University, 2121 Euclid Ave, Cleveland, OH, 44115, USA.
Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.

Dennis O Clegg (DO)

Center for Stem Cell Biology and Engineering, Neuroscience Research Institute, Mail Code 5060, University of California, Santa Barbara, CA, 93016, USA.

Erich D Jarvis (ED)

The Rockefeller University, Box 54, 1230 York Avenue, New York, NY, 10065, USA.

James A Thomson (JA)

Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA. jthomson@morgridge.org.
Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA. jthomson@morgridge.org.
Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, WI, 53715, USA. jthomson@morgridge.org.

Ron Stewart (R)

Bioinformatics and Regenerative Biology, Morgridge Institute for Research, Madison, WI, USA. rstewart@morgridge.org.

Mark J P Chaisson (MJP)

Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA. mchaisso@usc.edu.

Yury V Bukhman (YV)

Bioinformatics and Regenerative Biology, Morgridge Institute for Research, Madison, WI, USA. ybukhman@morgridge.org.
ORCID: 0000-0002-8111-7651

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › A haplotype-resolved genome assembly of the...
questionsmedicales.fr › Eucaryotes › Animaux › A haplotype-resolved genome assembly of the...
questionsmedicales.fr › Phénomènes génétiques › Génotype › Haplotypes › A haplotype-resolved genome assembly of the...
questionsmedicales.fr › Maladies endocriniennes › Diabète › Diabète de type 2 › A haplotype-resolved genome assembly of the...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › A haplotype-resolved genome assembly of the...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › A haplotype-resolved genome assembly of the...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › A haplotype-resolved genome assembly of the...