Chromosome level genome assembly of the Etruscan shrew Suncus etruscus.

Animals Mice Chromosomes / genetics Genome Genomics Molecular Sequence Annotation Shrews / genetics

Journal

Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192

Informations de publication

Date de publication:
07 Feb 2024
Historique:
received: 28 07 2023
accepted: 26 01 2024
medline: 8 2 2024
pubmed: 8 2 2024
entrez: 7 2 2024
Statut: epublish

Résumé

Suncus etruscus is one of the world's smallest mammals, with an average body mass of about 2 grams. The Etruscan shrew's small body is accompanied by a very high energy demand and numerous metabolic adaptations. Here we report a chromosome-level genome assembly using PacBio long read sequencing, 10X Genomics linked short reads, optical mapping, and Hi-C linked reads. The assembly is partially phased, with the 2.472 Gbp primary pseudohaplotype and 1.515 Gbp alternate. We manually curated the primary assembly and identified 22 chromosomes, including X and Y sex chromosomes. The NCBI genome annotation pipeline identified 39,091 genes, 19,819 of them protein-coding. We also identified segmental duplications, inferred GO term annotations, and computed orthologs of human and mouse genes. This reference-quality genome will be an important resource for research on mammalian development, metabolism, and body size control.

Identifiants

DOI: 10.1038/s41597-024-03011-x PMID: 38326333 PMC: PMC10850158
pubmed: 38326333
doi: 10.1038/s41597-024-03011-x
pii: 10.1038/s41597-024-03011-x
pmc: PMC10850158
doi:

Types de publication

Dataset Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

176

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM133840
Pays : United States

Informations de copyright

© 2024. The Author(s).

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Auteurs

Yury V Bukhman (YV)

Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA. ybukhman@morgridge.org.
ORCID: 0000-0002-8111-7651

Susanne Meyer (S)

Neuroscience Research Institute, University of California - Santa Barbara, 494 UCEN Rd, Isla Vista, CA, 93117, USA.

Li-Fang Chu (LF)

Department of Comparative Biology and Experimental Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
ORCID: 0000-0002-4738-4481

Linelle Abueg (L)

Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.

Jessica Antosiewicz-Bourget (J)

Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.

Jennifer Balacco (J)

Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.

Michael Brecht (M)

BCCN/Humboldt University Berlin, Philippstr, 13 House 6, 10115, Berlin, Germany.
ORCID: 0000-0002-5387-0953

Erica Dinatale (E)

Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany.
ORCID: 0000-0003-1500-1324

Olivier Fedrigo (O)

Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
ORCID: 0000-0002-6450-7551

Giulio Formenti (G)

Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, 1230 York Avenue, New York, NY, 10065, USA.
ORCID: 0000-0002-7554-5991

Arkarachai Fungtammasan (A)

DNAnexus Inc., 1975 W El Camino Real, Mountain View, CA, 94040, USA.

Swagarika Jaharlal Giri (SJ)

Department of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA.

Michael Hiller (M)

LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany.
Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany.
Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
ORCID: 0000-0003-3024-1449

Kerstin Howe (K)

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

Daisuke Kihara (D)

Department of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA.
Department of Biological Sciences, Purdue University, 249 S. Martin Jischke Dr., West Lafayette, IN, 47907, USA.
ORCID: 0000-0003-4091-6614

Daniel Mamott (D)

Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.

Jacquelyn Mountcastle (J)

Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.

Sarah Pelan (S)

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

Keon Rabbani (K)

Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way RRI 408, Los Angeles, CA, 90089, USA.
ORCID: 0009-0004-1448-2167

Ying Sims (Y)

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

Alan Tracey (A)

Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
ORCID: 0000-0002-4805-9058

Jonathan M D Wood (JMD)

Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
ORCID: 0000-0002-7545-2162

Erich D Jarvis (ED)

Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, 1230 York Avenue, New York, NY, 10065, USA.
ORCID: 0000-0001-8931-5049

James A Thomson (JA)

Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA.

Mark J P Chaisson (MJP)

Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way RRI 408, Los Angeles, CA, 90089, USA.
ORCID: 0000-0001-5395-1457

Ron Stewart (R)

Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
ORCID: 0000-0002-9041-1828

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chromosome level genome assembly of the...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › Souris › Chromosome level genome assembly of the...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Chromosomes › Chromosome level genome assembly of the...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Chromosome level genome assembly of the...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Chromosome level genome assembly of the...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › Chromosome level genome assembly of the...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Insectivora › Musaraignes › Chromosome level genome assembly of the...