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Chromosome level genome assembly of the Etruscan shrew Suncus etruscus.
Bukhman, Yury V; Meyer, Susanne; Chu, Li-Fang; Abueg, Linelle; Antosiewicz-Bourget, Jessica; Balacco, Jennifer; Brecht, Michael; Dinatale, Erica; Fedrigo, Olivier; Formenti, Giulio; Fungtammasan, Arkarachai; Giri, Swagarika Jaharlal; Hiller, Michael; Howe, Kerstin; Kihara, Daisuke; Mamott, Daniel; Mountcastle, Jacquelyn; Pelan, Sarah; Rabbani, Keon; Sims, Ying; Tracey, Alan; Wood, Jonathan M D; Jarvis, Erich D; Thomson, James A; Chaisson, Mark J P; Stewart, Ron.
Affiliation
  • Bukhman YV; Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA. ybukhman@morgridge.org.
  • Meyer S; Neuroscience Research Institute, University of California - Santa Barbara, 494 UCEN Rd, Isla Vista, CA, 93117, USA.
  • Chu LF; Department of Comparative Biology and Experimental Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
  • Abueg L; Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
  • Antosiewicz-Bourget J; Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
  • Balacco J; Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
  • Brecht M; BCCN/Humboldt University Berlin, Philippstr, 13 House 6, 10115, Berlin, Germany.
  • Dinatale E; Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany.
  • Fedrigo O; Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
  • Formenti G; Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, 1230 York Avenue, New York, NY, 10065, USA.
  • Fungtammasan A; DNAnexus Inc., 1975 W El Camino Real, Mountain View, CA, 94040, USA.
  • Giri SJ; Department of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA.
  • Hiller M; LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany.
  • Howe K; Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany.
  • Kihara D; Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
  • Mamott D; Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
  • Mountcastle J; Department of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA.
  • Pelan S; Department of Biological Sciences, Purdue University, 249 S. Martin Jischke Dr., West Lafayette, IN, 47907, USA.
  • Rabbani K; Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
  • Sims Y; Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
  • Tracey A; Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
  • Wood JMD; Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way RRI 408, Los Angeles, CA, 90089, USA.
  • Jarvis ED; Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
  • Thomson JA; Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
  • Chaisson MJP; Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
  • Stewart R; Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
Sci Data ; 11(1): 176, 2024 Feb 07.
Article in En | MEDLINE | ID: mdl-38326333
ABSTRACT
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Shrews / Chromosomes Limits: Animals Language: En Journal: Sci Data Year: 2024 Type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Shrews / Chromosomes Limits: Animals Language: En Journal: Sci Data Year: 2024 Type: Article Affiliation country: United States