Evidence map›Paper›PMID 38326333›Full record

ArticleScientific data2024

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus.

Yury V Bukhman, Susanne Meyer, Li-Fang Chu, Linelle Abueg, Jessica Antosiewicz-Bourget, Jennifer Balacco, Michael Brecht, Erica Dinatale, Olivier Fedrigo, Giulio Formenti and 16 more

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

26 authors.

Yury V BukhmanRegenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA. ybukhman@morgridge.org.ORCID 0000-0002-8111-7651
Susanne MeyerNeuroscience Research Institute, University of California - Santa Barbara, 494 UCEN Rd, Isla Vista, CA, 93117, USA.
Li-Fang ChuDepartment of Comparative Biology and Experimental Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.ORCID 0000-0002-4738-4481
Linelle AbuegVertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
Jessica Antosiewicz-BourgetRegenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
Jennifer BalaccoVertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
Michael BrechtBCCN/Humboldt University Berlin, Philippstr, 13 House 6, 10115, Berlin, Germany.ORCID 0000-0002-5387-0953
Erica DinataleMax Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany.ORCID 0000-0003-1500-1324
Olivier FedrigoVertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.ORCID 0000-0002-6450-7551
Giulio FormentiLaboratory of Neurogenetics of Language, The Rockefeller University/HHMI, 1230 York Avenue, New York, NY, 10065, USA.ORCID 0000-0002-7554-5991
Arkarachai FungtammasanDNAnexus Inc., 1975 W El Camino Real, Mountain View, CA, 94040, USA.
Swagarika Jaharlal GiriDepartment of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA.
Michael HillerLOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany.ORCID 0000-0003-3024-1449
Kerstin HoweTree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
Daisuke KiharaDepartment of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA.ORCID 0000-0003-4091-6614
Daniel MamottRegenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
Jacquelyn MountcastleVertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
Sarah PelanTree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
Keon RabbaniDepartment 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 SimsTree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
Alan TraceyTree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.ORCID 0000-0002-4805-9058
Jonathan M D WoodTree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.ORCID 0000-0002-7545-2162
Erich D JarvisVertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.ORCID 0000-0001-8931-5049
James A ThomsonRegenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
Mark J P ChaissonDepartment 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 StewartRegenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.ORCID 0000-0002-9041-1828

Funding

Building protein structure models for intermediate resolution cryo-electron microscopy mapsR01GM133840 · NIGMS · PURDUE UNIVERSITY · PI KIHARA, DAISUKE · 2020 to 2023
$1.6M
NIGMS NIH HHS R01 GM133840
6 · The paper itself

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.

Indexed as

ChromosomesShrewsAnimalsGenomeGenomicsMiceMolecular Sequence Annotation

Identifiers

PMID38326333
PMCPMC10850158

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.