Evidence map›Paper›PMID 39386456›Full record

ArticlebioRxiv : the preprint server for biology2024

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens.

Bernhard Bein, Ioannis Chrysostomakis, Larissa S Arantes, Tom Brown, Charlotte Gerheim, Tilman Schell, Clement Schneider, Evgeny Leushkin, Zeyuan Chen, Julia Sigwart and 10 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

5 · Who and what money

Authors and funding

20 authors.

Bernhard BeinLOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.
Ioannis ChrysostomakisCenter for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany.
Larissa S ArantesBerlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 2-4, 14195 Berlin, Germany.
Tom BrownBerlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 2-4, 14195 Berlin, Germany.ORCID 0000-0001-8293-4816
Charlotte GerheimLOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.
Tilman SchellLOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.
Clement SchneiderSenckenberg Research Institute, Am Museum 1, 02826 Görlitz, Germany.
Evgeny LeushkinLOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.
Zeyuan ChenSenckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.
Julia SigwartLOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.ORCID 0000-0002-3005-6246
Vanessa GonzalezGlobal Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
Nur Leena W S WongInternational Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, 71050 Negeri Sembilan, Malaysia.
Fabricio R SantosLaboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Mozes P K BlomMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany.
Frieder MayerMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany.
Camila J MazzoniBerlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 2-4, 14195 Berlin, Germany.
Astrid BöhneCenter for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany.
Sylke WinklerMax Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.
Carola GreveLOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.
Michael HillerLOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.ORCID 0000-0003-3024-1449

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.

Indexed as

genome assemblylong-read sequencingmuseum collectionsPCR amplification

Identifiers

PMID39386456
PMCPMC11463647

What OpenQuestion holds

Textmetadata
LicenceCC BY-ND
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.