Long-read sequencing and genome assembly of natural history collection samples and challenging specimens
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 assemble 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.
Authors
- Tilman Schell (ORCID: https://orcid.org/0000-0002-6431-6018)
- Mozes P. K. Blom (ORCID: https://orcid.org/0000-0002-6304-9827)
- Nur Leena W. S. Wong (ORCID: https://orcid.org/0000-0002-8008-6400)
- Evgeny V. Leushkin (ORCID: https://orcid.org/0000-0001-5959-6943)
- Julia D. Sigwart (ORCID: https://orcid.org/0000-0002-3005-6246)
- Frieder Mayer (ORCID: https://orcid.org/0000-0002-0594-9923)
- Astrid Böhne (ORCID: https://orcid.org/0000-0002-1284-3115)
- Zeyuan Chen (ORCID: https://orcid.org/0009-0000-1046-3744)
- Tom Brown (ORCID: https://orcid.org/0000-0001-8293-4816)
- Michael Hiller (ORCID: https://orcid.org/0000-0003-3024-1449)
- Clément Schneider (ORCID: https://orcid.org/0000-0003-3743-9319)
- Fabrício R. Santos (ORCID: https://orcid.org/0000-0001-9088-1750)
- Carola Greve (ORCID: https://orcid.org/0000-0003-4993-1378)
- Vanessa L. González (ORCID: https://orcid.org/0000-0002-1593-4469)
- Camila J. Mazzoni (ORCID: https://orcid.org/0000-0001-6758-5427)
- Larissa Souza Arantes (ORCID: https://orcid.org/0000-0003-1374-6701)
- Sylke Winkler (ORCID: https://orcid.org/0000-0002-0915-3316)
- Ioannis Chrysostomakis (ORCID: https://orcid.org/0009-0001-6749-774X)
- Bernhard Bein
- Charlotte Gerheim
Institutions
- Smithsonian Institution (US)
- Universidade Federal de Minas Gerais (BR)
- Goethe University Frankfurt (DE)
- Universiti Putra Malaysia (MY)
- Museum für Naturkunde (DE)
- National Museum of Natural History (US)
- Senckenberg Research Institute and Natural History Museum Frankfurt/M (DE)
- Zoological Research Museum Alexander Koenig (DE)
- Berlin Center for Genomics in Biodiversity Research (DE)
- LOEWE Centre for Translational Biodiversity Genomics (DE)
- Senckenberg Museum für Naturkunde Görlitz (DE)
- Leibniz Institute for Zoo and Wildlife Research (DE)
- Max Planck Institute of Molecular Cell Biology and Genetics (DE)
- Technische Universität Dresden (DE)
Publication Details
- Journal
- Genome biology
- Published
- 2025-02-10
- DOI
- https://doi.org/10.1186/s13059-025-03487-9
- Citations
- 14
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 11.28
Funders
- Deutsche Forschungsgemeinschaft
- Technische Universität Dresden
- Hessisches Ministerium für Wissenschaft und Kunst
- Universitat de Barcelona
- Radboud Universitair Medisch Centrum
- Freie Universität Berlin
- Leibniz-Gemeinschaft