Long-read sequencing and genome assembly of natural history collection samples and challenging specimens
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-bas...
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| Language: | English |
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BMC
2025-02-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03487-9 |
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| author | Bernhard Bein Ioannis Chrysostomakis Larissa S. Arantes Tom Brown Charlotte Gerheim Tilman Schell Clément Schneider Evgeny Leushkin Zeyuan Chen Julia Sigwart Vanessa Gonzalez Nur Leena W. S. Wong Fabricio R. Santos Mozes P. K. Blom Frieder Mayer Camila J. Mazzoni Astrid Böhne Sylke Winkler Carola Greve Michael Hiller |
| author_facet | Bernhard Bein Ioannis Chrysostomakis Larissa S. Arantes Tom Brown Charlotte Gerheim Tilman Schell Clément Schneider Evgeny Leushkin Zeyuan Chen Julia Sigwart Vanessa Gonzalez Nur Leena W. S. Wong Fabricio R. Santos Mozes P. K. Blom Frieder Mayer Camila J. Mazzoni Astrid Böhne Sylke Winkler Carola Greve Michael Hiller |
| author_sort | Bernhard Bein |
| collection | DOAJ |
| description | 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 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. |
| format | Article |
| id | doaj-art-e879aceac2c848f0bab2f68949557e8e |
| institution | DOAJ |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-e879aceac2c848f0bab2f68949557e8e2025-08-20T02:43:16ZengBMCGenome Biology1474-760X2025-02-0126112510.1186/s13059-025-03487-9Long-read sequencing and genome assembly of natural history collection samples and challenging specimensBernhard Bein0Ioannis Chrysostomakis1Larissa S. Arantes2Tom Brown3Charlotte Gerheim4Tilman Schell5Clément Schneider6Evgeny Leushkin7Zeyuan Chen8Julia Sigwart9Vanessa Gonzalez10Nur Leena W. S. Wong11Fabricio R. Santos12Mozes P. K. Blom13Frieder Mayer14Camila J. Mazzoni15Astrid Böhne16Sylke Winkler17Carola Greve18Michael Hiller19LOEWE Centre for Translational Biodiversity GenomicsCenter for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity ChangeBerlin Center for Genomics in Biodiversity Research (BeGenDiv)Berlin Center for Genomics in Biodiversity Research (BeGenDiv)LOEWE Centre for Translational Biodiversity GenomicsLOEWE Centre for Translational Biodiversity GenomicsSenckenberg Research InstituteLOEWE Centre for Translational Biodiversity GenomicsSenckenberg Research InstituteLOEWE Centre for Translational Biodiversity GenomicsGlobal Genome Initiative, National Museum of Natural History, Smithsonian InstitutionInternational Institute of Aquaculture and Aquatic Sciences, Universiti Putra MalaysiaLaboratório de Biodiversidade E Evolução Molecular, Departamento de Genética, Universidade Federal de Minas GeraisMuseum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceMuseum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlin Center for Genomics in Biodiversity Research (BeGenDiv)Center for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity ChangeMax Planck Institute of Molecular Cell Biology and GeneticsLOEWE Centre for Translational Biodiversity GenomicsLOEWE Centre for Translational Biodiversity GenomicsAbstract 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.https://doi.org/10.1186/s13059-025-03487-9Long-read sequencingPCR amplificationGenome assemblyMuseum collections |
| spellingShingle | Bernhard Bein Ioannis Chrysostomakis Larissa S. Arantes Tom Brown Charlotte Gerheim Tilman Schell Clément Schneider Evgeny Leushkin Zeyuan Chen Julia Sigwart Vanessa Gonzalez Nur Leena W. S. Wong Fabricio R. Santos Mozes P. K. Blom Frieder Mayer Camila J. Mazzoni Astrid Böhne Sylke Winkler Carola Greve Michael Hiller Long-read sequencing and genome assembly of natural history collection samples and challenging specimens Genome Biology Long-read sequencing PCR amplification Genome assembly Museum collections |
| title | Long-read sequencing and genome assembly of natural history collection samples and challenging specimens |
| title_full | Long-read sequencing and genome assembly of natural history collection samples and challenging specimens |
| title_fullStr | Long-read sequencing and genome assembly of natural history collection samples and challenging specimens |
| title_full_unstemmed | Long-read sequencing and genome assembly of natural history collection samples and challenging specimens |
| title_short | Long-read sequencing and genome assembly of natural history collection samples and challenging specimens |
| title_sort | long read sequencing and genome assembly of natural history collection samples and challenging specimens |
| topic | Long-read sequencing PCR amplification Genome assembly Museum collections |
| url | https://doi.org/10.1186/s13059-025-03487-9 |
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