Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1111/1755-0998.13433 http://hdl.handle.net/11449/228984 |
Resumo: | Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies. |
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Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimensancient DNAarchival DNAbiological collectionformalinsingle-stranded DNA librarytarget captureMillions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Deutsche ForschungsgemeinschaftUniversity Museum of BergenSNSB Bavarian State Collection of ZoologyDepartamento de Biodiversidade Instituto de Biociências and Centro de Aquicultura (CAUNESP) Laboratório de Herpetologia Universidade Estadual Paulista - UNESPZoological Institute Braunschweig University of TechnologyDepartment of Mathematics and Natural Sciences Evolutionary Adaptive Genomics Institute for Biochemistry and Biology University of PotsdamMuseum für Naturkunde– Leibniz Institute for Evolution and Biodiversity ScienceChair of Wildlife Ecology and Management Albert Ludwigs University FreiburgSection for Evolutionary Genomics The GLOBE Institute University of CopenhagenDepartment of Zoology Cambridge UniversityDepartment of Microbiology Immunology and Transplantation Division of Clinical and Epidemiological Virology Rega Institute for Medical ResearchSchool of Science and Technology Nottingham Trent UniversityDepartamento de Biodiversidade Instituto de Biociências and Centro de Aquicultura (CAUNESP) Laboratório de Herpetologia Universidade Estadual Paulista - UNESPFAPESP: #2013/50741-7FAPESP: #2017/2616-8FAPESP: #2018/15425-0CNPq: 306623/2018-8Deutsche Forschungsgemeinschaft: 351649567CNPq: 431589/2016-0University Museum of BergenSNSB Bavarian State Collection of ZoologyUniversidade Estadual Paulista (UNESP)Braunschweig University of TechnologyUniversity of PotsdamMuseum für Naturkunde– Leibniz Institute for Evolution and Biodiversity ScienceAlbert Ludwigs University FreiburgUniversity of CopenhagenCambridge UniversityRega Institute for Medical ResearchNottingham Trent UniversityStraube, NicolasLyra, Mariana L. [UNESP]Paijmans, Johanna L. A.Preick, MichaelaBasler, NikolasPenner, JohannesRödel, Mark-OliverWestbury, Michael V.Haddad, Célio F. B. [UNESP]Barlow, AxelHofreiter, Michael2022-04-29T08:29:39Z2022-04-29T08:29:39Z2021-10-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article2299-2315http://dx.doi.org/10.1111/1755-0998.13433Molecular Ecology Resources, v. 21, n. 7, p. 2299-2315, 2021.1755-09981755-098Xhttp://hdl.handle.net/11449/22898410.1111/1755-0998.134332-s2.0-85108119904Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Ecology Resourcesinfo:eu-repo/semantics/openAccess2024-04-09T15:29:47Zoai:repositorio.unesp.br:11449/228984Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:19:35.184693Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens |
title |
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens |
spellingShingle |
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens Straube, Nicolas ancient DNA archival DNA biological collection formalin single-stranded DNA library target capture |
title_short |
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens |
title_full |
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens |
title_fullStr |
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens |
title_full_unstemmed |
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens |
title_sort |
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens |
author |
Straube, Nicolas |
author_facet |
Straube, Nicolas Lyra, Mariana L. [UNESP] Paijmans, Johanna L. A. Preick, Michaela Basler, Nikolas Penner, Johannes Rödel, Mark-Oliver Westbury, Michael V. Haddad, Célio F. B. [UNESP] Barlow, Axel Hofreiter, Michael |
author_role |
author |
author2 |
Lyra, Mariana L. [UNESP] Paijmans, Johanna L. A. Preick, Michaela Basler, Nikolas Penner, Johannes Rödel, Mark-Oliver Westbury, Michael V. Haddad, Célio F. B. [UNESP] Barlow, Axel Hofreiter, Michael |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
University Museum of Bergen SNSB Bavarian State Collection of Zoology Universidade Estadual Paulista (UNESP) Braunschweig University of Technology University of Potsdam Museum für Naturkunde– Leibniz Institute for Evolution and Biodiversity Science Albert Ludwigs University Freiburg University of Copenhagen Cambridge University Rega Institute for Medical Research Nottingham Trent University |
dc.contributor.author.fl_str_mv |
Straube, Nicolas Lyra, Mariana L. [UNESP] Paijmans, Johanna L. A. Preick, Michaela Basler, Nikolas Penner, Johannes Rödel, Mark-Oliver Westbury, Michael V. Haddad, Célio F. B. [UNESP] Barlow, Axel Hofreiter, Michael |
dc.subject.por.fl_str_mv |
ancient DNA archival DNA biological collection formalin single-stranded DNA library target capture |
topic |
ancient DNA archival DNA biological collection formalin single-stranded DNA library target capture |
description |
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-10-01 2022-04-29T08:29:39Z 2022-04-29T08:29:39Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1111/1755-0998.13433 Molecular Ecology Resources, v. 21, n. 7, p. 2299-2315, 2021. 1755-0998 1755-098X http://hdl.handle.net/11449/228984 10.1111/1755-0998.13433 2-s2.0-85108119904 |
url |
http://dx.doi.org/10.1111/1755-0998.13433 http://hdl.handle.net/11449/228984 |
identifier_str_mv |
Molecular Ecology Resources, v. 21, n. 7, p. 2299-2315, 2021. 1755-0998 1755-098X 10.1111/1755-0998.13433 2-s2.0-85108119904 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Molecular Ecology Resources |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
2299-2315 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128790547660800 |