Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens

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Straube, Nicolas ^{[1, 2]} ; Lyra, Mariana L. ^{[3, 4, 5]} ; Paijmans, Johanna L. A. ^{[6, 7]} ; Preick, Michaela ^[7] ; Basler, Nikolas ^{[7, 8]} ; Penner, Johannes ^{[9, 10]} ; Rodel, Mark-Oliver ^[9] ; Westbury, V, Michael ; Haddad, Celio F. B. ^{[3, 4]} ; Barlow, Axel ^{[11, 7]} ; Hofreiter, Michael ^[7]

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^[1] Univ Museum Bergen, Allegaten 41, N-5020 Bergen - Norway

^[2] SNSB Bavarian State Collect Zool, Munich - Germany

^[3] Univ Estadual Paulista, Dept Biodiversidade, Inst Biociencias, UNESP, Rio Claro, SP - Brazil

^[4] Univ Estadual Paulista, Ctr Aquicultura CAUNESP, Lab Herpetol, UNESP, Rio Claro, SP - Brazil

^[5] Braunschweig Univ Technol, Zool Inst, Braunschweig - Germany

^[6] Univ Cambridge, Dept Zool, Cambridge - England

^[7] Univ Potsdam, Inst Biochem & Biol, Dept Math & Nat Sci Evolutionary Adapt Genom, Potsdam - Germany

^[8] Rega Inst Med Res, Dept Microbiol Immunol & Transplantat, Div Clin & Epidemiol Virol, Leuven - Belgium

^[9] Leibniz Inst Evolut & Biodivers Sci, Museum Nat Kunde, Berlin - Germany

^[10] Albert Ludwigs Univ Freiburg, Chair Wildlife Ecol & Management, Freiburg - Germany

^[11] Nottingham Trent Univ, Sch Sci & Technol, Nottingham - England

• Tipo de documento: Artigo Científico
• Fonte: MOLECULAR ECOLOGY RESOURCES; v. 21, n. 7, p. 2299-2315, OCT 2021.
• Citações Web of Science: 2

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. (AU)

• Processo FAPESP: 13/50741-7 - Diversidade e conservação dos anfíbios brasileiros
• Beneficiário: Célio Fernando Baptista Haddad
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOTA - Temático
• Processo FAPESP: 17/26162-8 - Diversidade e conservação dos anfíbios brasileiros
• Beneficiário: Mariana Lúcio Lyra
• Modalidade de apoio: Bolsas no Brasil - Programa Capacitação - Treinamento Técnico
• Processo FAPESP: 18/15425-0 - Uma abordagem multidisciplinar para o estudo da diversificação dos anfíbios: fase 2
• Beneficiário: Taran Grant
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores - Fase 2