{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T04:03:14Z","timestamp":1792814594556,"version":"4.5.0"},"reference-count":76,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2021,10,1]],"date-time":"2021-10-01T00:00:00Z","timestamp":1633046400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000943","name":"Commonwealth Scientific and Industrial Research Organisation","doi-asserted-by":"publisher","award":["R\u201010011"],"award-info":[{"award-number":["R\u201010011"]}],"id":[{"id":"10.13039\/501100000943","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000943","name":"Commonwealth Scientific and Industrial Research Organisation","doi-asserted-by":"publisher","award":["R\u201014486"],"award-info":[{"award-number":["R\u201014486"]}],"id":[{"id":"10.13039\/501100000943","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2022,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin\u2010preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1962 and 2006 and ranging in preservation quality, we compared the efficacy of several end\u2010to\u2010end whole genome sequencing workflows alongside a k\u2010mer\u2010based trimming\u2010free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3\u00d7 nuclear genome coverage from formalin\u2010preserved tissues. Hot alkaline lysis coupled with phenol\u2010chloroform extraction out\u2010performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Here, we demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target\u2010capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision\u2010making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin\u2010preserved specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.<\/jats:p>","DOI":"10.1111\/1755-0998.13505","type":"journal-article","created":{"date-parts":[[2021,9,22]],"date-time":"2021-09-22T06:28:03Z","timestamp":1632292083000},"page":"2130-2147","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":68,"title":["Unlocking inaccessible historical genomes preserved in formalin"],"prefix":"10.1111","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6459-9508","authenticated-orcid":false,"given":"Erin E.","family":"Hahn","sequence":"first","affiliation":[{"name":"National Research Collections Australia Commonwealth Scientific Industrial Research Organisation  Canberra ACT Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina R.","family":"Alexander","sequence":"additional","affiliation":[{"name":"National Research Collections Australia Commonwealth Scientific Industrial Research Organisation  Canberra ACT Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alicia","family":"Grealy","sequence":"additional","affiliation":[{"name":"National Research Collections Australia Commonwealth Scientific Industrial Research Organisation  Canberra ACT Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiri","family":"Stiller","sequence":"additional","affiliation":[{"name":"Agriculture and Food Commonwealth Scientific Industrial Research Organisation  St Lucia Qld Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donald M.","family":"Gardiner","sequence":"additional","affiliation":[{"name":"Agriculture and Food Commonwealth Scientific Industrial Research Organisation  St Lucia Qld Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5257-0019","authenticated-orcid":false,"given":"Clare E.","family":"Holleley","sequence":"additional","affiliation":[{"name":"National Research Collections Australia Commonwealth Scientific Industrial Research Organisation  Canberra ACT Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,10]]},"reference":[{"key":"e_1_2_9_2_1","volume-title":"FastQC: A quality control tool for high throughput sequence data","author":"Andrews S.","year":"2010"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/jfb.14687"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/0379\u20100738(88)90118\u20101"},{"key":"e_1_2_9_5_1","first-page":"1196","article-title":"Evaluation of DNA extraction method from formalin preserved skin samples of Panthera pardus for molecular genetic assessment","volume":"25","author":"Bibi S. 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