Unlocking inaccessible historical genomes preserved in formalin

• Published in: Molecular ecology resources Vol. 22; no. 6; pp. 2130 - 2147
• Main Authors: Hahn, Erin E., Alexander, Marina R., Grealy, Alicia, Stiller, Jiri, Gardiner, Donald M., Holleley, Clare E.
• Format: Journal Article
• Language: English
• Published: Oxford Wiley Subscription Services, Inc 01.08.2022
• Subjects: Chloroform; Climate change; Decision making; Deoxyribonucleic acid; DNA; DNA sequencing; Endopeptidase K; Formaldehyde; formalin; Gene mapping; genome sequencing; Genomes; Genomic analysis; hot alkaline lysis; Lysis; Mitochondria; museum, fixed; Museums; Nondestructive testing; Nucleotide sequence; Phenols; Preservation; Proteinase; Success; Whole genome sequencing
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.13505

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‐preserved 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‐to‐end whole genome sequencing workflows alongside a k‐mer‐based trimming‐free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3× nuclear genome coverage from formalin‐preserved tissues. Hot alkaline lysis coupled with phenol‐chloroform extraction out‐performed 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‐capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision‐making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin‐preserved 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.